Comparison of 3 Different Therapeutic Particles in Radioembolization of Locally Advanced Intrahepatic Cholangiocarcinoma.

Our objective was to compare 3 different therapeutic particles used for radioembolization in locally advanced intrahepatic cholangiocarcinoma. Methods: 90Y-glass, 90Y-resin, and 166Ho-labeled poly(l-lactic acid) microsphere prescribed activity was calculated as per manufacturer recommendations. Posttreatment quantitative 90Y PET/CT and quantitative 166Ho SPECT/CT were used to determine tumor-absorbed dose, whole-normal-liver-absorbed dose, treated-normal-liver-absorbed dose, tumor-to-nontumor ratio, lung-absorbed dose, and lung shunt fraction. Response was assessed using RECIST 1.1 and the [18F]FDG PET-based change in total lesion glycolysis. Hepatotoxicity was assessed using the radioembolization-induced liver disease classification. Results: Six 90Y-glass, 8 90Y-resin, and 7 166Ho microsphere patients were included for analysis. The mean administered activity was 2.6 GBq for 90Y-glass, 1.5 GBq for 90Y-resin, and 7.0 GBq for 166Ho microspheres. Tumor-absorbed dose and treated-normal-liver-absorbed dose were significantly higher for 90Y-glass than for 90Y-resin and 166Ho microspheres (mean tumor-absorbed dose, 197 Gy for 90Y-glass vs. 73 Gy for 90Y-resin and 50 Gy for 166Ho; mean treated-normal-liver-absorbed dose, 79 Gy for 90Y-glass vs. 37 Gy for 90Y-resin and 31 Gy for 166Ho). The whole-normal-liver-absorbed dose and tumor-to-nontumor ratio did not significantly differ between the particles. All patients had a lung-absorbed dose under 30 Gy and a lung shunt fraction under 20%. The 3 groups showed similar toxicity and response according to RECIST 1.1 and [18F]FDG PET-based total lesion glycolysis changes. Conclusion: The therapeutic particles used for radioembolization differed from each other and showed significant differences in absorbed dose, whereas toxicity and response were similar for all groups. This finding emphasizes the need for separate dose constraints and dose targets for each particle.

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter.

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

Infectious Bovine Rhinotracheitis Post-Eradication Program in the Autonomous Province of Bolzano, Italy: A Retrospective Study on Potential Bovine Herpesvirus Type 2 Cross-Reactivity.

Bovine alphaherpesviruses, BoAHV, can cause respiratory, genital and neurological disorders. In particular, bovine alphaherpesvirus type 1 (BoAHV1) is one of the most significant ruminant pathogens worldwide and it can heavily damage the livestock industry. BoAHV1 can cause infectious bovine rhinotracheitis (IBR) along with fertility disorders. Bovine alphaherpesvirus type 2 (BoAHV2) can cause two different conditions as well: pseudo-lumpy skin disease (PSLD) and bovine herpetic mammillitis (BHM). The autonomous province of Bolzano (Italy) has adopted several strategies to control and eradicate IBR, and it was declared in 2000 to be IBR-free by the European Commission. Since 2001, a post-eradication monitoring program has overseen the serological analysis of bulk milk and, in the presence of a positive result, a follow-up examination is performed on the individual blood serum of all bovines older than 24 months that belong to bulk milk-positive herds. Despite the detection of positives in both bulk milk and serum samples, South Tyrol has been declared IBR-free, as these positives have never been confirmed through seroneutralization. Between 2014 and 2022, approximately 41,000 bulk milk (averaging 4300 samples/year) and 3229 serum samples were tested for BoAHV1. The aim of this study was to evaluate the post-eradication program for IBR with a particular focus on the potential cross-reactivity with BoAHV2; for this reason, serum samples were also tested for BoAHV2 antibodies. This study could be of great importance for those countries that submit herds to an IBR monitoring and eradication program; performing further analyses to confirm and explain false positive outcomes would increase the reliability of the obtained results.

Quantitative 177Lu SPECT/CT imaging for personalized dosimetry using a ring-shaped CZT-based camera.

BACKGROUND: Dosimetry after radiopharmaceutical therapy with 177Lu (177Lu-RPT) relies on quantitative SPECT/CT imaging, for which suitable reconstruction protocols are required. In this study, we characterized for the first time the quantitative performance of a ring-shaped CZT-based camera using two different reconstruction algorithms: an ordered subset expectation maximization (OSEM) and a block sequential regularized expectation maximization (BSREM) combined with noise reduction regularization. This study lays the foundations for the definition of a reconstruction protocol enabling accurate dosimetry for patients treated with 177Lu-RPT. METHODS: A series of 177Lu-filled phantoms were acquired on a StarGuide™ (GE HealthCare), with energy and scatter windows centred at 208 (± 6%) keV and 185 (± 5%) keV, respectively. Images were reconstructed with the manufacturer implementations of OSEM (GE-OSEM) and BSREM (Q.Clear) algorithms, and various combinations of iterations and subsets. Additionally, the manufacturer-recommended Q.Clear-based reconstruction protocol was evaluated. Quantification accuracy, measured as the difference between the SPECT-based and the radionuclide calibrator-based activity, and noise were evaluated in a large cylinder. Recovery coefficients (RCs) and spatial resolution were assessed in a NEMA IEC phantom with sphere inserts. The reconstruction protocols considered suitable for clinical applications were tested on a cohort of patients treated with [177Lu]Lu-PSMA-I&T. RESULTS: The accuracy of the activity from the cylinder, although affected by septal penetration, was < 10% for all reconstructions. Both algorithms featured improved spatial resolution and higher RCs with increasing updates at the cost of noise build-up, but Q.Clear outperformed GE-OSEM in reducing noise accumulation. When the reconstruction parameters were carefully selected, similar values for noise (~0.15), spatial resolution (~1 cm) and RCs were found, irrespective of the reconstruction algorithm. Analogue results were found in patients. CONCLUSIONS: Accurate activity quantification is possible when imaging 177Lu with StarGuide™. However, the impact of septal penetration requires further investigations. GE-OSEM is a valid alternative to the recommended Q.Clear reconstruction algorithm, featuring comparable performances assessed on phantoms and patients.

Automatic healthy liver segmentation for holmium-166 radioembolization dosimetry.

BACKGROUND: For safe and effective holmium-166 (166Ho) liver radioembolization, dosimetry is crucial and requires accurate healthy liver definition. The current clinical standard relies on manual segmentation and registration of a separately acquired contrast enhanced CT (CECT), a prone-to-error and time-consuming task. An alternative is offered by simultaneous imaging of 166Ho and technetium-99m stannous-phytate accumulating in healthy liver cells (166Ho-99mTc dual-isotope protocol). This study compares healthy liver segmentation performed with an automatic method using 99mTc images derived from a 166Ho-99mTc dual-isotope acquisition to the manual segmentation, focusing on healthy liver dosimetry and corresponding hepatotoxicity. Data from the prospective HEPAR PLuS study were used. Automatic healthy liver segmentation was obtained by thresholding the 99mTc image (no registration step required). Manual segmentation was performed on CECT and then manually registered to the SPECT/CT and subsequently to the corresponding 166Ho SPECT to compute absorbed dose in healthy liver. RESULTS: Thirty-one patients (66 procedures) were assessed. Manual segmentation and registration took a median of 30 min per patient, while automatic segmentation was instantaneous. Mean ± standard deviation of healthy liver absorbed dose was 18 ± 7 Gy and 20 ± 8 Gy for manual and automatic segmentations, respectively. Mean difference ± coefficient of reproducibility between healthy liver absorbed doses using the automatic versus manual segmentation was 2 ± 6 Gy. No correlation was found between mean absorbed dose in the healthy liver and hepatotoxicity. CONCLUSIONS: 166Ho-99mTc dual-isotope protocol can automatically segment the healthy liver without hampering the 166Ho dosimetry assessment. TRIAL REGISTRATION: ClinicalTrials.gov, NCT02067988. Registered 20 February 2014. https://clinicaltrials.gov/ct2/show/NCT02067988.

Probing disorder in 2CzPN using core and valence states.

Molecules which exhibit thermally activated delayed fluorescence (TADF) show great promise for use in efficient, environmentally-friendly OLEDs, and thus the design of new TADF emitters is an active area of research. However, when used in devices, they are typically in the form of disordered thin films, where both the external molecular environment and thermally-induced internal variations in parameters such as the torsion angle can strongly influence their electronic structure. In this work, we use density functional theory and X-ray photoelectron spectroscopy to investigate the impact of disorder on both core and valence states in the TADF emitter 2CzPN (1,2-bis(carbazol-9-yl)-4,5-dicyanobenzene). By simulating gas phase molecules displaying varying levels of disorder, we assess the relative sensitivity of the different states to factors such as varying torsion angle. The theoretical results for both core and valence states show good agreement with experiment, thereby also highlighting the advantages of our approach for interpreting experimental spectra of large aromatic molecules, which are too complex to interpret based solely on experimental data.

Holmium-166 Radioembolization: Current Status and Future Prospective.

Since its first suggestion as possible option for liver radioembolization treatment, the therapeutic isotope holmium-166 (166Ho) caught the experts' attention due to its imaging possibilities. Being not only a beta, but also a gamma emitter and a lanthanide, 166Ho can be imaged using single-photon emission computed tomography and magnetic resonance imaging, respectively. Another advantage of 166Ho is the possibility to perform the scout and treatment procedure with the same particle. This prospect paves the way to an individualized treatment procedure, gaining more control over dosimetry-based patient selection and treatment planning. In this review, an overview on 166Ho liver radioembolization will be presented. The current clinical workflow, together with the most relevant clinical findings and the future prospective will be provided.

166Holmium-99mTechnetium dual-isotope imaging: scatter compensation and automatic healthy-liver segmentation for 166Holmium radioembolization dosimetry.

BACKGROUND: Partition modeling allows personalized activity calculation for holmium-166 (166Ho) radioembolization. However, it requires the definition of tumor and non-tumorous liver, by segmentation and registration of a separately acquired CT, which is time-consuming and prone to error. A protocol including 166Ho-scout, for treatment simulation, and technetium-99m (99mTc) stannous phytate for healthy-liver delineation was proposed. This study assessed the accuracy of automatic healthy-liver segmentation using 99mTc images derived from a phantom experiment. In addition, together with data from a patient study, the effect of different 99mTc activities on the 166Ho-scout images was investigated. To reproduce a typical scout procedure, the liver compartment, including two tumors, of an anthropomorphic phantom was filled with 250 MBq of 166Ho-chloride, with a tumor to non-tumorous liver activity concentration ratio of 10. Eight SPECT/CT scans were acquired, with varying levels of 99mTc added to the non-tumorous liver compartment (ranging from 25 to 126 MBq). For comparison, forty-two scans were performed in presence of only 99mTc from 8 to 240 MBq. 99mTc image quality was assessed by cold-sphere (tumor) contrast recovery coefficients. Automatic healthy-liver segmentation, obtained by thresholding 99mTc images, was evaluated by recovered volume and Sørensen-Dice index. The impact of 99mTc on 166Ho images and the role of the downscatter correction were evaluated on phantom scans and twenty-six patients' scans by considering the reconstructed 166Ho count density in the healthy-liver. RESULTS: All 99mTc image reconstructions were found to be independent of the 166Ho activity present during the acquisition. In addition, cold-sphere contrast recovery coefficients were independent of 99mTc activity. The segmented healthy-liver volume was recovered fully, independent of 99mTc activity as well. The reconstructed 166Ho count density was not influenced by 99mTc activity, as long as an adequate downscatter correction was applied. CONCLUSION: The 99mTc image reconstructions of the phantom scans all performed equally well for the purpose of automatic healthy-liver segmentation, for activities down to 8 MBq. Furthermore, 99mTc could be injected up to at least 126 MBq without compromising 166Ho image quality. Clinical trials The clinical study mentioned is registered with Clinicaltrials.gov (NCT02067988) on February 20, 2014.

Transition-Based Constrained DFT for the Robust and Reliable Treatment of Excitations in Supramolecular Systems.

Despite the variety of available computational approaches, state-of-the-art methods for calculating excitation energies, such as time-dependent density functional theory (TDDFT), are computationally demanding and thus limited to moderate system sizes. Here, we introduce a new variation of constrained DFT (CDFT), wherein the constraint corresponds to a particular transition (T), or a combination of transitions, between occupied and virtual orbitals, rather than a region of the simulation space as in traditional CDFT. We compare T-CDFT with TDDFT and ΔSCF results for the low-lying excited states (S1 and T1) of a set of gas-phase acene molecules and OLED emitters and with reference results from the literature. At the PBE level of theory, T-CDFT outperforms ΔSCF for both classes of molecules, while also proving to be more robust. For the local excitations seen in the acenes, T-CDFT and TDDFT perform equally well. For the charge transfer (CT)-like excitations seen in the OLED molecules, T-CDFT also performs well, in contrast to the severe energy underestimation seen with TDDFT. In other words, T-CDFT is equally applicable to both local excitations and CT states, providing more reliable excitation energies at a much lower computational cost than TDDFT cost. T-CDFT is designed for large systems and has been implemented in the linear-scaling BigDFT code. It is therefore ideally suited for exploring the effects of explicit environments on excitation energies, paving the way for future simulations of excited states in complex realistic morphologies, such as those which occur in OLED materials.

Lung Dose Measured on Postradioembolization 90Y PET/CT and Incidence of Radiation Pneumonitis.

Radiation pneumonitis is a rare but possibly fatal side effect of 90Y radioembolization. It may occur 1-6 mo after therapy, if a significant part of the 90Y microspheres shunts to the lungs. In current clinical practice, a predicted lung dose greater than 30 Gy is considered a criterion to exclude patients from treatment. However, contrasting findings regarding the occurrence of radiation pneumonitis and lung dose were previously reported in the literature. In this study, the relationship between the lung dose and the eventual occurrence of radiation pneumonitis after 90Y radioembolization was investigated. Methods: We retrospectively analyzed 317 90Y liver radioembolization procedures performed during an 8-y period (February 2012 to September 2020). We calculated the predicted lung mean dose (LMD) using 99mTc-MAA planar scintigraphy (LMDMAA) acquired during the planning phase and left LMD (LMDY-90) using the 90Y PET/CT acquired after the treatment. For the lung dose computation, we used the left lung as the representative lung volume, to compensate for scatter from the liver moving in the craniocaudal direction because of breathing and mainly affecting the right lung. Results: In total, 272 patients underwent 90Y procedures, of which 63% were performed with glass microspheres and 37% with resin microspheres. The median injected activity was 1,974 MBq (range, 242-9,538 MBq). The median LMDMAA was 3.5 Gy (range, 0.2-89.0 Gy). For 14 procedures, LMDMAA was more than 30 Gy. Median LMDY-90 was 1 Gy (range, 0.0-22.1 Gy). No patients had an LMDY-90 of more than 30 Gy. Of the 3 patients with an LMDY-90 of more than 12 Gy, 2 patients (one with an LMDY-90 of 22.1 Gy and an LMDMAA of 89 Gy; the other with an LMDY-90 of 17.7 Gy and an LMDMAA of 34.1 Gy) developed radiation pneumonitis and consequently died. The third patient, with an LMDY-90 of 18.4 Gy (LMDMAA, 29.1 Gy), died 2 mo after treatment, before the imaging evaluation, because of progressive disease. Conclusion: The occurrence of radiation pneumonitis as a consequence of a lung shunt after 90Y radioembolization is rare (<1%). No radiation pneumonitis developed in patients with a measured LMDY-90 lower than 12 Gy.

Does the Urinary Proteome Reflect ccRCC Stage and Grade Progression?

Due its ability to provide a global snapshot of kidney physiology, urine has emerged as a highly promising, non-invasive source in the search for new molecular indicators of disease diagnosis, prognosis, and surveillance. In particular, proteomics represents an ideal strategy for the identification of urinary protein markers; thus, a urinomic approach could also represent a powerful tool in the investigation of the most common kidney cancer, which is clear cell Renal Cell Carcinoma (ccRCC). Currently, these tumors are classified after surgical removal using the TNM and nuclear grading systems and prognosis is usually predicted based upon staging. However, the aggressiveness and clinical outcomes of ccRCC remain heterogeneous within each stratified group, highlighting the need for novel molecular indicators that can predict the progression of these tumors. In our study, we explored the association between the urinary proteome and the ccRCC staging and grading classification. The urine proteome of 44 ccRCC patients with lesions of varying severity was analyzed via label-free proteomics. MS data revealed several proteins with altered abundance according to clinicopathological stratification. Specifically, we determined a panel of dysregulated proteins strictly related to stage and grade, suggesting the potential utility of MS-based urinomics as a complementary tool in the staging process of ccRCC.

Gamma camera characterization at high holmium-166 activity in liver radioembolization.

BACKGROUND: High activities of holmium-166 (166Ho)-labeled microspheres are used for therapeutic radioembolization, ideally directly followed by SPECT imaging for dosimetry purposes. The resulting high-count rate potentially impacts dead time, affecting the image quality and dosimetric accuracy. This study assesses gamma camera performance and SPECT image quality at high 166Ho activities of several GBq. To this purpose, the liver compartment, including two tumors, of an anthropomorphic phantom was filled with 166Ho-chloride, with a tumor to non-tumorous liver activity concentration ratio of 10:1. Multiple SPECT/CT scans were acquired over a range of activities up to 2.7 GBq. Images were reconstructed using a commercially available protocol incorporating attenuation and scatter correction. Dead time effects were assessed from the observed count rate in the photopeak (81 keV, 15% width) and upper scatter (118 keV, 12% width) window. Post reconstruction, each image was scaled with an individual conversion factor to match the known total activity in the phantom at scanning time. The resulting activity concentration was measured in the tumors and non-tumorous liver. The image quality as a function of activity was assessed by a visual check of the absence of artifacts by a nuclear medicine physician. The apparent lung shunt fraction (nonzero due to scatter) was estimated on planar and SPECT images. RESULTS: A 20% count loss due to dead time was observed around 0.7 GBq in the photopeak window. Independent of the count losses, the measured activity concentration was up to 100% of the real value for non-tumorous liver, when reconstructions were normalized to the known activity at scanning time. However, for tumor spheres, activity concentration recovery was ~80% at the lowest activity, decreasing with increasing activity in the phantom. Measured lung shunt fractions were relatively constant over the considered activity range. CONCLUSIONS: At high 166Ho count rate, all images, visually assessed, presented no artifacts, even at considerable dead time losses. A quantitative evaluation revealed the possibility of reliable dosimetry within the healthy liver, as long as a post-reconstruction scaling to scanning activity is applied. Reliable tumor dosimetry, instead, remained hampered by the dead time.

Fast Molecular Compression by a Hyperthermal Collision Gives Bond-Selective Mechanochemistry.

Using electrospray ion beam deposition, we collide the complex molecule Reichardt's dye (C_{41}H_{30}NO^{+}) at low, hyperthermal translational energy (2-50 eV) with a Cu(100) surface and image the outcome at single-molecule level by scanning tunneling microscopy. We observe bond-selective reaction induced by the translational kinetic energy. The collision impulse compresses the molecule and bends specific bonds, prompting them to react selectively. This dynamics drives the system to seek thermally inaccessible reactive pathways, since the compression timescale (subpicosecond) is much shorter than the thermalization timescale (nanosecond), thereby yielding reaction products that are unobtainable thermally.

Monte Carlo-based scatter correction for the SMARTZOOM collimator.

BACKGROUND: Myocardial perfusion imaging is a commonly performed SPECT protocol and hence it would be beneficial if its scan duration could be shortened. For traditional gamma cameras, two developments have separately shown to allow for a shortened scan duration: (i) reconstructing with Monte Carlo-based scatter correction instead of dual-energy window scatter correction and (ii) acquiring projections with the SMARTZOOM collimator instead of a parallel-hole collimator. This study investigates which reduction in scan duration can be achieved when both methods are combined in a single system. RESULTS: The SMARTZOOM collimator was implemented in a Monte Carlo-based reconstruction package and the implementation was validated through image quality phantom experiments. The potential for scan duration reduction was evaluated with a phantom configuration that is realistic for myocardial perfusion imaging. The original reconstruction quality was achieved in 76 ± 8% of the original scan duration when switching from dual-energy window scatter correction to Monte Carlo-based scatter correction. The original reconstruction quality was achieved in 56 ± 13% of the original scan duration when switching from the parallel-hole to the SMARTZOOM collimator. After combining both methods in a single system, the original reconstruction quality was achieved in 34 ± 7% of the original scan duration. CONCLUSIONS: Monte Carlo-based scatter correction combined with the SMARTZOOM collimator can further decrease the scan duration in myocardial perfusion imaging.

Predicting Core Level Photoelectron Spectra of Amino Acids Using Density Functional Theory.

Core level photoelectron spectroscopy is a widely used technique to study amino acids. Interpretation of the individual contributions from functional groups and their local chemical environments to overall spectra requires both high-resolution reference spectra and theoretical insights, for example, from density functional theory calculations. This is a particular challenge for crystalline amino acids due to the lack of experimental data and the limitation of previous calculations to gas phase molecules. Here, a state of the art multiresolution approach is used for high-precision gas phase calculations and to validate core hole pseudopotentials for plane-wave calculations. This powerful combination of complementary numerical techniques provides a framework for accurate ΔSCF calculations for molecules and solids in systematic basis sets. It is used to successfully predict C and O 1s core level spectra of glycine, alanine, and serine and identify chemical state contributions to experimental spectra of crystalline amino acids.

Detecting Proteomic Indicators to Distinguish Diabetic Nephropathy from Hypertensive Nephrosclerosis by Integrating Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging with High-Mass Accuracy Mass Spectrometry.

INTRODUCTION: Diabetic nephropathy (DN) and hypertensive nephrosclerosis (HN) represent the most common causes of chronic kidney disease (CKD) and many patients progress to -end-stage renal disease. Patients are treated primarily through the management of cardiovas-cular risk factors and hypertension; however patients with HN have a more favorable outcome. A noninvasive clinical approach to separate these two entities, especially in hypertensive patients who also have diabetes, would allow for targeted treatment and more appropriate resource allocation to those patients at the highest risk of CKD progression. Meth-ods: In this preliminary study, high-spatial-resolution matrix-assisted laser desorption/ion-ization (MALDI) mass spectrometry imaging (MSI) was integrated with high-mass accuracy MALDI-FTICR-MS and nLC-ESI-MS/MS analysis in order to detect tissue proteins within kidney biopsies to discriminate cases of DN (n = 9) from cases of HN (n = 9). RESULTS: Differences in the tryptic peptide profiles of the 2 groups could clearly be detected, with these becoming even more evident in the more severe histological classes, even if this was not evident with routine histology. In particular, 4 putative proteins were detected and had a higher signal intensity within regions of DN tissue with extensive sclerosis or fibrosis. Among these, 2 proteins (PGRMC1 and CO3) had a signal intensity that increased at the latter stages of the disease and may be associated with progression. DISCUSSION/CONCLUSION: This preliminary study represents a valuable starting point for a future study employing a larger cohort of patients to develop sensitive and specific protein biomarkers that could reliably differentiate between diabetic and hypertensive causes of CKD to allow for improved diagnosis, fewer biopsy procedures, and refined treatment approaches for clinicians.

Flexibilities of wavelets as a computational basis set for large-scale electronic structure calculations.

The BigDFT project was started in 2005 with the aim of testing the advantages of using a Daubechies wavelet basis set for Kohn-Sham (KS) density functional theory (DFT) with pseudopotentials. This project led to the creation of the BigDFT code, which employs a computational approach with optimal features of flexibility, performance, and precision of the results. In particular, the employed formalism has enabled the implementation of an algorithm able to tackle DFT calculations of large systems, up to many thousands of atoms, with a computational effort that scales linearly with the number of atoms. In this work, we recall some of the features that have been made possible by the peculiar properties of Daubechies wavelets. In particular, we focus our attention on the usage of DFT for large-scale systems. We show how the localized description of the KS problem, emerging from the features of the basis set, is helpful in providing a simplified description of large-scale electronic structure calculations. We provide some examples on how such a simplified description can be employed, and we consider, among the case-studies, the SARS-CoV-2 main protease.

The management of haemoglobin interference for the MALDI-MSI proteomics analysis of thyroid fine needle aspiration biopsies.

MALDI-MSI represents an ideal tool to explore the spatial distribution of proteins directly in situ, integrating molecular and cytomorphological information, enabling the discovery of potential diagnostic markers in thyroid cytopathology. However, red cells present in the fine needle aspiration biopsy (FNAB) specimens caused ion suppression of other proteins during the MALDI-MSI analysis due to large amount of haemoglobin. Aim of this study was to set up a sample preparation workflow able to manage this haemoglobin interference. Three protocols were compared using ex vivo cytological samples collected from fresh thyroid nodules of 9 patients who underwent thyroidectomy: (A) conventional air-dried smears, (B) cytological smears immediately fixed in ethanol, and (C) ThinPrep liquid-based preparation. Protocols C and A were also evaluated using real FNABs. Results show that protocol C markedly decreased the amount of haemoglobin, with respect to protocols A and B. Protein profiles obtained with protocols A and B were characterised by high inter-patient variability, probably related to the abundance of the haemoglobin, whereas similar spectra were observed for protocol C, where haemoglobin contents were lower. Our findings suggest protocol C as the sample preparation method for MALDI-MSI analysis. Graphical abstract.

Study of Anopheles gambiae 3-hydroxykynurenine transaminase activity and inhibition by LC-MS/MS method.

In Anopheles gambiae, the most efficient vector of the malaria parasite Plasmodium falciparum, 3-hydroxykynurenine is endowed with a toxic potential. In adult mosquitoes, the excess of 3-hydroxykynurenine is removed by a specific transaminase (3-hydroxykynurenine transaminase, 3-HKT) which converts the compound into the more stable xanthurenic acid. Interfering with 3-hydroxykynurenine metabolism in A. gambiae is a potential approach for the development of transmission-blocking drugs and insecticides. Hence, the aims of this work were to develop and validate a new LC-MS/MS method for the evaluation of A. gambiae 3-hydroxykynurenine transaminase (Ag-HKT) activity and the determination of the potency of inhibitors of the enzyme. We set up a LC-MS/MS based enzymatic assay for the determination of kinetic constants values of the recombinant Ag-HKT enzyme and for the evaluation of Ag-HKT inhibition by a known protein inhibitor used as reference and a newly synthesized compound. The chromatographic separation was performed in a gradient mode on a Phenomenex Synergi Polar-RP (150 mm × 2.0, 4 µm) with methanol and water containing both 0.2% formic acid. Mass spectrometric detection was achieved with an ion trap equipped with an ESI source, in positive ionization scan, operating in SRM mode. The LC-MS/MS method was validated in terms of selectivity, linearity, precision and accuracy.

Proteomics of liquid biopsies: Depicting RCC infiltration into the renal vein by MS analysis of urine and plasma.

Liquid biopsies, as blood and urine, could offer an invaluable, easily accessible source of biomarkers, and evidences for elucidating the pathological processes. Only few studies integrated the proteomes driven by more than one biofluid. Furthermore, it is not clear which biofluid better mirrors the alterations triggered by disease. Venous infiltrating RCC(Renal Cell Carcinoma) could represent an advantageous model for exploring this aspect. Herein, we investigate how blood and urine "proteomically" reflect the changes occurring during RCC infiltration into renal vein(RV) by label-free nLC-ESI-MS/MS. We found 574 and 58 differentially expressed proteins(DEPs) in response to vascular involvement. To the augment of vascular involvement, the abundance of only three proteins in urine(UROM,RALA,CNDP1) and two in plasma(APOA1,K2C1) diminished while increased for twenty-six urinary proteins. 80 proteins were found both in urine and plasma, among which twenty-eight were DEPs. A huge overlap between the two biofluids was highlighted, as expected, being urine the filtrate of blood. However, this consistency decreases when RV-occlusion occurs suggesting alternative protein releases, and a loss of kidney architecture. Moreover, several proteomic and functional signatures were biofluid-specific. In conclusion, the complementarity between the specimens allowed to achieve a deeper level of molecular complexity of the RCC venous infiltration. SIGNIFICANCE: Although plasma and urine are strongly interconnected, only few proteomic studies investigated the complementarity of these fluids as bio-sources of information. Moreover, none of them was focused to their analysis and comparison in the context of vascular infiltration of renal cancer. Herein, new insights were gained regarding the impact into urinary and plasma proteome of the changes triggered by the ccRCC invasion into vascular system and renal vein. Furthermore, the integration of the information driven by the two liquid biopsies permits to unravel biological processes otherwise lost.