Estimation of protein folding probability from equilibrium simulations

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide or protein. The procedure utilizes a structurally homogeneous clustering and does not require any additional simulation. It can be used to detect multiple folding pathways as shown for a three-stranded antiparallel $\beta$-sheet peptide investigated by implicit solvent molecular dynamics simulations.Comment: 7 pages, 4 figures, supplemetary material

Animated GIF optimization by adaptive color local table management

After thirty years of the GIF file format, today is becoming more popular than ever: being a great way of communication for friends and communities on Instant Messengers and Social Networks. While being so popular, the original compression method to encode GIF images have not changed a bit. On the other hand popularity means that storage saving becomes an issue for hosting platforms. In this paper a parametric optimization technique for animated GIFs will be presented. The proposed technique is based on Local Color Table selection and color remapping in order to create optimized animated GIFs while preserving the original format. The technique achieves good results in terms of byte reduction with limited or no loss of perceived color quality. Tests carried out on 1000 GIF files demonstrate the effectiveness of the proposed optimization strategy

Early detection of hip periprosthetic joint infections through CNN on Computed Tomography images

Early detection of an infection prior to prosthesis removal (e.g., hips, knees or other areas) would provide significant benefits to patients. Currently, the detection task is carried out only retrospectively with a limited number of methods relying on biometric or other medical data. The automatic detection of a periprosthetic joint infection from tomography imaging is a task never addressed before. This study introduces a novel method for early detection of the hip prosthesis infections analyzing Computed Tomography images. The proposed solution is based on a novel ResNeSt Convolutional Neural Network architecture trained on samples from more than 100 patients. The solution showed exceptional performance in detecting infections with an experimental high level of accuracy and F-score

Boosting multiple sclerosis lesion segmentation through attention mechanism

Magnetic resonance imaging is a fundamental tool to reach a diagnosis of multiple sclerosis and monitoring its progression. Although several attempts have been made to segment multiple sclerosis lesions using artificial intelligence, fully automated analysis is not yet available. State-of-the-art methods rely on slight variations in segmentation architectures (e.g. U-Net, etc.). However, recent research has demonstrated how exploiting temporal-aware features and attention mechanisms can provide a significant boost to traditional architectures. This paper proposes a framework that exploits an augmented U-Net architecture with a convolutional long short-term memory layer and attention mechanism which is able to segment and quantify multiple sclerosis lesions detected in magnetic resonance images. Quantitative and qualitative evaluation on challenging examples demonstrated how the method outperforms previous state-of-the-art approaches, reporting an overall Dice score of 89% and also demonstrating robustness and generalization ability on never seen new test samples of a new dedicated under construction dataset

A Robust Document Identification Framework through f-BP Fingerprint

© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/)The identification of printed materials is a critical and challenging issue for security purposes, especially when it comes to documents such as banknotes, tickets, or rare collectable cards: eligible targets for ad hoc forgery. State-of-the-art methods require expensive and specific industrial equipment, while a low-cost, fast, and reliable solution for document identification is increasingly needed in many contexts. This paper presents a method to generate a robust fingerprint, by the extraction of translucent patterns from paper sheets, and exploiting the peculiarities of binary pattern descriptors. A final descriptor is generated by employing a block-based solution followed by principal component analysis (PCA), to reduce the overall data to be processed. To validate the robustness of the proposed method, a novel dataset was created and recognition tests were performed under both ideal and noisy conditions.Peer reviewedFinal Published versio

A Novel Approach for Multiple Material Extrusion in Arthroscopic Knee Surgery

Articular cartilage defects and degenerative diseases are pathological conditions that cause pain and the progressive loss of joint functionalities. The most severe cases are treated through partial or complete joint replacement with prostheses, even if the interest in cartilage regeneration and re-growth methods is steadily increasing. These methods consist of the targeted deposition of biomaterials. Only a few tools have been developed so far for performing these procedures in a minimally invasive way. This work presents an innovative device for the direct deposition of multiple biomaterials in an arthroscopic scenario. The tool is easily handleable and allows the extrusion of three different materials simultaneously. It is also equipped with a flexible tip to reach remote areas of the damaged cartilage. Three channels are arranged coaxially and a spring-based dip-coating approach allows the fabrication and assembly of a bendable polymeric tip. Experimental tests were performed to characterize the tip, showing the ability to bend it up to 90 degrees (using a force of similar to 1.5 N) and to extrude three coaxial biomaterials at the same time with both tip straight and tip fully bent. Rheometric analysis and fluid-dynamic computational simulations were performed to analyze the fluids' behavior; the maximum shear stresses were observed in correspondence to the distal tip and the channel convergence chamber, but with values up to similar to 1.2 kPa, compatible with a safe extrusion of biomaterials, even laden with cells. The cells viability was assessed after the extrusion with Live/Dead assay, confirming the safety of the extrusion procedures. Finally, the tool was tested arthroscopically in a cadaveric knee, demonstrating its ability to deliver the biomaterial in different areas, even ones that are typically hard-to-reach with traditional tools

Soft Perfusable Device to Culture Skeletal Muscle 3D Constructs in Air

Devices for in vitro culture of three-dimensional (3D) skeletal muscle tissues have multiple applications, including tissue engineering and muscle-powered biorobotics. In both cases, it is crucial to recreate a biomimetic environment by using tailored scaffolds at multiple length scales and to administer prodifferentiative biophysical stimuli (e.g., mechanical loading). On the contrary, there is an increasing need to develop flexible biohybrid robotic devices capable of maintaining their functionality beyond laboratory settings. In this study, we describe a stretchable and perfusable device to sustain cell culture and maintenance in a 3D scaffold. The device mimics the structure of a muscle connected to two tendons: Tendon−Muscle−Tendon (TMT). The TMT device is composed of a soft (E ∼ 6 kPa) porous (pore diameter: ∼650 μm) polyurethane scaffold, encased within a compliant silicone membrane to prevent medium evaporation. Two tendon-like hollow channels interface the scaffold with a fluidic circuit and a stretching device. We report an optimized protocol to sustain C2C12 adhesion by coating the scaffold with polydopamine and fibronectin. Then, we show the procedure for the soft scaffold inclusion in the TMT device, demonstrating the device’s ability to bear multiple cycles of elongations, simulating a protocol for cell mechanical stimulation. By using computational fluid dynamic simulations, we show that a flow rate of 0.62 mL/min ensures a wall shear stress value safe for cells (<2 Pa) and 50% of scaffold coverage by an optimal fluid velocity. Finally, we demonstrate the effectiveness of the TMT device to sustain cell viability under perfusion for 24 h outside of the CO2 incubator. We believe that the proposed TMT device can be considered an interesting platform to combine several biophysical stimuli, aimed at boosting skeletal muscle tissue differentiation in vitro, opening chances for the development of muscle-powered biohybrid soft robots with long-term operability in real-world environments

Case report: A Saprochaete clavata (Magnusiomyces clavatus) severe infection effectively treated with granulocyte transfusion in a young patient with myeloid sarcoma

Myeloid sarcoma is a hematologic malignancy consisting of extramedullary tissue involvement by myeloid blasts, usually considered as acute myeloid leukemia and treated accordingly. The disease itself, together with chemotherapy and disease-associated factors, may have an impact in increasing the risk of developing severe and frequently life-threatening infections. Herein, we describe the case of a patient with a right breast skin lesion, histologically diagnosed myeloid sarcoma, who developed a severe disseminated fungal infection by Saprochaete clavata (Magnusiomyces clavatus), during the first consolidation course of chemotherapy. Despite maximum antifungal therapy, the infection progressed and the fungus continued to be isolated until granulocyte transfusion therapy was initiated. Our experience suggests that patients with profound and long-lasting neutropenia could benefit from granulocyte transfusions as additional therapy in severe fungal infections resistant to broad-spectrum antimicrobial therapy

In BCR-ABL1 Positive B-Cell Acute Lymphoblastic Leukemia, Steroid Therapy Induces Hypofibrinogenemia

Hypofibrinogenemia (HF) in adult acute lymphoblastic leukemia (ALL) of B lineage is uncommon and mostly associated with asparaginase (ASP) delivery. Since we noticed a significant reduction in fibrinogen (FBG) plasma levels even before the first ASP dose, we aim to assess the levels of FBG during induction treatment and explore if the FBG fall correlated with therapies other than asparaginase and/or specific leukemia biological features. We retrospectively analyzed FBG levels in 115 patients with B-ALL. In 74 (64%) out of 115 patients FBG decline occurred during the steroid prephase. In univariate analysis, such a steroid-related HF was significantly associated with BCR-ABL1 rearrangement (p = 0.00158). None of those experiencing HF had significant modifications of liver function tests during induction treatment. Our retrospective study suggests that in B-ALL, steroid therapy can also induce HF and that such an event is preferentially observed in patients carrying BCR-ABL1 rearrangements. The pathogenesis of this phenomenon is still unclear. We attempt to explain it by applying the International Society of Thrombosis and Hemostasis-Disseminated Intravascular Coagulation score (ISTH-DIC score); nonetheless additional studies are needed to clarify further the mechanisms of HF in this subset of patients