Predicting Topics of Scientific Papers from Co-Authorship Graphs: a Case Study

In this paper, we present a case study of predicting topics of scientific papers using a co-authorship graph. Co-authorship graphs constitute a specific view on bibliographic data, where scientific publications are modelled as a graph’s nodes, and two nodes are linked by an undirected edge whenever the two corresponding papers share at least one author. We apply a simple collective classification algorithm based on relaxation labelling to the ILPnet2 bibliographic database. The approach is based on the assumption that papers in the same neighbourhood of the co-authorship graph tend to be on the same topics, and that the predicted topic for one node in the graph depends on the actual or predicted topics of the nodes linked to it. We evaluate the performance of this method on the ILPnet2 data in terms of ROC analysis, and explain the results in terms of the co-authorship graph and the position and properties of papers on a certain topic in the graph.

Unique case of inverted papilloma of septum with nasopharyngeal carcinoma:Is it a metachronous tumour?

Inverted papilloma is a rare and benign tumour. It affects the nasal cavity and paranasal sinuses, has a high rate of recurrence and is associated with malignant transformation. Only few cases of a poorly differentiated carcinoma arising from inverted papilloma have been reported, none of which in the nasopharynx. We report a case of a 37-year-old female, who presented originally in 2012 with inverted papilloma of the nasal septum which was surgically resected. Nasopharyngeal biopsy from 2014 was reported as carcinoma in situ and treated with local endoscopic resection. Three years later she presented with a solitary lesion of the right Eustachian tube opening, confirmed as invasive poorly differentiated carcinoma. Imaging revealed T4 N2b M0 malignancy with skull base and prevertebral space invasion, likely extension into right temporal lobe and malignant adenopathy. Although rare, malignant transformation of inverted papilloma in unusual places should be considered during workup and monitoring of patients

The molecular characteristics of recurrent/metastatic HPV-positive head and neck squamous cell carcinoma:A systematic review of the literature

Objectives: About 17% of patients with human papillomavirus (HPV)-positive head and neck squamous cell carcinoma (HNSCC), which is mainly comprised of oropharyngeal SCC (OPSCC), will experience disease recurrence, which is often considered incurable when manifested at a metastatic and/or recurrent stage. We conducted a critical qualitative systematic review. Our objectives were to provide an overview of the molecular landscape of recurrent/metastatic HPV-positive HNSCC as well as novel molecular biomarkers. Design: A literature review was conducted to identify studies reporting on the molecular characteristics of recurrent/metastatic HPV-positive HNSCC, novel molecular biomarkers and treatment options. The reviews of abstracts, full articles, and revision of the included studies, followed by data extraction and quality assessment were performed by three independent assessors. All primary literature, such as retrospective, prospective, and clinical trials as well as basic research studies were considered, and the final search was conducted at the end of February 2023. The level of evidence was rated using the guidelines published by the Oxford Centre for Evidence-based Medicine and quality was assessed using the Newcastle-Ottawa Scale criteria. Results and Conclusions: The literature search resulted in the identification of 1991 articles. A total of 181 full articles were screened, and 66 articles were included in this analysis. Several studies reported that recurrent/metastatic HPV-positive HNSCC had higher rates of TP53 mutation and were genomically similar to HPV-negative HNSCC. The detection of circulating tumour tissue-modified HPV DNA (ctHPVDNA) as a specific biomarker has shown promising results for monitoring treatment response and recurrence in the subset of HPV-positive HNSCC. In addition, evidence for targeted therapy in recurrent/metastatic HPV-positive HNSCC has emerged, including agents that inhibit overexpressed EGFR. Studies of combination immunotherapy are also underway. Our review outlines the latest evidence on the distinct molecular profiles of recurrent/metastatic HPV-positive HNSCC as well as the clinical potential of ctHPVDNA testing in routine practice. More controlled and longitudinal studies are needed to identify additional molecular targets and to assess the performance and benefits of novel molecular biomarkers in clinical practice.</p

Molecular characterization of the evolution of premalignant lesions in the upper aerodigestive tract

IntroductionEarly relapse and development of metastatic disease are some of the primary reasons for the poor prognosis of patients with head and neck squamous cell carcinoma (HNSCC). HNSCC is a heterogeneous disease which may develop in large premalignant fields of genetically altered cells. Yet knowing which individuals will progress and develop clinically significant cancers during their lifetimes remains one of the most important challenges of reducing HNSCC morbidity and mortality. To further elucidate the molecular mechanisms, we performed a focused analysis of the genome and immune microenvironment from multiple, matched normal squamous tissue, premalignant lesions, as well as primary and recurrent tumors from seven patients with p16-negative HNSCC.MethodsWe performed targeted panel Next Generation Sequencing (161 genes) to analyze somatic variants from sequentially collected, matched formalin-fixed paraffin-embedded tissue (normal, premalignant, HNSCC) from two patients. These samples plus samples from five additional patients were analyzed with the Nanostring PanCancer Immune Panel. In addition, we performed shallow whole genome sequencing (0.5x coverage on average) on samples from three of these patients. Patients were, apart from one case, primarily treated with curative-intent surgery, and received subsequent adjuvant treatment, if indicated.ResultsThe most frequently mutated genes were TP53 and NOTCH1. Other mutated genes included NOTCH3 and CDKN2A, among others. A significant number of mutations were private to dysplasia and invasive carcinoma, respectively, however, almost 20% were shared between them. Increasing genomic instability was observed when comparing histologically normal squamous mucosa with higher levels of dysplasia. High-grade dysplasia showed similarly rearranged genomes as invasive carcinoma. Pathways related to interferon alpha and gamma response were upregulated even in moderate dysplastic lesions with increasing expression in higher grades of dysplasia and carcinoma. SPINK5, a known tumor suppressor gene in HNSCC, was already downregulated in low-grade dysplastic lesions, indicating an early deactivation in the evolution of the disease.ConclusionGenomic alterations as well as aberrant immune gene expression can be observed early in the evolution of tumors of the upper aerodigestive tract, highlighting the potential for targeting early mechanisms of disease progression

Benefit of postoperative radiotherapy for early tumors with single ipsilateral lymph node metastasis

Objectives/Hypothesis Indication for postoperative radiotherapy in patients with locally circumscribed tumors (pT1–pT2) and a single ipsilateral lymph node metastasis (pN1) is debatable. The aim of this study was to evaluate the oncological long‐term outcome of patients with pT1‐pT2 pN1 squamous cell carcinoma (SCC) of the oral cavity, the oropharynx, and the hypopharynx without extracapsular spread (ECS) after a margin‐negative surgical resection, who either received or did not receive postoperative (chemo)radiotherapy. Study Design Retrospective case series. Methods The oncological outcome of patients with pT1‐pT2 pN1 SCC without ECS was evaluated retrospectively. All patients underwent primary tumor resection that included transoral laser microsurgery and neck dissection at an academic tertiary referral center. Results Of 65 identified patients treated between 1986 and 2015 (18 oral cavity, 30 oropharynx, 17 hypopharynx), 21 (32%) received postoperative radiotherapy, and 44 (68%) were treated by surgery alone. The group of patients receiving postoperative treatment showed a significantly superior 5‐year disease‐specific (94.4% vs. 73.2%, P = .029) and recurrence‐free survival (85.2% vs. 43.2%, P = .002), as well as a higher local control rate (90.2% vs. 64.9%, P = .042). The overall survival was 71.4% vs. 62.6% (P = .53). The mean follow‐up was 80.7 months. Conclusions Patients with locally circumscribed carcinomas and a single ipsilateral ECS‐negative lymph node metastasis seem to benefit from postoperative radiotherapy. Level of Evidence 4 Laryngoscope, 130:E530–E538, 202