Biological Semantic Segmentation on CT Medical Images for Kidney Tumor Detection Using nnU-Net Framework

Healthcare systems are constantly challenged with bottlenecks due to human-reliant operations, such as analyzing medical images. High precision and repeatability is necessary when performing a diagnostics on patients with tumors. Throughout the years an increasing number of advancements have been made using various machine learning algorithms for the detection of tumors helping to fast track diagnosis and treatment decisions. “Black Box” systems such as the complex deep learning networks discussed in this paper rely heavily on hyperparameter optimization in order to obtain the most ideal performance. This requires a significant time investment in the tuning of such networks to acquire cutting-edge results. The approach of this paper relies on implementing a state of the art deep learning framework, the nn-UNet, in order to label computed tomography (CT) images from patients with kidney cancer through semantic segmentation by feeding raw CT images through a deep architecture and obtaining pixel-wise mask classifications. Taking advantage of nn-UNet’s framework versatility, various configurations of the architecture are explored and applied, benchmarking and assorting resulting performance, including variations of 2D and 3D convolutions as well as the use of distinct cost functions such as the Sørensen-Dice coefficient, Cross Entropy, and a compound of them. 79% is the accuracy currently reported for the detection of benign and malign tumors using CT imagery performed by medical practitioners. The best iteration and mixture of parameters in this work resulted in an accuracy of 83% for tumor labelling. This study has further exposed the performance of a versatile and groundbreaking approach to deep learning framework designed for biomedical image segmentation

Positron emission tomography of sodium glucose cotransport activity in high grade astrocytomas.

A novel glucose transporter, the sodium glucose cotransporter 2 (SGLT2), has been demonstrated to contribute to the demand for glucose by pancreatic and prostate tumors, and its functional activity has been imaged using a SGLT specific PET imaging probe, α-methyl-4-[F-18]fluoro-4-deoxy-D-glucopyaranoside (Me-4FDG). In this study, Me-4FDG PET was extended to evaluate patients with high-grade astrocytic tumors. Me-4FDG PET scans were performed in four patients diagnosed with WHO Grade III or IV astrocytomas and control subjects, and compared with 2-deoxy-2-[F-18]fluoro-D-glucose (2-FDG) PET and magnetic resonance imaging (MRI) of the same subjects. Immunocytochemistry was carried out on Grade IV astrocytomas to determine the cellular location of SGLT proteins within the tumors. Me-4FDG retention was pronounced in astrocytomas in dramatic contrast to the lack of uptake into the normal brain, resulting in a high signal-to-noise ratio. Macroscopically, the distribution of Me-4FDG within the tumors overlapped with that of 2-FDG uptake and tumor definition using contrast-enhanced MRI images. Microscopically, the SGLT2 protein was found to be expressed in neoplastic glioblastoma cells and endothelial cells of the proliferating microvasculature. This preliminary study shows that Me-4FDG is a highly sensitive probe for visualization of high-grade astrocytomas by PET. The distribution of Me-4FDG within tumors overlapped that for 2-FDG, but the absence of background brain Me-4FDG resulted in superior imaging sensitivity. Furthermore, the presence of SGLT2 protein in astrocytoma cells and the proliferating microvasculature may offer a novel therapy using the SGLT2 inhibitors already approved by the FDA to treat type 2 diabetes mellitus

Robust Peak Recognition in Intracranial Pressure Signals

<p>Abstract</p> <p>Background</p> <p>The waveform morphology of intracranial pressure pulses (ICP) is an essential indicator for monitoring, and forecasting critical intracranial and cerebrovascular pathophysiological variations. While current ICP pulse analysis frameworks offer satisfying results on most of the pulses, we observed that the performance of several of them deteriorates significantly on abnormal, or simply more challenging pulses.</p> <p>Methods</p> <p>This paper provides two contributions to this problem. First, it introduces MOCAIP++, a generic ICP pulse processing framework that generalizes MOCAIP (Morphological Clustering and Analysis of ICP Pulse). Its strength is to integrate several peak recognition methods to describe ICP morphology, and to exploit different ICP features to improve peak recognition. Second, it investigates the effect of incorporating, automatically identified, challenging pulses into the training set of peak recognition models.</p> <p>Results</p> <p>Experiments on a large dataset of ICP signals, as well as on a representative collection of sampled challenging ICP pulses, demonstrate that both contributions are complementary and significantly improve peak recognition performance in clinical conditions.</p> <p>Conclusion</p> <p>The proposed framework allows to extract more reliable statistics about the ICP waveform morphology on challenging pulses to investigate the predictive power of these pulses on the condition of the patient.</p

Analysis of SARS-CoV-2 infection associated cell entry proteins ACE2, CD147, PPIA, and PPIB in datasets from non SARS-CoV-2 infected neuroblastoma patients, as potential prognostic and infection biomarkers in neuroblastoma

SARS-CoV-2 viral contagion has given rise to a worldwide pandemic. Although most children experience minor symptoms from SARS-CoV-2 infection, some have severe complications including Multisystem Inflammatory Syndrome in Children. Neuroblastoma patients may be at higher risk of severe infection as treatment requires immunocompromising chemotherapy and SARS-CoV-2 has demonstrated tropism for nervous cells. To date, there is no sufficient epidemiological data on neuroblastoma patients with SARS-CoV-2. Therefore, we evaluated datasets of non-SARS-CoV-2 infected neuroblastoma patients to assess for key genes involved with SARS-CoV-2 infection as possible neuroblastoma prognostic and infection biomarkers. We hypothesized that ACE2, CD147, PPIA and PPIB, which are associated with viral-cell entry, are potential biomarkers for poor prognosis neuroblastoma and SARS-CoV-2 infection. We have analysed three publicly available neuroblastoma gene expression datasets to understand the specific molecular susceptibilities that high-risk neuroblastoma patients have to the virus. Gene Expression Omnibus (GEO) GSE49711 and GEO GSE62564 are the microarray and RNA-Seq data, respectively, from 498 neuroblastoma samples published as part of the Sequencing Quality Control initiative. TARGET, contains microarray data from 249 samples and is part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. ACE2, CD147, PPIA and PPIB were identified through their involvement in both SARS-CoV-2 infection and cancer pathogenesis. In-depth statistical analysis using Kaplan-Meier, differential gene expression, and Cox multivariate regression analysis, demonstrated that overexpression of ACE2, CD147, PPIA and PPIB is significantly associated with poor-prognosis neuroblastoma samples. These results were seen in the presence of amplified MYCN, unfavourable tumour histology and in patients older than 18 months of age. Previously, we have shown that high levels of the nerve growth factor receptor NTRK1 together with low levels of the phosphatase PTPN6 and TP53 are associated with increased relapse-free survival of neuroblastoma patients. Interestingly, low levels of expression of ACE2, CD147, PPIA and PPIB are associated with this NTRK1-PTPN6-TP53 module, suggesting that low expression levels of these genes are associated with good prognosis. These findings have implications for clinical care and therapeutic treatment. The upregulation of ACE2, CD147, PPIA and PPIB in poor-prognosis neuroblastoma samples suggests that these patients may be at higher risk of severe SARS-CoV-2 infection. Importantly, our findings reveal ACE2, CD147, PPIA and PPIB as potential biomarkers and therapeutic targets for neuroblastoma

Residual Tumor Confers a 10-Fold Increased Risk of Regrowth in Clinically Nonfunctioning Pituitary Tumors.

ObjectiveWe evaluated tumor recurrence and regrowth rates following endoscopic transnasal transsphenoidal (TNTS) surgical removal in a consecutive series of clinically nonfunctioning pituitary adenomas (CNFTs).DesignRetrospective chart review of clinical, biochemical, and sellar MRI findings in all TNTS surgeries in patients with CNFT, performed by a single surgeon, between 2008 and 2015 (n = 280).PatientsNinety-three patients met eligibility criteria, with complete clinical, biochemical, and imaging follow-up for a 3-year minimum.ResultsOf 85 patients who were not irradiated, 3-month postsurgical MRI demonstrated no residual tumor in 58 of 85 (68.2%), equivocal findings in 12 of 85 (14.1%), and definite residual tumor in 15 of 85 (17.6%) patients. Six of 85 (7.1%) demonstrated tumor regrowth by 3 years, and 2 further patients demonstrated true tumor recurrence at 3 and 6 years after surgery, respectively, for a total recurrence rate of 9.4% (8 of 85). Eight of the 93 patients were irradiated between 3 months and 4 years after pituitary surgery. In 3 patients with tumor regrowth, 2 exhibited residual tumor and 1 had no residual findings at the 3-month postoperative imaging. Overall, Ki-67 labeling index or Knosp grading did not predict recurrence.ConclusionTumor recurrence at 3 years was low (1 of 58; 1.7%) if the 3-month postoperative MRI showed no residual tumor. The findings support a less frequent imaging schedule for this group. Patients with definite residual tumor visible at 3 months harbor the greatest risk for tumor growth, but regrowth does not occur in all patients (6 of 15; 40%)

Cómic, memoria y representación : el pasado en movimiento en Maus de Art Spiegelman

En 1991 se publicó la edición final de la historieta Maus del estadounidense Art Spiegelman, cómic acerca de Vladek, padre del autor y sobreviviente de Auschwitz. A medida que la narración del cómic avanza, se presenta un relato que construye una interpretación histórica del pasado, que parte de la narración oral para articular un documento que logra con éxito plasmar las implicaciones de pertenecer a lo que la autora Marianne Hirsch, denomina la generación de la post-memoria. Término que se utiliza para referirse a la relación entre los descendientes de los sobrevivientes de eventos violentos y traumáticos como el llamado Holocausto, con los poderosos recuerdos de la generación que los precedió, que logró de alguna manera seguir con vida después de algo casi incontable. La investigación indaga sobre la identidad construida y configurada en sus cómics por el autor, como judío secular estadounidense, moldeado por el pasado y los recuerdos de sus padres acerca de una violencia inimaginable.In 1991 the final edition of the comic Maus by American author Art Spiegelman. was published The book is about Vladek, Spiegelman's father and Auschwitz's survivor. While the narration of the comic goes forward, it is presented a story that builds an historic representation of the past, starting from oral narration to form a document that successfully captures the implications of being part of what Marianne Hirsch calls the Generation of Post memory. This term is used to refer to the relationship between the descendants of the survivors of violent and traumatic events like the so called Holocaust, with the powerful memories of the previous generation that somehow managed to survive something almost impossible to describe and retell. One of this investigation's goals is to inquire about the identity constructed and configurated by the author in his comics as a Secular-American-Jewish, molded by the past and the memories of his parents about an unimaginable violence.Historiador (a)Pregrad

Characterization of lower urinary tract symptoms in patients with idiopathic normal pressure hydrocephalus

AIMS: The purpose of this study was to evaluate lower urinary tract symptoms (LUTS) in idiopathic normal pressure hydrocephalus (iNPH). METHODS: Patients with new-onset iNPH were prospectively evaluated for LUTS via detailed history and physical, and administration of questionnaires from the International Consultation on Incontinence to assess incontinence (ICIq-UI), overactive bladder (ICIq-OAB), and quality of life (ICIq-LUTqol), as well as the American Urological Association Symptom Score bother scale. All patients with moderate-to-severe LUTS were offered urodynamic testing. Sub-analysis was performed based on gender, medical comorbidities, and age. RESULTS: Fifty-five consecutive patients with iNPH completed the initial evaluation and surveys. Total urinary incontinence score was mild to moderate (8.710.64: 0-21 scale) with 90.9% experiencing leakage and 74.5% reporting urge incontinence. The most common OAB symptom was nocturia (2.2 +/- 0.14: 0-4 scale) with urge incontinence the most bothersome (3.71 +/- 0.44: 0-10 scale). Quality-of-life impact was moderate (4.47 +/- 0.4: 0-10 scale) and American Urological Association Symptom Score bother scale was 2.89 +/- 0.22 (0-6 scale). Urodynamics testing revealed 100% detrusor overactivity and mean bladder capacity of 200mL. Several differences were identified based on gender, medical comorbidities, and age. CONCLUSIONS: Patients with iNPH present with mild-moderate incontinence of which nocturia is the most common symptom, urge incontinence the most bothersome, with 100% of patients having detrusor overactivity. Younger patients experienced greater bother related to LUTS. To our knowledge, this is the only prospective evaluation of urinary symptoms in patients with new-onset iNPH

Extraparenchymal neurocysticercosis in the United States: a case report

<p>Abstract</p> <p>Introduction</p> <p>Neurocysticercosis is endemic in the developing world, but is becoming more common in the United States due to immigration.</p> <p>Case presentation</p> <p>A 26-year-old Caucasian man presented with headache, nausea and vomiting and was found to have hydrocephalus and meningitis. Brain imaging and immunological studies were suggestive of neurocysticercosis. Endoscopic removal of the cyst resulted in resolution of symptoms. This case represents a combination of two rare presentations of extraparenchymal neurocysticercosis; intraventricular neurocysticercosis and subarachnoid neurocysticercosis.</p> <p>Conclusion</p> <p>Although neurocysticercosis is pleomorphic in its presentation, extraparenchymal neurocysticercosis may be challenging to diagnose and treat. Clinicians should be aware of this condition given increasing incidence in the United States.</p

Regression analysis for peak designation in pulsatile pressure signals

Following recent studies, the automatic analysis of intracranial pressure (ICP) pulses appears to be a promising tool for forecasting critical intracranial and cerebrovascular pathophysiological variations during the management of many disorders. A pulse analysis framework has been recently developed to automatically extract morphological features of ICP pulses. The algorithm is able to enhance the quality of ICP signals, to segment ICP pulses, and to designate the locations of the three ICP sub-peaks in a pulse. This paper extends this algorithm by utilizing machine learning techniques to replace Gaussian priors used in the peak designation process with more versatile regression models. The experimental evaluations are conducted on a database of ICP signals built from 700 h of recordings from 64 neurosurgical patients. A comparative analysis of different state-of-the-art regression analysis methods is conducted and the best approach is then compared to the original pulse analysis algorithm. The results demonstrate a significant improvement in terms of accuracy in favor of our regression-based recognition framework. It reaches an average peak designation accuracy of 99% using a kernel spectral regression against 93% for the original algorithm