BR-Bodies Provide Selectively Permeable Condensates that Stimulate mRNA Decay and Prevent Release of Decay Intermediates.

Biomolecular condensates play a key role in organizing RNAs and proteins into membraneless organelles. Bacterial RNP-bodies (BR-bodies) are a biomolecular condensate containing the RNA degradosome mRNA decay machinery, but the biochemical function of such organization remains poorly defined. Here, we define the RNA substrates of BR-bodies through enrichment of the bodies followed by RNA sequencing (RNA-seq). We find that long, poorly translated mRNAs, small RNAs, and antisense RNAs are the main substrates, while rRNA, tRNA, and other conserved non-coding RNAs (ncRNAs) are excluded from these bodies. BR-bodies stimulate the mRNA decay rate of enriched mRNAs, helping to reshape the cellular mRNA pool. We also observe that BR-body formation promotes complete mRNA decay, avoiding the buildup of toxic endo-cleaved mRNA decay intermediates. The combined selective permeability of BR-bodies for both enzymes and substrates together with the stimulation of the sub-steps of mRNA decay provide an effective organization strategy for bacterial mRNA decay.

Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae.

Genetic networks are surprisingly robust to perturbations caused by new mutations. This robustness is conferred in part by compensation for loss of a gene's activity by genes with overlapping functions, such as paralogs. Compensation occurs passively when the normal activity of one paralog can compensate for the loss of the other, or actively when a change in one paralog's expression, localization, or activity is required to compensate for loss of the other. The mechanisms of active compensation remain poorly understood in most cases. Here we investigate active compensation for the loss or reduction in expression of the Saccharomyces cerevisiae gene TDH3 by its paralog TDH2. TDH2 is upregulated in a dose-dependent manner in response to reductions in TDH3 by a mechanism requiring the shared transcriptional regulators Gcr1p and Rap1p. TDH1, a second and more distantly related paralog of TDH3, has diverged in its regulation and is upregulated by another mechanism. Other glycolytic genes regulated by Rap1p and Gcr1p show changes in expression similar to TDH2, suggesting that the active compensation by TDH3 paralogs is part of a broader homeostatic response mediated by shared transcriptional regulators.

The Afrotropical breeding grounds of the Palearctic-African migratory painted lady butterflies (Vanessa cardui).

Migratory insects are key players in ecosystem functioning and services, but their spatiotemporal distributions are typically poorly known. Ecological niche modeling (ENM) may be used to predict species seasonal distributions, but the resulting hypotheses should eventually be validated by field data. The painted lady butterfly (Vanessa cardui) performs multigenerational migrations between Europe and Africa and has become a model species for insect movement ecology. While the annual migration cycle of this species is well understood for Europe and northernmost Africa, it is still unknown where most individuals spend the winter. Through ENM, we previously predicted suitable breeding grounds in the subhumid regions near the tropics between November and February. In this work, we assess the suitability of these predictions through i) extensive field surveys and ii) two-year monitoring in six countries: a large-scale monitoring scheme to study butterfly migration in Africa. We document new breeding locations, year-round phenological information, and hostplant use. Field observations were nearly always predicted with high probability by the previous ENM, and monitoring demonstrated the influence of the precipitation seasonality regime on migratory phenology. Using the updated dataset, we built a refined ENM for the Palearctic-African range of V. cardui. We confirm the relevance of the Afrotropical region and document the missing natural history pieces of the longest migratory cycle described in butterflies.

Endovascular thrombectomy plus medical care versus medical care alone for large ischaemic stroke: 1-year outcomes of the SELECT2 trial.

BACKGROUND: Multiple randomised trials have shown efficacy and safety of endovascular thrombectomy in patients with large ischaemic stroke. The aim of this study was to evaluate long-term (ie, at 1 year) evidence of benefit of thrombectomy for these patients. METHODS: SELECT2 was a phase 3, open-label, international, randomised controlled trial with blinded endpoint assessment, conducted at 31 hospitals in the USA, Canada, Spain, Switzerland, Australia, and New Zealand. Patients aged 18-85 years with ischaemic stroke due to proximal occlusion of the internal carotid artery or of the first segment of the middle cerebral artery, showing large ischaemic core on non-contrast CT (Alberta Stroke Program Early Computed Tomographic Score of 3-5 [range 0-10, with lower values indicating larger infarctions]) or measuring 50 mL or more on CT perfusion and MRI, were randomly assigned, within 24 h of ischaemic stroke onset, to thrombectomy plus medical care or to medical care alone. The primary outcome for this analysis was the ordinal modified Rankin Scale (range 0-6, with higher scores indicating greater disability) at 1-year follow-up in an intention-to-treat population. The trial is registered at ClinicalTrials.gov (NCT03876457) and is completed. FINDINGS: The trial was terminated early for efficacy at the 90-day follow-up after 352 patients had been randomly assigned (178 to thrombectomy and 174 to medical care only) between Oct 11, 2019, and Sept 9, 2022. Thrombectomy significantly improved the 1-year modified Rankin Scale score distribution versus medical care alone (Wilcoxon-Mann-Whitney probability of superiority 0·59 [95% CI 0·53-0·64]; p=0·0019; generalised odds ratio 1·43 [95% CI 1·14-1·78]). At the 1-year follow-up, 77 (45%) of 170 patients receiving thrombectomy had died, compared with 83 (52%) of 159 patients receiving medical care only (1-year mortality relative risk 0·89 [95% CI 0·71-1·11]). INTERPRETATION: In patients with ischaemic stroke due to a proximal occlusion and large core, thrombectomy plus medical care provided a significant functional outcome benefit compared with medical care alone at 1-year follow-up. FUNDING: Stryker Neurovascular.

SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort.

Identifying the potential for SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4,411 United States employees in 4 states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an odds ratio for reinfection ranging from 0.14 (95% CI: 0.019 to 0.63) to 0.28 (95% CI: 0.05 to 1.1), implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 72% to 86% reduced odds of a subsequent PCR positive test based on our point estimates. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a 6-month time period. We also highlight 2 major sources of bias and uncertainty to be considered when estimating the relative risk of reinfection, confounders and the choice of baseline time point, and show how to account for both in reinfection analysis.

TRP channel regulates EGFR signaling in hair morphogenesis and skin barrier formation.

A plethora of growth factors regulate keratinocyte proliferation and differentiation that control hair morphogenesis and skin barrier formation. Wavy hair phenotypes in mice result from naturally occurring loss-of-function mutations in the genes for TGF-alpha and EGFR. Conversely, excessive activities of TGF-alpha/EGFR result in hairless phenotypes and skin cancers. Unexpectedly, we found that mice lacking the Trpv3 gene also exhibit wavy hair coat and curly whiskers. Here we show that keratinocyte TRPV3, a member of the transient receptor potential (TRP) family of Ca(2+)-permeant channels, forms a signaling complex with TGF-alpha/EGFR. Activation of EGFR leads to increased TRPV3 channel activity, which in turn stimulates TGF-alpha release. TRPV3 is also required for the formation of the skin barrier by regulating the activities of transglutaminases, a family of Ca(2+)-dependent crosslinking enzymes essential for keratinocyte cornification. Our results show that a TRP channel plays a role in regulating growth factor signaling by direct complex formation.

Therapy-induced senescent cancer cells exhibit complement activation and increased complement regulatory protein expression.

Therapy-induced senescence (TIS) is a primary response to chemotherapy, contributing to untoward treatment outcomes such as evasion of immunosurveillance. Despite the established role of the complement system in the immune response to cancer, the role of complement in mediating the immune response against senescent tumor cells remains poorly understood. To explore this relationship, we exposed lung adenocarcinoma (A549), breast adenocarcinoma (MCF7) and pancreatic carcinoma (Panc-1) cell lines to sublethal doses of either etoposide or doxorubicin to trigger TIS. Identification of TIS was based on morphological changes, upregulation of the senescence-associated ß-galactosidase, p21Cip1 induction and lamin B1 downregulation. Using immunofluorescence microscopy, quantitative PCR, ELISA of conditioned media and in silico analysis, we investigated complement activation, complement protein expression, C3 levels in the conditioned media of senescent cells and secreted complement proteins as part of the senescence-associated secretory phenotype (SASP), respectively. In cell lines undergoing TIS, complement-related changes included (i) activation of the terminal pathway, evidenced by the deposition of C5b-9 on senescent cells; (ii) an increase in the expression of CD59 and complement factor H and (iii) in A549 cells, an elevation in the expression of C3 with its secretion into the medium. In addition, increased C3 expression was observed in breast cancer samples expressing TIS hallmarks following exposure to neoadjuvant chemotherapy. In conclusion, TIS led to the activation of complement, upregulation of complement regulatory proteins and increased C3 expression. Complement appears to play a role in shaping the cancer microenvironment upon senescence induction.

Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages.

The opportunistic pathogen Acinetobacter baumannii possesses stress tolerance strategies against host innate immunity and antibiotic killing. However, how the host-pathogen-antibiotic interaction affects the overall molecular regulation of bacterial pathogenesis and host response remains unexplored. Here, we simultaneously investigate proteomic changes in A. baumannii and macrophages following infection in the absence or presence of the polymyxins. We discover that macrophages and polymyxins exhibit complementary effects to disarm several stress tolerance and survival strategies in A. baumannii, including oxidative stress resistance, copper tolerance, bacterial iron acquisition and stringent response regulation systems. Using the spoT mutant strains, we demonstrate that bacterial cells with defects in stringent response exhibit enhanced susceptibility to polymyxin killing and reduced survival in infected mice, compared to the wild-type strain. Together, our findings highlight that better understanding of host-pathogen-antibiotic interplay is critical for optimization of antibiotic use in patients and the discovery of new antimicrobial strategy to tackle multidrug-resistant bacterial infections.

Dual-Function Antibody Conjugate-Enabled Photoimmunotherapy Complements Fluorescence and Photoacoustic Imaging of Head and Neck Cancer Spheroids.

Several molecular-targeted imaging and therapeutic agents are in clinical trials for image-guided surgery and photoimmunotherapy (PIT) for head and neck cancers. In this context, we have previously reported the development, characterization, and specificity of a dual-function antibody conjugate (DFAC) for multimodal imaging and photoimmunotherapy (PIT) of EGFR-overexpressing cancer cells. The DFAC reported previously and used in the present study comprises an EGFR-targeted antibody, cetuximab, conjugated to benzoporphyrin derivative (BPD) for fluorescence imaging and PIT and a Si-centered naphthalocyanine dye for photoacoustic imaging. We report here the evaluation and performance of DFAC in detecting microscopic cancer spheroids by fluorescence and photoacoustic imaging along with their treatment by PIT. We demonstrate that while fluorescence imaging can detect spheroids with volumes greater than 0.049 mm3, photoacoustic imaging-based detection was possible even for the smallest spheroids (0.01 mm3) developed in the study. When subjected to PIT, the spheroids showed a dose-dependent response, with smaller spheroids (0.01 and 0.018 mm3) showing a complete response with no recurrence when treated with 100 J/cm2. Together our results demonstrate the complementary imaging and treatment capacity of DFAC. This potentially enables fluorescence imaging to assess the presence of tumor on a macroscopic scale, followed by photoacoustic imaging for delineating tumor margins guiding surgical resection and elimination of any residual microscopic disease by PIT, in a single intraoperative setting.

Effects of Chronic Pain Diagnoses on the Antidepressant Efficacy of Transcranial Magnetic Stimulation.

OBJECTIVE: Major depressive disorder (MDD) and chronic pain are highly comorbid and bidirectionally related. Repetitive transcranial magnetic stimulation (rTMS) over the dorsolateral prefrontal cortex is effective in treating MDD, but additional research is needed to determine if chronic pain interferes with rTMS for MDD. METHODS: Participants were 124 veterans ( Mage = 49.14, SD = 13.83) scheduled for 30 sessions of rTMS across 6 weeks. Depression severity was monitored weekly using the Patient Health Questionnaire-9 (PHQ-9). Having any pain diagnosis, low back pain, or headache/migraine were assessed by chart review. We fit latent basis models to estimate total change by pain diagnosis in depression scores and quadratic latent growth models to examine differences in growth rates. Then, we computed χ2 tests of group differences in response (PHQ-9 reduction ≥50%) and remission rates (final PHQ-9 < 5). RESULTS: A total of 92 participants (74%) had a documented pain diagnosis, 58 (47%) had low back pain, and 32 (26%) had headache/migraine. In growth models, depression scores initially decreased (linear slope estimate = -2.04, SE = 0.26, p < .0001), but the rate of decrease slowed over time (quadratic slope estimate = 0.18, SE = 0.04, p < .001). Overall change was not different as a function of any pain diagnosis ( p = .42), low back pain (p = .11 ), or headache/migraine ( p = .28). However, we found that low back pain was a negative predictor of response ( p = .032). CONCLUSIONS: These data support rTMS as a viable treatment option for comorbid populations. Although patients with comorbid chronic pain conditions are likely to receive benefit from rTMS for depression, adjunctive pain treatment may be indicated.

A Broadened Class of Donor-Acceptor Stacked Macrometallacyclic Adducts of Different Coinage Metals.

A yet-outstanding supramolecular chemistry challenge is isolation of novel varieties of stacked complexes with finely-tuned donor-acceptor bonding and optoelectronic properties, as herein reported for binary adducts comprising two different cyclic trinuclear complexes (CTC@CTC'). Most previous attempts focused only on 1-2 factors among metal/ligand/substituent combinations, resulting in heterobimetallic complexes. Instead, here we show that, when all 3 factors are carefully considered, a broadened variety of CTC@CTC' stacked pairs with intuitively-enhanced intertrimer coordinate-covalent bonding strength and ligand-ligand/metal-ligand dispersion are attained (dM-M' 2.868(2) Å; ΔE>50 kcal/mol, an order of magnitude higher than aurophilic/metallophilic interactions). Significantly, CTC@CTC' pairs remain intact/strongly-bound even in solution (Keq 4.67×105 L/mol via NMR/UV-vis titrations), and the gas phase (mass spectrometry revealing molecular peaks for the entire CTC@CTC' units in sublimed samples), rather than simple co-crystal formation. Photo-/electro-luminescence studies unravel metal-centered phosphorescence useful for novel all metal-organic light-emitting diodes (MOLEDs) optoelectronic device concepts. This work manifests systematic design of supramolecular bonding and multi-faceted spectral properties of pure metal-organic macrometallacyclic donor/acceptor (inorganic/inorganic) stacks with remarkably-rich optoelectronic properties akin to well-established organic/organic and organic/inorganic analogues.

Elucidating the Mechanism of Efficient Eu(III) and Yb(III) Sensitisation from a Re(I) Tetrazolato Triangular Assembly.

The reaction of Re(CO)5Br with deprotonated 1H-(5-(2,2':6',2''-terpyridine)pyrid-2-yl)tetrazole yields a triangular assembly formed by tricarbonyl Re(I) vertices. Photophysical measurements reveal blue-green emission with a maximum at 520 nm, 32% quantum yield, and 2430 ns long-lived excited state decay lifetime in deaerated dichloromethane solution. Coordination of lanthanoid ions to the terpyridine units red-shifts the emission to 570 nm and also reveals efficient (90%) and fast sensitisation to both Eu(III) and Yb(III) at room temperature, with a similar rate constant kET of the order of 107 s-1. Efficient sensitisation of Eu(III) from Re(I) is unprecedented, especially when considering the close proximity in energy between the donor and acceptor excited states. On the other hand, comparative measurements at 77 K reveal that energy transfer to Yb(III) is two orders of magnitude slower than that to Eu(III). A two-step mechanism of sensitisation is therefore proposed, whereby the rate-determining step is a thermally activated energy transfer step between the Re(I) centre and the terpyridine functionality, followed by rapid energy transfer to the respective Ln(III) excited states. At 77 K, the direct Re(I) to Eu(III) energy transfer seems to proceed via a ligand-mediated superexchange Dexter-type mechanism.

Factors predictive of hospital length of stay in patients with an index episode of acute necrotizing pancreatitis.

INTRODUCTION: Acute necrotizing pancreatitis (ANP) complicates 15 % of acute pancreatitis cases and is associated with prolonged length of stay (LOS). There are limited studies exploring potential predictors. METHODS: We carried out a retrospective study of all consecutive patients presenting to a large referral healthcare system with ANP. Patients younger than 18 years of age, without confirmed glandular necrosis and with in-hospital mortality were excluded. Poisson regression was carried out to identify potential predictors of prolonged hospital stay. RESULTS: One hundred and sixty-two patients hospitalized between December 2016 and June 2020 were included. The median LOS was 12 days (range: 1-155 days). On multivariate analysis, organ dysfunction at presentation (Incidence rate ratio (IRR) 1.21, p = 0.01) or during admission (IRR 1.32, p = 0.001), Charlson Comorbidity Index scores (IRR 1.1 per CCI point, p < 0.001), known chronic pancreatitis (IRR 1.19, p = 0.03), concurrent (non-pancreas related) infections (IRR 1.13, p = 0.04), need for enteral tube placement (IRR 3.42, p < 0.001) and in-hospital interventions (IRR 1.48-2.85 depending on intervention, p < 0.001) were associated with increased LOS. For patients in the cohort to whom this applied, delayed hospital transfers (IRR 1.02, p < 0.001) and delayed start of enteral feeds (IRR 1.01, p = 0.017) contributed to increased overall LOS. CONCLUSION: We demonstrate that multiple factors including delayed transfers to hospitals with pancreaticobiliary expertise lead to increased length of hospitalization. We suggest various strategies that can be considered to target those gaps and may have a favorable effect on LOS.

Impact of proteins and protein fouling on virus retention during virus removal filtration.

Virus filtration is a crucial step in ensuring the high levels of viral clearance required in the production of biotherapeutics produced in mammalian cells or derived from human plasma. Previous studies have reported that virus retention is often reduced in the presence of therapeutic proteins due to membrane fouling; however, the underlying mechanisms controlling this behavior are still not well understood. Experimental studies were performed with a single layer of the commercially available dual-layer PegasusTM SV4 virus removal filter to more easily interpret the experimental results. Bacteriophage ФX174 was used as a model parvovirus, and human immunoglobulin (hIgG) and Bovine Serum Albumin (BSA) were used as model proteins. Data obtained with 5 g/L solutions of hIgG showed more than a 100-fold reduction in virus retention compared to that in the protein-free solution. Similar effects were seen with membranes that were pre-fouled with hIgG and then challenged with ФX174. The experimental data were well-described using an internal polarization model that accounts for virus capture and accumulation within the virus filter, with the hIgG nearly eliminating the irreversible virus capture while also facilitating the release of previously captured virus. These results provide important insights into the performance and validation of virus removal filters in bioprocessing.

Predictive and diagnostic measures for kernicterus spectrum disorder: a prospective cohort study.

BACKGROUND: Kernicterus spectrum disorder (KSD) resulting from neonatal hyperbilirubinemia remains a common cause of cerebral palsy worldwide. This 12-month prospective cohort study followed neonates with hyperbilirubinemia to determine which clinical measures best predict KSD. METHODS: The study enrolled neonates ≥35 weeks gestation with total serum bilirubin (TSB) ≥ 20 mg/dl admitted to Aminu Kano Hospital, Nigeria. Clinical measures included brain MRI, TSB, modified bilirubin-induced neurologic dysfunction (BIND-M), Barry-Albright Dystonia scale (BAD), auditory brainstem response (ABR), and the modified KSD toolkit. MRI signal alteration of the globus pallidus was scored using the Hyperbilirubinemia Imaging Rating Tool (HIRT). RESULTS: Of 25 neonates enrolled, 13/25 completed 12-month follow-up and six developed KSD. Neonatal BIND-M ≥ 3 was 100% sensitive and 83% specific for KSD. Neonatal ABR was 83% specific and sensitive for KSD. Neonatal HIRT score of 2 was 67% sensitive and 75% specific for KSD; this increased to 100% specificity and sensitivity at 12 months. BAD ≥ 2 was 100% specific for KSD at 3-12 months, with 50-100% sensitivity. CONCLUSIONS: Neonatal MRIs do not reliably predict KSD. BIND-M is an excellent screening tool for KSD, while the BAD or HIRT score at 3 or 12 months can confirm KSD, allowing for early diagnosis and intervention. IMPACT: The first prospective study of children with acute bilirubin encephalopathy evaluating brain MRI findings over the first year of life. Neonatal MRI is not a reliable predictor of kernicterus spectrum disorders (KSD). Brain MRI at 3 or 12 months can confirm KSD. The modified BIND scale obtained at admission for neonatal hyperbilirubinemia is a valuable screening tool to assess risk for developing KSD. The Barry Albright Dystonia scale and brain MRI can be used to establish a diagnosis of KSD in at-risk infants as early as 3 months.

Safety and Effectiveness of Fibrin Sheath Stripping of Pediatric Chest Ports.

PURPOSE: To report the safety and effectiveness of fibrin sheath stripping of pediatric chest ports. MATERIALS AND METHODS: Fibrin sheath stripping procedures for pediatric chest ports between 2018 and 2023 were retrospectively reviewed. The treatment indication was the inability to aspirate blood from the port. The technical success, adverse events, days of primary and secondary service intervals, fluoroscopy time, and fluoroscopy dose were recorded. RESULTS: Fibrin sheath stripping procedures were performed in 15 patients for a total of 18 procedures. All patients treated with fibrin sheath stripping had failed fibrinolytic treatment and a preprocedural fluoroscopy examination suggestive of fibrin sheath before attempting stripping. All fibrin sheath stripping procedures were technically successful. The median and mean total days of primary service interval from the date of port placement to the date of suspected fibrin sheath were 666 and 617 days, respectively. The median and mean total number of days of secondary service interval were 385 and 561 days, respectively. The mean fluoroscopy time was 16.9 minutes. The mean fluoroscopy air kerma was 29.8 mGy. No adverse events were observed. CONCLUSIONS: Fibrin sheath stripping is a safe and effective minimally invasive option to maintain the function of pediatric chest ports.

A Copper-Based Metal-Organic Framework for Selective Separation of C2 Hydrocarbons from Methane at Ambient Conditions: Experiment and Simulation.

C2 hydrocarbon separation from methane represents a technological challenge for natural gas upgrading. Herein, we report a new metal-organic framework, [Cu2L(DEF)2]·2DEF (UNT-14; H4L = 4,4',4″,4‴-((1E,1'E,1″E,1‴E)-benzene-1,2,4,5-tetrayltetrakis(ethene-2,1-diyl))tetrabenzoic acid; DEF = N,N-diethylformamide; UNT = University of North Texas). The linker design will potentially increase the surface area and adsorption energy owing to π(hydrocarbon)-π(linker)/M interactions, hence increasing C2 hydrocarbon/CH4 separation. Crystallographic data unravel an sql topology for UNT-14, whereby [Cu2(COO)4]···[L]4- paddle-wheel units afford two-dimensional porous sheets. Activated UNT-14a exhibits moderate porosity with an experimental Brunauer-Emmett-Teller (BET) surface area of 480 m2 g-1 (vs 1868 m2 g-1 from the crystallographic data). UNT-14a exhibits considerable C2 uptake capacity under ambient conditions vs CH4. GCMC simulations reveal higher isosteric heats of adsorption (Qst) and Henry's coefficients (KH) for UNT-14a vs related literature MOFs. Ideal adsorbed solution theory yields favorable adsorption selectivity of UNT-14a for equimolar C2Hn/CH4 gas mixtures, attaining 31.1, 11.9, and 14.8 for equimolar mixtures of C2H6/CH4, C2H4/CH4, and C2H2/CH4, respectively, manifesting efficient C2 hydrocarbon/CH4 separation. The highest C2 uptake and Qst being for ethane are also desirable technologically; it is attributed to the greatest number of "agostic" or other dispersion C-H bond interactions (6) vs 4/2/4 for ethylene/acetylene/methane.

Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter.

The ability to conduct effective high throughput screening (HTS) campaigns in drug discovery is often hampered by the detection of false positives in these assays due to small colloidally aggregating molecules (SCAMs). SCAMs can produce artifactual hits in HTS by nonspecific inhibition of the protein target. In this work, we present a new computational prediction tool for detecting SCAMs based on their 2D chemical structure. The tool, called the boosted aggregation detection (BAD) molecule filter, employs decision tree ensemble methods, namely, the CatBoost classifier and the light gradient-boosting machine, to significantly improve the detection of SCAMs. In developing the filter, we explore models trained on individual data sets, a consensus approach using these models, and, third, a merged data set approach, each tailored for specific drug discovery needs. The individual data set method emerged as most effective, achieving 93% sensitivity and 90% specificity, outperforming existing state-of-the-art models by 20 and 5%, respectively. The consensus models offer broader chemical space coverage, exceeding 90% for all testing sets. This feature is an important aspect particularly for early stage medicinal chemistry projects, and provides information on applicability domain. Meanwhile, the merged data set models demonstrated robust performance, with a notable sensitivity of 79% in the comprehensive 10-fold cross-validation test set. A SHAP analysis of model features indicates the importance of hydrophobicity and molecular complexity as primary factors influencing the aggregation propensity. The BAD molecule filter is readily accessible for the public usage on https://molmodlab-aau.com/Tools.html. This filter provides a new, more robust tool for aggregate prediction in the early stages of drug discovery to optimize hit rates and reduce associated testing and validation overheads.

Molecular dynamics simulations as a guide for modulating small molecule aggregation.

Small colloidally aggregating molecules (SCAMs) can be problematic for biological assays in drug discovery campaigns. However, the self-associating properties of SCAMs have potential applications in drug delivery and analytical biochemistry. Consequently, the ability to predict the aggregation propensity of a small organic molecule is of considerable interest. Chemoinformatics-based filters such as ChemAGG and Aggregator Advisor offer rapid assessment but are limited by the assay quality and structural diversity of their training set data. Complementary to these tools, we explore here the ability of molecular dynamics (MD) simulations as a physics-based method capable of predicting the aggregation propensity of diverse chemical structures. For a set of 32 molecules, using simulations of 100 ns in explicit solvent, we find a success rate of 97% (one molecule misclassified) as opposed to 75% by Aggregator Advisor and 72% by ChemAGG. These short timescale MD simulations are representative of longer microsecond trajectories and yield an informative spectrum of aggregation propensities across the set of solutes, capturing the dynamic behaviour of weakly aggregating compounds. Implicit solvent simulations using the generalized Born model were less successful in predicting aggregation propensity. MD simulations were also performed to explore structure-aggregation relationships for selected molecules, identifying chemical modifications that reversed the predicted behaviour of a given aggregator/non-aggregator compound. While lower throughput than rapid cheminformatics-based SCAM filters, MD-based prediction of aggregation has potential to be deployed on the scale of focused subsets of moderate size, and, depending on the target application, provide guidance on removing or optimizing a compound's aggregation propensity.

Electrochemical Methods for Water Purification, Ion Separations, and Energy Conversion.

Agricultural development, extensive industrialization, and rapid growth of the global population have inadvertently been accompanied by environmental pollution. Water pollution is exacerbated by the decreasing ability of traditional treatment methods to comply with tightening environmental standards. This review provides a comprehensive description of the principles and applications of electrochemical methods for water purification, ion separations, and energy conversion. Electrochemical methods have attractive features such as compact size, chemical selectivity, broad applicability, and reduced generation of secondary waste. Perhaps the greatest advantage of electrochemical methods, however, is that they remove contaminants directly from the water, while other technologies extract the water from the contaminants, which enables efficient removal of trace pollutants. The review begins with an overview of conventional electrochemical methods, which drive chemical or physical transformations via Faradaic reactions at electrodes, and proceeds to a detailed examination of the two primary mechanisms by which contaminants are separated in nondestructive electrochemical processes, namely electrokinetics and electrosorption. In these sections, special attention is given to emerging methods, such as shock electrodialysis and Faradaic electrosorption. Given the importance of generating clean, renewable energy, which may sometimes be combined with water purification, the review also discusses inverse methods of electrochemical energy conversion based on reverse electrosorption, electrowetting, and electrokinetic phenomena. The review concludes with a discussion of technology comparisons, remaining challenges, and potential innovations for the field such as process intensification and technoeconomic optimization.