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Upon infection of host cells, Legionella pneumophilareleases a multitude of effector enzymes into the cell's cytoplasm that hijack a plethora of cellular activities, including the host ubiquitination pathways. Effectors belonging to the SidE-family are involved in noncanonical serine phosphoribosyl ubiquitination of host substrate proteins contributing to the formation of a Legionella-containing vacuole that is crucial in the onset of Legionnaires’ disease. This dynamic process is reversed by effectors called Dups that hydrolyze the phosphodiester in the phosphoribosyl ubiquitinated protein. We installed reactive warheads on chemically prepared ribosylated ubiquitin to generate a set of probes targeting these Legionella enzymes. In vitro tests on recombinant DupA revealed that a vinyl sulfonate warhead was most efficient in covalent complex formation. Mutagenesis and X-ray crystallography approaches were used to identify the site of covalent cross-linking to be an allosteric cysteine residue. The subsequent application of this probe highlights the potential to selectively enrich the Dup enzymes from Legionella-infected cell lysates.

The integration of diverse chemical tools like small-molecule inhibitors, activity-based probes (ABPs), and proteolysis targeting chimeras (PROTACs) advances clinical drug discovery and facilitates the exploration of various biological facets of targeted proteins. Here, we report the development of such a chemical toolbox for the human Parkinson disease protein 7 (PARK7/DJ-1) implicated in Parkinson’s disease and cancers. By combining structure-guided design, miniaturized library synthesis, and high-throughput screening, we identified two potent compounds, JYQ-164and JYQ-173, inhibiting PARK7 invitroand in cells by covalently and selectively targeting its critical residue, Cys106. Leveraging JYQ-173, we further developed a cell-permeable Bodipy probe, JYQ-196, for covalent labeling of PARK7 in living cells and a first-in-class PARK7 degrader JYQ-194that selectively induces its proteasomal degradation in human cells. Our study provides a valuable toolbox to enhance the understanding of PARK7 biology in cellular contexts and opens new opportunities for therapeutic interventions.

This paper proposes a non-linear analytical model for bread-loaf permanent magnet (PM) machines, combining magnetic equivalent circuit (MEC) and conformal mapping (CM) techniques. It examines both no-load and on-load conditions for two different machine structures. The fundamental principle of the proposed model is its consideration of winding flux leakage and iron saturation. Additionally, the model is analyzed for two different winding schemes: distributed winding and concentrated winding. An iterative process is implemented to estimate the electromagnetic performance when the stator iron core is saturated under heavy load conditions. Furthermore, this non-linear model sets a standard for bread-loaf PM machines. In conclusion, the accuracy and practicality of the MEC-CM combined model are verified through finite element analysis (FEA) and experimental results.

Objective:Major lower limb amputation is generally associated with a high risk of early and late-term mortality. In this study, 30-day, one-year and three-year mortality of non-traumatic major lower extremity amputations and comorbidities affecting the mortality rate were investigated.Method:Patients who underwent a major lower limb amputation secondary to diabetes or peripheral artery disease between the years 2010–2015 were retrospectively evaluated. Additional to patient demographic data and comorbidities, amputation level, survival and mortality time were extracted. Mortality rates after 30 days, one year and three years were analysed. The associations of the survival to different parameters were evaluated with Kaplan–Meier analysis and log rank test, while the impact of the risk factors on mortality was evaluated with the Cox regression test.Results:A total of 193 patients were enrolled in the study. Approximately 60% of patients were aged ≥65 years, and 65.8% were male. Below-knee amputation was performed in 64.8% of patients and above-knee amputation in 35.2% of patients. The mean follow-up of patients was 29.48 months (range: 0–101 months). After non-traumatic major lower extremity amputation, 30-day, one-year and three-year mortality were 16.6%, 38.3% and 60.1%, respectively. On Cox regression analysis, age ≥65 years was the only variable that had significant impact on the 30-day mortality (hazard ratio (HR): 3.4; p=0.012), while age ≥65 years (HR: 2.5, p=0.000), diabetes (HR: 2, p=0.006) and renal failure (HR: 2, p=0.001) were found to have significant impacts on three-year mortality.Conclusion:The findings of this study showed that >50% of patients with non-traumatic major lower limb amputations died within three years. Advanced age, diabetes and renal failure were the risk factors that increased the mortality. The high mortality rates revealed the importance of employing all hard-to-heal wound treatment options before making an amputation decision. Further, prospective studies are needed to determine the effects of primary disease status and timing of amputation on mortality.

Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.

Thermal energy content of sewage sludge offers opportunities in terms of energy production. Incineration is extensively used for energy conversion of sludge. Dewatered sludge needs to be dried prior to incineration or supplementary fuel should be supplied to the incinerator. Energy production rate is exaggerated when dryer energy is neglected. Net energy production rate depends on dryer energy consumption. The effect of the dryer energy consumption on the net energy production is not emphasized. Energy consumption data of the sludge management process is collected from wastewater management utilities. Thermal and electrical energy conversion of sludge is studied within a scenario analysis. Energy consumption of the examining drying plants (11000–3900 kJ/kg water) is higher than literature (4320–3000 kJ/kg water) data. In order for the dewatered sludge to be burned and dried with its own energy (90% solid), the ratio of its lower calorific value to the specific energy consumption of drying should be 2.8. Net energy production with fully dried sludge is only possible in Plant 4. In the case of auto-thermal combustion, with partially dried (50% solid) sludge, net energy production is possible in 3 of the 4 plants examined. Twenty-five to seventy-five percent of the energy consumption of the wastewater treatment plant can be met by electricity generated using biogas and sludge.

The cornerstones of an efficient circular waste management strategy aiming for enhanced resource efficiency are maximizing organic waste valorization and improving residual conversion to biochemicals. In this regard, this study focuses on the production of volatile fatty acids (VFAs) from the effluent of fungi biomass cultivation on low-grade residues from the potato starch industry with batch and semi-continuous membrane bioreactors (MBRs) containing the effluent of already fermented potato protein liquor (FPPL) inoculated with chicken and cow manure. The effect of pH in the batch experiments on the production and yield of VFAs during acidogenic digestion was evaluated. Rapid generation of VFAs at a concentration of up to 11.8 g/L could be successfully achieved in the MBR. Under the optimal conditions, a high yield of 0.65 g VFAs/g VSfedwas obtained for the organic loading rate (OLR) of 1 g VS/L/d using FPPL substrate and chicken manure as inoculum. The results show that the application of sequential multi-step bioconversion of potato starch industry residues has the potential to increase the variety of value-added products generated from a single organic residue while enhancing nutrient recovery capacity.

ALBATROSS is a European Funded project by the European Commission that addresses the needs of European Electric and Hybrid-Electric passenger vehicle market by overcoming driver concerns relating to battery range and anxiety, cost, long-term reliability, and excessive charging times. ALBATROSS will develop an integrated approach based on smart batteries combined with lightweight designs. Using innovative cooling technologies, we will achieve pack temperature range 5-40°C, with <3°C variation between battery cells and optimal operating temperature 20-23°C. The light weighting solutions, based on modular multi-material systems for battery modules and trays, will be fabricated and joined using cutting edge, fast and cost-effective processes, with disassembly, recycling and reuse designed in as a part of an eco-design approach. The modular approach provides solutions for BEVs and PHEVs.

ObjectivesThe long-term consequences of COVID-19 infection on the gastrointestinal tract remain unclear. Here, we aimed to evaluate the prevalence of gastrointestinal symptoms and post-COVID-19 disorders of gut–brain interaction after hospitalisation for SARS-CoV-2 infection.DesignGI-COVID-19 is a prospective, multicentre, controlled study. Patients with and without COVID-19 diagnosis were evaluated on hospital admission and after 1, 6 and 12 months post hospitalisation. Gastrointestinal symptoms, anxiety and depression were assessed using validated questionnaires.ResultsThe study included 2183 hospitalised patients. The primary analysis included a total of 883 patients (614 patients with COVID-19 and 269 controls) due to the exclusion of patients with pre-existing gastrointestinal symptoms and/or surgery. At enrolment, gastrointestinal symptoms were more frequent among patients with COVID-19 than in the control group (59.3% vs 39.7%, p<0.001). At the 12-month follow-up, constipation and hard stools were significantly more prevalent in controls than in patients with COVID-19 (16% vs 9.6%, p=0.019 and 17.7% vs 10.9%, p=0.011, respectively). Compared with controls, patients with COVID-19 reported higher rates of irritable bowel syndrome (IBS) according to Rome IV criteria: 0.5% versus 3.2%, p=0.045. Factors significantly associated with IBS diagnosis included history of allergies, chronic intake of proton pump inhibitors and presence of dyspnoea. At the 6-month follow-up, the rate of patients with COVID-19 fulfilling the criteria for depression was higher than among controls.ConclusionCompared with controls, hospitalised patients with COVID-19 had fewer problems of constipation and hard stools at 12 months after acute infection. Patients with COVID-19 had significantly higher rates of IBS than controls.Trial registration numberNCT04691895.

The multifunctional human Parkinson’s disease protein 7 (PARK7/DJ1) is an attractive therapeutic target due to its link with early-onset Parkinson’s disease, upregulation in various cancers, and contribution to chemoresistance. However, only a few compounds have been identified to bind PARK7 due to the lack of a dedicated chemical toolbox. We report the creation of such a toolbox and showcase the application of each of its components. The selective PARK7 submicromolar inhibitor with a cyanimide reactive group covalently modifies the active site Cys106. Installment of different dyes onto the inhibitor delivered two PARK7 probes. The Rhodamine110 probe provides a high-throughput screening compatible FP assay, showcased by screening a compound library (8000 molecules). The SulfoCy5-equipped probe is a valuable tool to assess the effect of PARK7 inhibitors in a cell lysate. Our work creates new possibilities to explore PARK7 function in a physiologically relevant setting and develop new and improved PARK7 inhibitors.

ABSTRACTVolatile fatty acids (VFAs) produced during anaerobic digestion (AD) of organic waste are a promising alternative carbon source for various biological processes; however, their applications are limited due to the presence of impurities such as ammonium (NH4+). This study investigates the potential for removal of ammonium using a naturally occurring zeolite (clinoptilolite) from chicken manure (CKM) derived VFA effluent recovered from an anaerobic membrane bioreactor (MBR). Experiments were conducted for both synthetic and actual VFA (AD-VFA) solutions, and the effects of different parameters were investigated with batch and continuous studies. It was observed that the Langmuir-type isotherm provided the best fit to the equilibrium data in the isotherm investigations carried out with the AD-VFA solution. The maximum adsorption capacity (qm) was found as 15.7 mg NH4+/g clinoptilolite. The effect of some operational parameters on process performance such as pH, initial NH4+loading and potassium ion (K+) concentration was investigated. The pH had a negligible effect on ammonium removal for a pH range of 3–7, while the removal efficiency of ammonium decreased with the increase of initial NH4+loading and K+concentration. At the optimum conditions determined in batch experiments, the ammonium removal from synthetic and AD-VFA solutions were compared and average ammonium removal efficiencies of 93 and 94% were found in 12 h equilibrium time for synthetic and AD-VFA solutions, respectively. Overall findings indicated that clinoptilolite has excellent potential for ion exchange when combined with biological processes such as acidogenic fermentation of VFAs to purify the solution from high-ammonium content.

Soft sensors have proven themselves as a valuable tool in terms of quality prediction, process monitoring, process control and minimizing operating cost. Compared to traditional hardware sensors, a soft sensor is a technology that consists of all combinations of mathematical model, data processing and software techniques. Deep learning method has the great potential to be data-driven soft sensors. In this paper, Gated Recurrent Unit (GRU) which is one of the deep learning model was developed as soft sensors for prediction of Total Suspended Solids (TSS) concentration having a role of water quality of New Water Treatment Plant (NWTP) in oil refinery. A real dataset consisting of 39 parameters (41,123 observations) over 6 months from different sensor measurements including flow, temperature, pressure and turbidity etc. was used for GRU model. Also, Principal Component Analysis (PCA) was used for reducing the dimensionality of datasets, providing data interpretation and examining data that correlates with each other. In this case, three different scenarios were created using 5, 10 and 39 process variables as input based on the PCA results. The results show that acceptable estimation has been achieved through the developed algorithm. The minimum mean absolute errors of 0.0108 % for testing dataset and R2of 0.899 for using 10 input variables that affect TSS concentration were achieved. The motivation in this study is that the data-driven predictive model is realized from historical data in large scale system, so it is valuable for the theory to take shape in an industrial application.

ABSTRACTSustainable provision of chemicals and materials is undoubtedly a defining factor in guaranteeing economic, environmental, and social stability of future societies. Among the most sought-after chemical building blocks are volatile fatty acids (VFAs). VFAs such as acetic, propionic, and butyric acids have numerous industrial applications supporting from food and pharmaceuticals industries to wastewater treatment. The fact that VFAs can be produced synthetically from petrochemical derivatives and also through biological routes, for example, anaerobic digestion of organic mixed waste highlights their provision flexibility and sustainability. In this regard, this review presents a detailed overview of the applications associated with petrochemically and biologically generated VFAs, individually or in mixture, in industrial and laboratory scale, conventional and novel applications.

The thermal energy content of sewage sludge (SS) is close to that of low-grade fuels. Drying is the most energy-consuming process in the conversion of sludge to biofuel. However, the energy efficiency of the drying system is not sufficiently emphasized. In this study, the energy efficiency of the sludge drying process is investigated using an experimental contact-type dryer. The effects of wall temperature, rotation speed, and waste heat usage alternatives are investigated. Waste heat usage has the highest impact on energy efficiency. Flue gas feeding increases the drying rate and reduces the total drying duration. Energy efficiency is increased with increasing temperatures. The rotation speed does not considerably affect energy efficiency. Sludge passes through 3 distinct phases regarding the specific energy consumption (SEC). In the first phase, the sludge temperature increases to the saturation temperature. A rather long period of constant energy consumption follows this phase. Most of the water evaporation and drying period occurs in this phase. SECvalues begin to increase in the last phase when humidity is in the range of 0.5–1 (30–50% wb). Considering the first drying stage, a 32–20% higher evaporation rate is obtained with waste heat recovery application depending on the temperature.

ABSTRACTIntroduction:Children with neurodevelopmental disorders are at high risk for malnutrition. We aimed to investigate the impact of nutritional interventions to children with neurodevelopmental disorders and the quality of life of caregivers.Materials/Method:This is a prospective interventional study of 91 children with neurodevelopmental disorders. The children were separated into two groups: the intervention group and control group. The intervention group was selected from among children who had not been evaluated for nutrition and feeding problems by a pediatric gastroenterologist or dietician for the past one year. Children in the intervention group were called for follow-up visits and their nutritional intervention and anthropometric measurements were initiated by a pediatric gastroenterologist and dietician, at one month, three months, six months, and one year. The WHOQoL-BREF quality of life scale was completed by the caregivers of the children at baseline and at one year.Results:The intervention group had increased malnutrition (p < 0.001) and gastrointestinal system pathologies such as dysphagia (p < 0.001), constipation (p = 0.02), gastroesophageal reflux (p = 0.03) at baseline. After the nutritional intervention, 77.7% of the intervention group gained weight and 55.5% reached the target weight. The quality of life scale scores at baseline were lower among caregivers of the intervention group; however, they reached those of the control group after the nutritional intervention.Conclusion:Close multidisciplinary nutrition monitoring enables children with neurodevelopmental disorders to thrive appropriately and improves the quality of life of caregivers.

During the extrusion of magnesium alloys, temperature change could have a significant effect on the outcome. When this effect is not considered, some commonly known defects might be observed, such as hot cracking. In this study, all samples consist of extruded AZ31 and AM50 magnesium alloys as a solid profile, but the methods by which they are cooled, such as air cooling and water quenching, vary. The effects of cooling methods on tensile-compression behavior and the microstructural properties of the samples were investigated. Test samples were obtained in extrusion direction and perpendicular to the extrusion direction separately for mechanical tests. The main purpose of this study was to investigate the effect of different cooling methods on the mechanical properties and microstructural behavior of AZ31 and AM50 magnesium alloys after extrusion, once different cooling methods were applied. According to the microstructural investigation results, an AM50 magnesium alloy has a finer grain structure as compared with an AZ31 alloy according to both cooling methods in the extrusion process. The average grain size values of both alloys were found to be higher for water cooling. Cooling methods have significant effects on the tensile properties of both alloys, depending on their extrusion directions.

The Th17 pathway has been implicated in autoimmune diseases. The retinoic acid receptor-related orphan receptor C2 (RORγt) is a master regulator of Th17 cells and controls the expression of IL-17A. RORγt is expressed primarily in IL-17A-producing lymphoid cells. Here we describe a virtual screen of the ligand-binding pocket and subsequent screen in a binding assay that identified the 1-benzyl-4′,5′-dihydrospiro[piperidine-4,7′-thieno[2,3-c]pyran]-2′-carboxamide scaffold as a starting point for optimization of binding affinity and functional activity guided by structure-based design. Compound 12demonstrated activity in a mouse PK/PD model and efficacy in an inflammatory arthritis mouse model that were used to define the level and duration of target engagement required for efficacy in vivo. Further optimization to improve ADME and physicochemical properties with guidance from simulations and modeling provided compound 22, which is projected to achieve the level and duration of target engagement required for efficacy in the clinic.

Background: The aim of this study is to evaluate the quality of the most commonly viewed total extraperitoneal laparoscopic inguinal hernia repair (TEP) videos on Youtube, which is the largest social and medical media broadcasting service, concerning educational purposes. Method: A search with the keyword “total extraperitoneal laparoscopic inguinal hernia repair” was performed on Youtube. The first 120 videos among the search results were downloaded and 55 of them were included in the study. A scoring system developed by the authors according to the recent literature was utilized for evaluation of the videos. Video demographics were evaluated for the quality and upload source. Results: Among the enrolled videos, video quality was rated as good in 13 (23.6%), as moderate in 22 (40%), and as poor in 20 (36.4%). Video length, presence of narration, number of likes, and comments were significantly higher in the good group. Upload source was an academic center in 14 (25.5%), a community hospital in 22 (40.0%), and a physician in 19 (34.5%). The mean video score of the academic center group (8 ± 4.095) and community hospital group (8.64 ± 3.259) was significantly higher than the physician group (5.47 ± 2.632) (p= 0.010). Video quality was not correlated with total views or views per day. Conclusion: Total extraperitoneal laparoscopic inguinal hernia repair procedure videos uploaded to Youtube demonstrate considerable heterogeneity in terms of educational quality and the number of good quality videos is significantly low. This heterogeneity is attributed to the lack of peer review process for the evaluation of educational quality of the videos. Therefore, a physician intending to learn and practice a surgical procedure properly (TEP repair in this situation) should not consider a broadcasting service without a peer review process as a reliable training source.

Epidermal growth factor receptor (EGFR) has critical roles in epithelial cell physiology. Over-expression and over-activation of EGFR have been implicated in diverse cancers, including triple-negative breast cancers (TNBCs), prompting anti‐EGFR therapies. Therefore, developing potent therapies and addressing the inevitable drug resistance mechanisms necessitates deciphering of EGFR related networks. Here, we describe Sorting Nexin 3 (SNX3), a member of the recycling retromer complex, as a critical player in the epidermal growth factor (EGF) stimulated EGFR network in TNBCs. We show that SNX3 is an immediate and sustained target of EGF stimulation initially at the protein level and later at the transcriptional level, causing increased SNX3 abundance. Using a proximity labeling approach, we observed increased interaction of SNX3 and EGFR upon EGF stimulation. We also detected colocalization of SNX3 with early endosomes and endocytosed EGF. Moreover, we show that EGFR protein levels are sensitive to SNX3 loss. Transient RNAi models of SNX3downregulation have a temporary reduction in EGFR levels. In contrast, long-term silencing forces cells to recover and overexpress EGFRmRNA and protein, resulting in increased proliferation, colony formation, migration, invasion in TNBC cells, and increased tumor growth and metastasis in syngeneic models. Consistent with these results, low SNX3and high EGFRmRNA levels correlate with poor relapse-free survival in breast cancer patients. Overall, our results suggest that SNX3 is a critical player in the EGFR network in TNBCs with implications for other cancers dependent on EGFR activity.

Many reagents have emerged to study the function of specific enzymes in vitro.On the other hand, target specific reagents are scarce or need improvement, allowing investigations of the function of individual enzymes in their native cellular context. Here we report the development of a target-selective fluorescent small-molecule activity-based DUB probe that is active in live cells and an in vivoanimal model. The probe labels active ubiquitin carboxy-terminal hydrolase L1 (UCHL1), also known as neuron-specific protein PGP9.5 (PGP9.5) and Parkinson disease 5 (PARK5), a DUB active in neurons that constitutes 1 to 2% of the total brain protein. UCHL1 variants have been linked with neurodegenerative disorders Parkinson’s and Alzheimer’s diseases. In addition, high levels of UCHL1 also correlate often with cancer and especially metastasis. The function of UCHL1 activity or its role in cancer and neurodegenerative disease is poorly understood and few UCHL1-specific activity tools exist. We show that the reagents reported here are specific to UCHL1 over all other DUBs detectable by competitive activity-based protein profiling and by mass spectrometry. Our cell-penetrable probe, which contains a cyanimide reactive moiety, binds to the active-site cysteine residue of UCHL1 in an activity-dependent manner. Its use is demonstrated by the fluorescent labeling of active UCHL1 both in vitroand in live cells. We furthermore show that this probe can selectively and spatiotemporally report UCHL1 activity during the development of zebrafish embryos. Our results indicate that our probe has potential applications as a diagnostic tool for diseases with perturbed UCHL1 activity.

Septal perforation is a condition characterized by loss of cartilage and/or bony structures along with the mucoperichondrium and mucoperiosteum lining them. The etiology includes a history of nasal surgery or trauma, nose picking, bilateral septal cauterization, overuse of nasal sprays, cocaine abuse, vasculitis, and malignancies.