Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Vimentin Layers on Solid Substrates: Adsorption Kinetics and Corona Formation Investigations

Adsorption kinetics of human vimentin on negatively charged substrates (mica, silica, and polymer particles) was analyzed using atomic force microscopy (AFM), quartz microbalance (QCM), and the laser doppler velocimetry (LDV) method. AFM studies realized under diffusion conditions proved that the adsorbed protein layer mainly consisted of aggregates in the form of compact tetramers and hexamers of a size equal to 11–12 nm. These results were consistent with vimentin adsorption kinetics under flow conditions investigated by QCM. It was established that vimentin aggregates efficiently adsorbed on the negatively charged silica sensor at pH 3.5 and 7.4, forming compact layers with the coverage reaching 3.5 mg m–2. Additionally, the formation of the vimentin corona at polymer particles was examined using the LDV method and interpreted in terms of the electrokinetic model. This allowed us to determine the zeta potential of the corona as a function of pH and the electrokinetic charge of aggregates, which was equal to −0.7 e nm–2 at pH 7.4 in a 10 mM NaCl solution. The anomalous adsorption of aggregates exhibiting an average negative charge on the negatively charged substrates was interpreted as a result of a heterogeneous charge distribution. These investigations confirmed that it is feasible to deposit stable vimentin layers both at planar substrates and at carrier particles with well-controlled coverage and zeta potential. They can be used for investigations of vimentin interactions with various ligands including receptors of the innate immune system, immunoglobulins, bacterial virulence factors, and spike proteins of viruses.
WATER-WAVES AND REVERSIBLE SPATIAL DYNAMICS

The introduction of spatial dynamics by K.Kirchgassner in the eighties allowed big progresses in the mathematical theory of water waves. Several new forms of localized waves were discovered, as well in 2D as in 3D. The talk gives elements of the reduction methods used in spatial dynamics (Center manifold reduction and normal forms for infinite dimensional reversible systems ) and examples of results for water wave theory as depression solitary waves with damped oscillations, or generalized solitary waves with a very small (nonzero) periodic amplitude at infinity. We shall also mention the limitations of the method in physical limiting cases.
PHF20 is crucial for epigenetic control of starvation-induced autophagy through enhancer activation

Abstract Autophagy is a catabolic pathway that maintains cellular homeostasis under various stress conditions, including conditions of nutrient deprivation. To elevate autophagic flux to a sufficient level under stress conditions, transcriptional activation of autophagy genes occurs to replenish autophagy components. Thus, the transcriptional and epigenetic control of the genes regulating autophagy is essential for cellular homeostasis. Here, we applied integrated transcriptomic and epigenomic profiling to reveal the roles of plant homeodomain finger protein 20 (PHF20), which is an epigenetic reader possessing methyl binding activity, in controlling the expression of autophagy genes. Phf20 deficiency led to impaired autophagic flux and autophagy gene expression under glucose starvation. Interestingly, the genome-wide characterization of chromatin states by Assay for Transposase-Accessible Chromatin (ATAC)-sequencing revealed that the PHF20-dependent chromatin remodelling occurs in enhancers that are co-occupied by dimethylated lysine 36 on histone H3 (H3K36me2). Importantly, the recognition of H3K36me2 by PHF20 was found to be highly correlated with increased levels of H3K4me1/2 at the enhancer regions. Collectively, these results indicate that PHF20 regulates autophagy genes through enhancer activation via H3K36me2 recognition as an epigenetic reader. Our findings emphasize the importance of nuclear events in the regulation of autophagy.
Association between serum calcium and in-hospital mortality in critical patients with multiple myeloma: a cohort study

ABSTRACT Background Elevated serum calcium levels may serve as a useful clinical biomarker of mortality in patients with multiple myeloma(MM). However, the clinical significance of the relationship between serum calcium levels and in-hospital mortality in MM patients admitted to the Intensive Care Unit (ICU) remains unclear. Objectives This study aimed to explore the association between serum calcium levels and in-hospital mortality in patients with MM in the ICU. Methods Patients with MM were identified from the Medical Information Mart for Intensive Care IV(MIMIC-IV) database. The outcome was in-hospital mortality. Multivariable-adjusted Cox regression analysis, curve fitting, and threshold effects analysis were used to assess the relationship between serum calcium levels and in-hospital mortality in patients with MM in the ICU. Results Our study included 262 patients with MM with a mean age of 72.3 ± 11.0 years, 63.4% of whom were male. The in-hospital mortality was 19.5% (51/262). The relationship between serum calcium levels and in-hospital mortality was nonlinear. The effect size on the left and right sides of the inflection point, were 0.270 (HR: 0.270, 95% CI 0.106-0.687, P < 0.05) and 2.104 (HR: 2.104, 95% CI 1.069-4.142, P < 0.05), respectively. The results of the sensitivity analysis remained stable. Conclusion Our findings show that a nonlinear relationship exists between serum calcium levels and in-hospital mortality in critically ill patients with MM. A serum calcium level of approximately 8.40 mg/dL was associated with the lowest risk of in-hospital mortality, which increases with rising serum calcium levels, and should be of concern to ICU physicians.
Improving yield of a recombinant biologic in a Brassica hairy root manufacturing process

Hairy root systems have proven to be a viable alternative for recombinant protein production. For recalcitrant proteins, maximizing the productivity of hairy root cultures is essential. The aim of this study was to optimize a Brassica rapa rapa hairy root process for secretion of alpha‐ l‐iduronidase (IDUA), a biologic of medical value. The process was first optimized with hairy roots expressing eGFP. For the biomass optimization, the highest biomass yields were achieved in modified Gamborg B5 culture medium. For the secretion induction, the optimized secretion media was obtained with additives (1.5 g/l PVP + 1 mg/l 2,4‐ d + 20.5 g/l KNO3) resulting in 3.4 fold eGFP secretion when compared to the non‐induced control. These optimized conditions were applied to the IDUA‐expressing hairy root clone, confirming that the highest yields of secreted IDUA occurred when using the defined additive combination. The functionality of the IDUA protein, secreted and intracellular, was confirmed with an enzymatic activity assay. A > 150‐fold increase of the IDUA activity was observed using an optimized secretion medium, compared with a non‐induced medium. We have proven that our B. rapa rapa hairy root system can be harnessed to secrete recalcitrant proteins, illustrating the high potential of hairy roots in plant molecular farming.
Non-intubated Uniportal Subxiphoid Video-Assisted Thoracoscopic Surgery for Extended Thymectomy in Myasthenia Gravis Patients: A Case Series

Minimally invasive strategies are increasingly popular in patients with myasthenia gravis (MG)-associated thymomas. Within the context of video-assisted thoracoscopic surgery (VATS) as a widely known minimally invasive option, the most recent achievement is uniportal subxiphoid VATS. In MG patients, it is mandatory (1) to minimize perioperative interference with administered anesthetics to avoid complications and (2) to achieve a complete surgical resection, as the prognosis essentially depends on radical tumor resection. In order to fulfill these criteria, we merged this surgical technique with its anesthesiologic counterpart: regional anesthesia with the maintenance of spontaneous ventilation via a laryngeal mask. Non-intubated uniportal subxiphoid VATS for extended thymectomy allowed radical thymectomy in all MG patients with both rapid symptom control and fast recovery.
Analysis of lower limb prosthetic socket interface based on stress and motion measurements

The study was designed to establish a biomechanical assessment platform for the lower limb residuum/socket interface as a function of duration and speed of movement. The approach exploits an interface sensor which measures multi-directional stresses at the interface. The corresponding interface coupling motion was assessed using a 3D motion capture system. A longitudinal study, involving a trans-femoral amputee, was conducted with nine repeated level walking sessions over a 12-month period. The effect of walking speed on interface biomechanics was also assessed. Interface peak pressures and shear stresses in the range of 55–59 kPa and 12–19 kPa were measured, respectively, over all sessions in the 12 months study period at the posterior-proximal location of the residuum. The peak pressure and longitudinal shear values were found to fluctuate approximately 11% and 40% as against its maximum value, respectively, over 12 months. In addition, up to 12° of angular coupling and up to 28 mm of pistoning were recorded over a gait cycle, which was found to change by 29% and 45% respectively over the study period. The variation in walking speed, by altering self-selected cadence, resulted in changes of pressure and shear stresses at mid-stance of the gait cycle. In particular, as compared with self-selected cadence, for fast speed, peak pressure and peak longitudinal shear stress decreased by 5% and 33%, respectively. For slow speed, peak pressure and peak longitudinal shear stress increased by 7% and 17%, respectively. The corresponding angular and pistoning revealed a variation of up to 29% and 45%, respectively. This biomechanical assessment approach shows promise in the quantitative assessment of interface kinematics and kinetics for lower limb prosthetics, the usage of which could assist the clinical assessment of prosthetic socket fit. Graphical Abstract
High‐throughput Method for Novel Medium Development for Culture of Anaerobic Gut Bacteria

Gut microbiota play important roles in the health of their host and detailed investigation of these organisms requires in vitro culture. Culturing strictly anaerobic bacteria can be a challenge as the gut environment they inhabit is nutritionally complex. Use of complex media containing nutritionally rich but undefined gut fluid reduces the accuracy of physiological and metabolomic studies. Here we present a high‐throughput protocol for comparing growth rates of fastidiously anaerobic bacteria on different media. These protocols can be used to develop a solid medium made up of commercially sourced ingredients, providing replicable growth conditions for previously uncultured anaerobic bacteria. As many fastidious bacteria grow poorly in a liquid broth, these protocols measure bacterial growth rate on solid media. These protocols speed up and simplify the growth rate measurement process by using a multiwell format and equations in place of physical McFarland standards to calculate approximate cell density. Bacterial strains belonging to the families Erysipelotrichaceae and Lachnospiraceae (phylum Firmicutes) isolated from the hindgut of Kyphosus sydneyanus were used to demonstrate the efficacy of these protocols. Bacterial growth rates were compared between a nutritionally rich medium with gut fluid versus a novel replicable medium with mannitol. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
Sex disparity of lung cancer risk in non-smokers: a multicenter population-based prospective study based on China National Lung Cancer Screening Program

Abstract Background: Non-smokers account for a large proportion of lung cancer patients, especially in Asia, but the attention paid to them is limited compared with smokers. In non-smokers, males display a risk for lung cancer incidence distinct from the females—even after excluding the influence of smoking; but the knowledge regarding the factors causing the difference is sparse. Based on a large multicenter prospective cancer screening cohort in China, we aimed to elucidate the interpretable sex differences caused by known factors and provide clues for primary and secondary prevention. Methods: Risk factors including demographic characteristics, lifestyle factors, family history of cancer, and baseline comorbidity were obtained from 796,283 Chinese non-smoking participants by the baseline risk assessment completed in 2013 to 2018. Cox regression analysis was performed to assess the sex difference in the risk of lung cancer, and the hazard ratios (HRs) that were adjusted for different known factors were calculated and compared to determine the proportion of excess risk and to explain the existing risk factors. Results: With a median follow-up of 4.80 years, 3351 subjects who were diagnosed with lung cancer were selected in the analysis. The lung cancer risk of males was significantly higher than that of females; the HRs in all male non-smokers were 1.29 (95% confidence interval [CI]: 1.20–1.38) after adjusting for the age and 1.38 (95% CI: 1.28–1.50) after adjusting for all factors, which suggested that known factors could not explain the sex difference in the risk of lung cancer in non-smokers. Known factors were 7% (|1.29–1.38|/1.29) more harmful in women than in men. For adenocarcinoma, women showed excess risk higher than men, contrary to squamous cell carcinoma; after adjusting for all factors, 47% ([1.30–1.16]/[1.30–1]) and 4% ([7.02–6.75]/[7.02–1])) of the excess risk was explainable in adenocarcinoma and squamous cell carcinoma. The main causes of gender differences in lung cancer risk were lifestyle factors, baseline comorbidity, and family history. Conclusions: Significant gender differences in the risk of lung cancer were discovered in China non-smokers. Existing risk factors did not explain the excess lung cancer risk of all non-smoking men, and the internal causes for the excess risk still need to be explored; most known risk factors were more harmful to non-smoking women; further exploring the causes of the sex difference would help to improve the prevention and screening programs and protect the non-smoking males from lung cancers.
Effects of Resistance Priming Exercise on Within-day Jumping Performance and its Relationship with Strength Level

Abstract This study aimed to identify the effects of same-day resistance priming exercise on countermovement jump parameters and subjective readiness, and to identify whether baseline strength level influenced these outcomes. Fourteen participants performed two separate conditions (Priming [2 sets high-load parallel squats with a 20% velocity loss cut-off] and Control) in a randomized, counterbalanced crossover design. Countermovement jump was assessed at pre, post and 6 h while readiness was assessed at pre and at 6 h only. All countermovement jump force-time metrics were similar between conditions ( p >0.05), but different individual responses were noted 6 h after priming. Jump height was increased for 4/14, decreased for another 4/14, and maintained for 6/14 participants at 6 h. Higher perceived physical performance capability ( p <0.001) and activation balance ( p =0.005) were observed after priming only. Positive relationships were observed between strength and the percentage change in jump height (r=0.47–0.50; p =0.033–0.042), concentric peak velocity (r=0.48–0.51; p =0.030–0.041) and im p ulse (r=0.47; p =0.030–0.045) at post and 6 h after priming exercise. These findings suggest that velocity-based high-load low-volume priming exercise has potential to positively impact jump performance and subjective readiness later that day in certain individuals. Participant absolute strength level may influence this response but should be confirmed in subsequent studies.
Influence of the allometric scale on the relationships between running economy, mechanical efficiency and performance in long distance runners : running efficiency and long-distance performance prediction

The aim of this thesis was to use allometric models to analyze the relationship that running economy(ECO) and mechanical efficiency (Ef) have on the performance of middle- and long-distance runners.Based on the results of three original studies, we concluded that allometric scaling can improve therelationship between ECO and performance in recreational middle- and long-distance runners, mainlydue to morphofunctional aspects. Similarly, the mechanical works, especially the external mechanicalwork, may be considered to be predictive of running performance and a specific allometric exponentcan improve these predictions. The results also showed that Ef is an important predictor of theperformance of long-distance runners. However, when the specific allometric exponents were applied,there was no improvement in the prediction of this performance. The results also showed that it isimportant to consider the contribution of anaerobic energy expenditure when calculating Ef, becauseotherwise the results may be overestimated, as already reported in other studies. In general, when theobjective is to predict the performance of middle- or long-distance runners through metabolic ormechanical powers, it is useful to adopt a specific allometric exponent of the group investigated.However, when this prediction is performed considering the Ef, particularly in high-performance longdistancerunners, the allometric application is not necessary.
Predicting drug response and toxicity in metastatic colorectal cancer: the role of germline markers

ABSTRACT Introduction Despite the introduction of targeted agents leading to therapeutic advances, clinical management of patients with metastatic colorectal cancer (mCRC) is still challenged by significant interindividual variability in treatment outcomes, both in terms of toxicity and therapy efficacy. The study of germline genetic variants could help to personalize and optimize therapeutic approaches in mCRC. Areas covered A systematic review of pharmacogenetic studies in mCRC patients published on PubMed between 2011 and 2021, evaluating the role of germline variants as predictive markers of toxicity and efficacy of drugs currently approved for treatment of mCRC, was perfomed. Expert opinion Despite the large amount of pharmacogenetic data published to date, only a few genetic markers (i.e. DPYD and UGT1A1 variants) reached the clinical practice, mainly to prevent the toxic effects of chemotherapy. The large heterogeneity of available studies represents the major limitation in comparing results and identifying potential markers for clinical use, the role of which remains exploratory in most cases. However, the available published findings are an important starting point for future investigations. They highlighted new promising pharmacogenetic markers within the network of inflammatory and immune response signaling. In addition, the emerging role of previously overlooked rare variants has been pointed out.
Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee

To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee’s role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants–in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee’s functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.
Influence Maximization With Visual Analytics

In social networks, individuals’ decisions are strongly influenced by recommendations from their friends, acquaintances, and favorite renowned personalities. The popularity of online social networking platforms makes them the prime venues to advertise products and promote opinions. The <italic>Influence Maximization</italic> (IM) problem entails selecting a <italic>seed set</italic> of users that maximizes the influence spread, i.e., the expected number of users positively influenced by a stochastic diffusion process triggered by the seeds. Engineering and analyzing IM algorithms remains a difficult and demanding task due to the NP-hardness of the problem and the stochastic nature of the diffusion processes. Despite several heuristics being introduced, they often fail in providing enough information on how the network topology affects the diffusion process, precious insights that could help researchers improve their seed set selection. In this paper, we present VAIM, a visual analytics system that supports users in analyzing, evaluating, and comparing information diffusion processes determined by different IM algorithms. Furthermore, VAIM provides useful insights that the analyst can use to modify the seed set of an IM algorithm, so to improve its influence spread. We assess our system by: <inline-formula><tex-math notation="LaTeX">$(i)$</tex-math><alternatives><mml:math><mml:mrow><mml:mo>(</mml:mo><mml:mi>i</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="arleo-ieq1-3190623.gif"/></alternatives></inline-formula> a qualitative evaluation based on a guided experiment with two domain experts on two different data sets; <inline-formula><tex-math notation="LaTeX">$(ii)$</tex-math><alternatives><mml:math><mml:mrow><mml:mo>(</mml:mo><mml:mi>i</mml:mi><mml:mi>i</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="arleo-ieq2-3190623.gif"/></alternatives></inline-formula> a quantitative estimation of the value of the proposed visualization through the ICE-T methodology by Wall <italic>et al.</italic> (IEEE TVCG - 2018). The twofold assessment indicates that VAIM effectively supports our target users in the visual analysis of the performance of IM algorithms.