Polimi at CLinkaRT: a Conditional Random Field vs a BERT-based approach

In the context of the EVALITA 2023 challenge, we present the models we have developed for the CLinkaRT task, which aims to identify medical examinations and their corresponding results in Italian clinical documents. We propose two distinct approaches: one utilising a Conditional Random Field (CRF), a probabilistic graphical model traditionally used for Named Entity Recognition, and the other based on BERT, the transformer-based model that is currently state-of-the-art for many Natural Language Processing tasks. Both models incorporate external knowledge from publicly available medical resources and are enhanced with heuristic rules to establish associations between exams and results. Our comparative analysis elects the CRF-based model as the winner, securing the third position in the competition ranking, but the BERT-based model demonstrated competitive performance

Fast method for the determination of short-chain-length polyhydroxyalkanoates (scl-PHAs) in bacterial samples by In Vial-Thermolysis (IVT)

none8siA new method based on the GC–MS analysis of thermolysis products obtained by treating bacterial samples at a high temperature (above 270 C) has been developed. This method, here named “In-Vial- Thermolysis” (IVT), allowed for the simultaneous determination of short-chain-length polyhydrox- yalkanoates (scl-PHA) content and composition. The method was applied to both single strains and microbial mixed cultures (MMC) fed with different carbon sources. The IVT procedure provided similar analytical performances compared to previous Py-GC–MS and Py- GC-FID methods, suggesting a similar application for PHA quantitation in bacterial cells. Results from the IVT procedure and the traditional methanolysis method were compared; the correlation between the two datasets was fit for the purpose, giving a R2 of 0.975. In search of further simplification, the rationale of IVT was exploited for the development of a “field method” based on the titration of thermolyzed samples with sodium hydrogen carbonate to quantify PHA inside bacterial cells. The accuracy of the IVT method was fit for the purpose. These results lead to the possibility for the on-line measurement of PHA productivity. Moreover, they allow for the fast and inexpensive quantification/characterization of PHA for biotechnological process control, as well as investigation over various bacterial communities and/or feeding strategies.mixedF. Abbondanzi; G. Biscaro; G. Carvalho; L. Favaro; P. Lemos; M. Paglione; C. Samorì; C. TorriF. Abbondanzi; G. Biscaro; G. Carvalho; L. Favaro; P. Lemos; M. Paglione; C. Samorì; C. Torr

Clustering Italian medical texts: a case study on referrals

In the medical domain, there is a large amount of valuable information that is stored in textual format. These unstructured data have long been ignored, due to the difficulties of introducing them in statistical models, but in the last years, the field of Natural Language Processing (NLP) has seen relevant improvements, with models capable of achieving relevant results in various tasks, including information extraction, classification and clustering. NLP models are typically language-specific and often domain-specific, but most of the work to date has been focused on the English language, especially in the medical domain. In this work, we propose a pipeline for clustering Italian medical texts, with a case study on clinical questions reported in referral

Hilbert Series for Flavor Invariants of the Standard Model

The Hilbert series is computed for the lepton flavor invariants of the Standard Model with three generations including the right-handed neutrino sector needed to generate light neutrino masses via the see-saw mechanism. We also compute the Hilbert series of the quark flavor invariants for the case of four generations.Comment: 6 page

Wheat germ stabilization by heat-treatment or sourdough fermentation: effects on dough rheology and bread properties

The aim of this work was to evaluate the effects of wheat germ - stabilized by toasting or by sourdough fermentation - on dough and bread properties. Doughs were produced by adding increasing amounts of each type of stabilized germ, starting with the current recommended level of 3 g/100 g up to 20 g/100 g. Sourdough fermentation ensured the presence of lactic acid bacteria (LAB) in amounts comparable to those found in conventional sourdough. The acidification induced by LAB inactivates lipase and lipoxygenase, as does the toasting process. These results account for the decrease in rancidity, as demonstrated by the low development of hexanal during storage. Fermentation significantly decreased the content of glutathione, responsible for the deterioration of the rheological characteristics and workability of dough containing high levels of germ. Dough enriched with fermented germ exhibited high stability during mixing and development. Positive effects (high specific volume and low firmness) associated with the use of germ stabilized by fermentation have been detected both in fresh bread and in samples stored up to 4 days in controlled conditions of humidity and temperature. Finally, the sensory consumers' test confirmed that the addition of fermented germ did not diminish the liking of the sample

Neoadjuvant eribulin mesylate following anthracycline and taxane in triple negative breast cancer: Results from the HOPE study

Background Eribulin mesylate (E) is indicated for metastatic breast cancer patients previously treated with anthracycline and taxane. We argued that E could also benefit patients eligible for neoadjuvant chemotherapy. Methods Patients with primary triple negative breast cancer 2 cm received doxorubicin 60 mg/m2 and paclitaxel 200 mg/m2 x 4 cycles (AT) followed by E 1.4 mg/m2 x 4 cycles. Primary endpoint was pathological complete response (pCR) rate; secondary and explorative endpoints included clinical/metabolic response rates and safety, and biomarker analysis, respectively. Using a two-stage Simon design, 43 patients were to be included provided that 4 of 13 patients had achieved pCR in the first stage of the study. Results In stage I of the study 13 women were enrolled, median age 43 years, tumor size 2–5 cm in 9/13 (69%), positive nodal status in 8/13 (61%). Main grade 3 adverse event was neutropenia (related to AT and E in 4 and 2 cases, respectively). AT followed by E induced clinical complete + partial responses in 11/13 patients (85%), pCR in 3/13 (23%). Median measurements of maximum standardized uptake value (SUVmax) resulted 13, 3, and 1.9 at baseline, after AT and E, respectively. Complete metabolic response (CMR) occurred after AT and after E in 2 and 3 cases, respectively. Notably, 2 of the 5 (40%) patients with CMR achieved pCR at surgery. Immunostaining of paired pre-/post-treatment tumor specimens showed a reduction of β-catenin, CyclinD1, Zeb-1, and c-myc expression, in the absence of N-cadherin modulation. The study was interrupted at stage I due to the lack of the required patients with pCR. Conclusions Despite the early study closure, preoperative E following AT showed clinical and biological activity in triple negative breast cancer patients. Furthermore, the modulation of β-catenin pathway core proteins, supposedly outside the domain of epithelial–mesenchymal transition, claims for further investigation. Trial registration EU Clinical Trial Register, EudraCT number 2012-004956-12

Flow cytometric analysis of DNA content in human ovarian cancers.

A total of 155 samples from 101 patients with ovarian cancer were investigated using flow cytometry to evaluate the DNA index and the percentage of cells in the various cell cycle phases. Thirty-four samples were DNA diploid tumours, while the other 121 were DNA aneuploid tumours. The DNA index was very stable in different sites and over time in the same patient. Tumour stage and ploidy were significantly associated: stages III and IV tumour stage were more likely to be DNA aneuploid. Patients with residual tumour size at first surgery greater than 2 cm had a significantly larger number of DNA aneuploid than DNA diploid tumours. The DNA index was also related to the degree of differentiation of the tumours. The percentage of cells in the S phase of the cell cycle was significantly higher in DNA aneuploid and in poorly differentiated tumours than DNA diploid and well differentiated tumours. Multivariate analysis using the Cox model showed that the DNA index and the percentage of cells in S phase were not independent prognostic variables in this study. Prospectively collected data should be accumulated before assigning the DNA index an important role as a biological prognostic factor in ovarian cancer