bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABPEPserver: a web application for documentation and analysis of substitutants
Authors: Pataskar Abhijeet , Montenegro Navarro Jasmine , Agami Reuven 
Published: June 2023

Abstract
Background
Cancer immunotherapy is implemented by identifying antigens that are presented on the cell surface of cancer cells and illicit T-cell response (Schumacher and Schreiber, Science 348:69–74, 2015; Waldman et al., Nat Rev Immunol 20:651–668, 2020; Zhang et al., Front Immunol 12:672,356, 2021b). Classical candidates of such antigens are the peptides resulting from genetic alterations and are named “neoantigen" (Schumacher and Schreiber, Science 348:69–74, 2015). Neoantigens have been widely catalogued across several human cancer types (Tan et al., Database (Oxford) 2020;2020b; Vigneron et al., Cancer Immun 13:15, 2013; Yi et al., iScience 24:103,107, 2021; Zhang et al., BMC Bioinformatics 22:40, 2021a). Recently, a new class of inducible antigens has been identified, namely Substitutants, that are produced as a result of aberrant protein translation (Pataskar et al., Nature 603:721–727, 2022).

Main
Catalogues of Substitutant expression across human cancer types, their specificity and association to gene expression signatures remain elusive for the scientific community's access. As a solution, we present ABPEPserver, an online database and analytical platform that can visualize a large-scale tumour proteomics analysis of Substitutant expression across eight tumour types sourced from the CPTAC database (Edwards et al., J Proteome Res 14:2707–2713, 2015). Functionally, ABPEPserver offers the analysis of gene-association signatures of Substitutant peptides, a comparison of enrichment between tumour and tumour-adjacent normal tissues, and a list of peptides that serve as candidates for immunotherapy design. ABPEPserver will significantly enhance the exploration of aberrant protein production in human cancer, as exemplified in a case study.

Conclusion
ABPEPserver is designed on an R SHINY platform to catalogue Substitutant peptides in human cancer. The application is available at https://rhpc.nki.nl/sites/shiny/ABPEP/. The code is available under GNU General public license from GitHub (https://github.com/jasminesmn/ABPEPserver).
Attenuated post-movement beta rebound reflects psychomotor alterations in major depressive disorder during a simple visuomotor task: a MEG study
Authors: Xia Yi , Hua Lingling , Dai Zhongpeng , Han Yinglin , Du Yishan , Zhao Shuai , Zhou Hongliang , Wang Xiaoqin , Yan Rui , Wang Xumiao , Zou HaoWen , Sun Hao , Huang YingHong , Yao ZhiJian , Lu Qing 
Published: June 2023

Abstract
Background
Psychomotor alterations are a common symptom in patients with major depressive disorder (MDD). The primary motor cortex (M1) plays a vital role in the mechanism of psychomotor alterations. Post-movement beta rebound (PMBR) in the sensorimotor cortex is abnormal in patients with motor abnormalities. However, the changes in M1 beta rebound in patients with MDD remain unclear. This study aimed to primarily explore the relationship between psychomotor alterations and PMBR in MDD.

Methods
One hundred thirty-two subjects were enrolled in the study, comprising 65 healthy controls (HCs) and 67 MDD patients. All participants performed a simple right-hand visuomotor task during MEG scanning. PMBR was measured in the left M1 at the source reconstruction level with the time–frequency analysis method. Retardation factor scores and neurocognitive test performance, including the Digit Symbol Substitution Test (DSST), the Making Test Part A (TMT-A), and the Verbal Fluency Test (VFT), were used to measure psychomotor functions. Pearson correlation analyses were used to assess relationships between PMBR and psychomotor alterations in MDD.

Results
The MDD group showed worse neurocognitive performance than the HC group in all three neurocognitive tests. The PMBR was diminished in patients with MDD compared to HCs. In a group of MDD patients, the reduced PMBR was negatively correlated with retardation factor scores. Further, there was a positive correlation between the PMBR and DSST scores. PMBR is negatively associated with the TMT-A scores.

Conclusion
Our findings suggested that the attenuated PMBR in M1 could illustrate the psychomotor disturbance in MDD, possibly contributing to clinical psychomotor symptoms and deficits of cognitive functions.
Identifying patient subgroups with different trends of patient-reported outcomes (PROMs) after elective knee arthroplasty
Authors: Golinelli Davide , Grassi Alberto , Sanmarchi Francesco , Tedesco Dario , Esposito Francesco , Rosa Simona , Rucci Paola , Amabile Marilina , Cosentino Monica , Bordini Barbara , Fantini Maria Pia , Zaffagnini Stefano 
Published: June 2023

Abstract
Background
Patient-reported outcome measures (PROMs) are increasingly being used to assess the effectiveness of elective total knee arthroplasty (TKA). However, little is known about how PROMs scores change over time in these patients. The aim of this study was to identify the trajectories of quality of life and joint functioning, and their associated demographic and clinical features in patients undergoing elective TKA.

Methods
A prospective, cohort study was conducted, in which PROMs questionnaires (Euro Quality 5 Dimensions 3L, EQ-5D-3L, and Knee injury and Osteoarthritis Outcome Score Patient Satisfaction, KOOS-PS) were administered to patients at a single center undergoing elective TKA before surgery, and at 6 and 12 months after surgery. Latent class growth mixture models were used to analyze the patterns of change in PROMs scores over time. Multinomial logistic regression was used to investigate the association between patient characteristics and PROMs trajectories.

Results
A total of 564 patients were included in the study. The analysis highlighted differential patterns of improvement after TKA. Three distinct PROMs trajectories were identified for each PROMs questionnaire, with one trajectory indicating the most favorable outcome. Female gender appears to be associated with a presentation to surgery with worse perceived quality of life and joint function than males, but also more rapid improvement after surgery. Having an ASA score greater than 3 is instead associated with a worse functional recovery after TKA.

Conclusion
The results suggest three main PROMs trajectories in patients undergoing elective TKA. Most patients reported improved quality of life and joint functioning at 6 months, which then stabilized. However, other subgroups showed more varied trajectories. Further research is needed to confirm these findings and to explore the potential clinical implications of these results.
Needle tract seeding of a sclerosing epithelioid fibrosarcoma in a biopsy tract: a case report
Authors: Kawai Masafumi , Miwa Shinji , Yamamoto Norio , Hayashi Katsuhiro , Takeuchi Akihiko , Igarashi Kentaro , Taniguchi Yuta , Araki Yoshihiro , Yonezawa Hirotaka , Nojima Takayuki , Tsuchiya Hiroyuki 
Published: June 2023

Abstract
Background
A sclerosing epithelioid fibrosarcoma (SEF) is an uncommon tumor of the deep soft tissue. An SEF has been described as a low-grade tumor with high local recurrence and metastatic rates. Generally, in bone and soft tissue tumors, a resection of the biopsy route is recommended; however, there is limited evidence with respect to the dissemination of the tumor tissue during a needle biopsy.

Case presentation
A mass in the right pelvic cavity, with no symptoms, was observed in a 45-year-old woman during a gynecological examination. Computed tomography (CT) revealed a multilocular mass with calcification in the pelvic cavity. The magnetic resonance imaging (MRI) showed an iso-signal intensity on T1 weighted images and hypo- and iso-signal intensity on T2 weighted images. The CT-guided core needle biopsy was performed using a dorsal approach, and the biopsy diagnosis was a low-grade spindle cell tumor. The tumor was excised using an anterior approach. The tumor tissue comprised spindle cells and epithelioid cells with irregular nuclei, and the immunohistological analysis was positive for vimentin and epithelial membrane antigen, which was consistent with a diagnosis of sclerosing epithelioid fibrosarcoma. Five years after the surgery, the MRI showed a tumor recurrence in the subcutaneous tissue of the right buttock, which was consistent with the needle biopsy tract. The patient underwent a tumor excision, and the resected tumor was similar to the primary tumor.

Conclusions
The recurrent tumor was excised with a surgical margin, and the tumor specimen had the histological features of a sclerosing epithelioid fibrosarcoma. It was difficult to investigate the association of the core needle biopsy with the tumor recurrence because the approach of the biopsy tract is usually same as that used in a tumor excision. However, the present case indicated the tumor may recur in the biopsy tract of a soft tissue sarcoma. Surgeons should be aware of the possibility of disseminating tumor tissues in a needle biopsy.
Ankle-foot orthoses among children with cerebral palsy: a cross-sectional population-based register study of 8,928 children living in Northern Europe
Authors: Stockman Jessica , Eggertsdóttir Guðbjörg , Gaston Mark S. , Jeglinsky-Kankainen Ira , Hollung Sandra Julsen , Nordbye-Nielsen Kirsten , von Rosen Philip , Alriksson-Schmidt Ann I. 
Published: June 2023

AbstractBackgroundCerebral palsy (CP) is an umbrella term where an injury to the immature brain affects muscle tone and motor control, posture, and at times, the ability to walk and stand. Orthoses can be used to improve or maintain function. Ankle-foot orthoses (AFOs) are the most frequently used orthoses in children with CP. However, how commonly AFOs are used by children and adolescents with CP is still unknown. The aims of this study were to investigate and describe the use of AFOs in children with CP in Sweden, Norway, Finland, Iceland, Scotland, and Denmark, and compare AFO use between countries and by gross motor function classification system (GMFCS) level, CP subtype, sex, and age.MethodAggregated data on 8,928 participants in the national follow-up programs for CP for the respective countries were used. Finland does not have a national follow-up program for individuals with CP and therefore a study cohort was used instead. Use of AFOs were presented as percentages. Logistic regression models were used to compare the use of AFOs among countries adjusted for age, CP subtype, GMFCS level, and sex.ResultsThe proportion of AFO use was highest in Scotland (57%; CI 54–59%) and lowest in Denmark (35%; CI 33–38%). After adjusting for GMFCS level, children in Denmark, Finland, and Iceland had statistically significantly lower odds of using AFOs whereas children in Norway and Scotland reported statistically significantly higher usage than Sweden.ConclusionIn this study, the use of AFOs in children with CP in countries with relatively similar healthcare systems, differed between countries, age, GMFCS level, and CP subtype. This indicates a lack of consensus as to which individuals benefit from using AFOs. Our findings present an important baseline for the future research and development of practical guidelines in terms of who stands to benefit from using AFOs.
Risk factors and predictive model for pulmonary complications in patients transferred to ICU after hepatectomy
Authors: Wang Bin , Liang HanSheng , Zhao HuiYing , Shen JiaWei , An YouZhong , Feng Yi 
Published: June 2023

Abstract
Objective
Postoperative pulmonary complications (PPCs) seriously harm the recovery and prognosis of patients undergoing surgery. However, its related risk factors in critical patients after hepatectomy have been rarely reported. This study aimed at analyzing the factors related to PPCs in critical adult patients after hepatectomy and create a nomogram for prediction of the PPCs.

Methods
503 patients’ data were collected form the Peking University People’s Hospital. Multivariate logistic regression analysis was used to identify independent risk factors to derive the nomogram. Nomogram’s discriminatory ability was assessed using the area under the receiver operating characteristic curve (AUC), and calibration was assessed using the Hosmer–Lemeshow goodness-of-fit test and calibration curve.

Results
The independent risk factor for PPCs are advanced age (odds ratio [OR] = 1.026; P = 0.008), higher body mass index (OR = 1.139; P < 0.001), lower preoperative serum albumin level (OR = 0.961; P = 0.037), and intensive care unit first day infusion volume (OR = 1.152; P = 0.040). And based on this, we created a nomogram to predict the occurrence of PPCs. Upon assessing the nomogram’s predictive ability, the AUC for the model was 0.713( 95% CI: 0.668–0.758, P<0.001). The Hosmer–Lemeshow test (P = 0.590) and calibration curve showed good calibration for the prediction of PPCs.

Conclusions
The prevalence and mortality of postoperative pulmonary complications in critical adult patients after hepatectomy are high. Advanced age, higher body mass index, lower preoperative serum albumin and intensive care unit first day infusion volume were found to be significantly associated with PPCs. And we created a nomogram model which can be used to predict the occurrence of PPCs.
Pure testicular choriocarcinoma with gastrointestinal metastasis and paraneoplastic symptoms: a case report
Authors: Namavari Negin , Taheri Lohrasb , Hooshmand Farhang , Dousthaghi Mohammad H. , Rahmanian Vahid 
Published: June 2023

Abstract
Background
Pure testicular choriocarcinoma is a rare type of non-seminomatous germ cell tumor extremely poor prognostic with the tendency to bleed at the metastatic site. At the time of the diagnosis, 70% of patients have metastatic lesions. Depending on the site of the metastasis, symptoms vary. Gastrointestinal involvement is seen in less than 5% of cases, mostly in the duodenum.

Case presentation
We present a 47 years old male with testicular choriocarcinoma involving the jejunum, lung, liver, and kidney presenting with acute abdominal pain, melena, and dyspnea with some paraneoplastic symptoms. The patient had increased, severe and constant pain in the right lower quadrant for the previous four days. Additionally, he was complaining of nausea, vomiting, anorexia, and a history of melena for the last 10 days. Dyspnea on exertion, hemoptysis, and dry cough were the symptoms he was suffering from, for almost one year. The patient’s general appearance was pale, ill, and thin with 10 kg of weight loss during the last some months. The computed tomography (CT) scan reported multiple metastatic lesions in both liver lobes and the left kidney. Pathologic study of the samples of small bowel lesions showed metastatic choriocarcinoma. Following the patient had been referred to an oncologist to start the chemotherapy regime. Finally, the patient has expired after 40 days of his first admission.

Conclusions
Testicular choriocarcinoma is a rare but fatal malignancy among young men. Gastrointestinal metastases are infrequent involvement represented by melena and acute abdominal pain, obstruction, and mass. Physicians should consider it as a differential diagnosis for acute abdomen and gastrointestinal bleeding causation.
Artificial intelligence in the diagnosis of dental diseases on panoramic radiographs: a preliminary study
Authors: Zhu Junhua , Chen Zhi , Zhao Jing , Yu Yueyuan , Li Xiaojuan , Shi Kangjian , Zhang Fan , Yu Feifei , Shi Keying , Sun Zhe , Lin Nengjie , Zheng Yuanna 
Published: June 2023

AbstractBackgroundArtificial intelligence (AI) has been introduced to interpret the panoramic radiographs (PRs). The aim of this study was to develop an AI framework to diagnose multiple dental diseases on PRs, and to initially evaluate its performance.MethodsThe AI framework was developed based on 2 deep convolutional neural networks (CNNs), BDU-Net and nnU-Net. 1996 PRs were used for training. Diagnostic evaluation was performed on a separate evaluation dataset including 282 PRs. Sensitivity, specificity, Youden’s index, the area under the curve (AUC), and diagnostic time were calculated. Dentists with 3 different levels of seniority (H: high, M: medium, L: low) diagnosed the same evaluation dataset independently. Mann-Whitney U test and Delong test were conducted for statistical analysis (ɑ=0.05).ResultsSensitivity, specificity, and Youden’s index of the framework for diagnosing 5 diseases were 0.964, 0.996, 0.960 (impacted teeth), 0.953, 0.998, 0.951 (full crowns), 0.871, 0.999, 0.870 (residual roots), 0.885, 0.994, 0.879 (missing teeth), and 0.554, 0.990, 0.544 (caries), respectively. AUC of the framework for the diseases were 0.980 (95%CI: 0.976–0.983, impacted teeth), 0.975 (95%CI: 0.972–0.978, full crowns), and 0.935 (95%CI: 0.929–0.940, residual roots), 0.939 (95%CI: 0.934–0.944, missing teeth), and 0.772 (95%CI: 0.764–0.781, caries), respectively. AUC of the AI framework was comparable to that of all dentists in diagnosing residual roots (p > 0.05), and its AUC values were similar to (p > 0.05) or better than (p < 0.05) that of M-level dentists for diagnosing 5 diseases. But AUC of the framework was statistically lower than some of H-level dentists for diagnosing impacted teeth, missing teeth, and caries (p < 0.05). The mean diagnostic time of the framework was significantly shorter than that of all dentists (p < 0.001).ConclusionsThe AI framework based on BDU-Net and nnU-Net demonstrated high specificity on diagnosing impacted teeth, full crowns, missing teeth, residual roots, and caries with high efficiency. The clinical feasibility of AI framework was preliminary verified since its performance was similar to or even better than the dentists with 3–10 years of experience. However, the AI framework for caries diagnosis should be improved.
Clinical outcomes of teeth adjacent to the site of mandibulotomy or mandibulectomy in patients with head and neck cancer: results from a multidisciplinary mono-institutional head and neck tumor board
Authors: Castagnola Raffaella , Rupe Cosimo , Gioco Gioele , Almadori Giovanni , Galli Jacopo , Tagliaferri Luca , Cassano Alessandra , Gallenzi Patrizia , Lajolo Carlo 
Published: June 2023

Abstract
Introduction
The aim of this case series was to evaluate the necrosis of teeth adjacent to the site of mandibulotomy or mandibulectomy in a cohort of patients suffering from head and neck cancers.

Methods
Fourteen patients who underwent segmental mandibulectomy or paramedian mandibulotomy for oral, oropharynx or major salivary gland cancer and a total of 23 teeth were included in this case series. Twelve patients underwent adjuvant head and neck radiotherapy. Cold sensitivity pulp testing and/or electric pulp testing were performed on teeth at the margin of mandibulectomy and on teeth adjacent to mandibulotomy after surgery. A “positive” response was considered the healthy state, and “negative” was considered the diseased state of the tooth.

Results
The 10 patients who underwent mandibulotomy had 12 teeth with a negative response. The 4 patients treated by mandibulectomy had two positive and three negative responses to cold and electric pulp tests. Fifteen out of 23 teeth (65.2%) showed a negative response to sensitivity testing.

Conclusions
Tooth necrosis seems to be a common event after mandibulectomy and mandibulotomy.

Clinical Relevance
To avoid post-surgery complications, performing root canal therapy before surgery on the teeth adjacent to the surgical site could be an appropriate strategy.
Evaluation of the chemical, physical, and biological properties of a newly developed bioceramic cement derived from cockle shells: an in vitro study
Authors: Wannakajeepiboon Monthip , Sathorn Chankhrit , Kornsuthisopon Chatvadee , Santiwong Busayarat , Wasanapiarnpong Thanakorn , Linsuwanont Pairoj 
Published: June 2023

AbstractBackgroundTricalcium silicate is the main component of commercial bioceramic cements that are widely used in endodontic treatment. Calcium carbonate, which is manufactured from limestone, is one of the substrates of tricalcium silicate. To avoid the environmental impact of mining, calcium carbonate can be obtained from biological sources, such as shelled mollusks, one of which is cockle shell. The aim of this study was to evaluate and compare the chemical, physical, and biological properties of a newly developed bioceramic cement derived from cockle shell (BioCement) with those of a commercial tricalcium silicate cement (Biodentine).MethodsBioCement was prepared from cockle shells and rice husk ash and its chemical composition was determined by X-ray diffraction and X-ray fluorescence spectroscopy. The physical properties were evaluated following the International Organization for Standardization (ISO) 9917-1;2007 and 6876;2012. The pH was tested after 3 h to 8 weeks. The biological properties were assessed using extraction medium from BioCement and Biodentine on human dental pulp cells (hDPCs) in vitro. The 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5[(phenylamino)carbonyl]-2 H-tetrazolium hydroxide assay was used to evaluate cell cytotoxicity following ISO 10993-5;2009. Cell migration was examined using a wound healing assay. Alizarin red staining was performed to detect osteogenic differentiation. The data were tested for a normal distribution. Once confirmed, the physical properties and pH data were analyzed using the independent t-test, and the biological property data were analyzed using one way ANOVA and Tukey’s multiple comparisons test at a 5% significance level.ResultsThe main components of BioCement and Biodentine were calcium and silicon. BioCement’s and Biodentine’s setting time and compressive strength were not different. The radiopacity of BioCement and Biodentine was 5.00 and 3.92 mmAl, respectively (p < 0.05). BioCement’s solubility was significantly higher than Biodentine. Both materials exhibited alkalinity (pH ranged from 9 to 12) and demonstrated > 90% cell viability with cell proliferation. The highest mineralization was found in the BioCement group at 7 days (p < 0.05).ConclusionsBioCement exhibited acceptable chemical and physical properties and was biocompatible to human dental pulp cells. BioCement promotes pulp cell migration and osteogenic differentiation.