Search

SUMMARY Computer simulations have become an indispensable tool for the empirical study of large-scale systems. The timely simulation of these systems, however, is not without its challenges. Simulators have to be able to harness the full computational power of modern multicore architectures through parallel execution and overcome the memory limitations of a single computer. In this paper, we evaluate the performance of a parallel and distributed simulator using several conventional time synchronization protocols executed on modern multicore hardware. In addition, we comprehensively analyze a hybrid approach, combining two traditional protocols, increasing robustness, and enabling improved performance in a wider range of simulation scenarios. Finally, an adaptive algorithm to automatically configure this hybrid protocol is introduced and evaluated, eliminating manual user intervention and further improving robustness with respect to varying simulation conditions. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: Alkali-promoted hydrotalcite-based materials have showed CO2 sorption capacity up to 1.6 mmol⋅g−1 when CO2 separation is carried out at relatively high temperature (300–500 °C) and high partial pressure of steam and CO2, conditions that are prevalent in pre-combustion CO2 capture conditions. In addition to CO2 breakthrough experiments in situ XRD experiments have allowed identifying magnesium carbonate crystalline phase formation during CO2 sorption. The alkali promoted hydrotalcite-based material (Mg/Al ratio 2.9) has revealed that high CO2 capacities can potentially be achieved by using the extra storage capacity offered by the presence of excess magnesium oxide that can be converted into magnesium carbonate. The use of this extra capacity in Pressure Swing Adsorption process is further discussed. [Copyright &y& Elsevier]

Background: Ultrafast cerebral Doppler ultrasound enables simultaneous quantification and visualization of cerebral blood flow velocity. The aim of this study is to compare the use of conventional and ultrafast spectral Doppler during anesthesia and their potential to show the effect of anesthesiologic procedures on cerebral blood flow velocities, in relation to blood pressure and cerebral oxygenation in infants undergoing inguinal hernia repair., Methods: A single-center prospective observational cohort study in infants up to six months of age. We evaluated conventional and ultrafast spectral Doppler cerebral ultrasound measurements in terms of number of successful measurements during the induction of anesthesia, after sevoflurane induction, administration of caudal analgesia, a fluid bolus and emergence of anesthesia. Cerebral blood flow velocity was quantified in pial arteries using conventional spectral Doppler and in the cerebral cortex using ultrafast Doppler by peak systolic velocity, end diastolic velocity and resistivity index., Results: Twenty infants were included with useable conventional spectral Doppler images in 72/100 measurements and ultrafast Doppler images in 51/100 measurements. Intraoperatively, the success rates were 53/60 (88.3%) and 41/60 (68.3%), respectively. Cerebral blood flow velocity increased after emergence for both conventional (end diastolic velocity, from 2.01 to 2.75 cm/s, p < 0.001) and ultrafast spectral Doppler (end diastolic velocity, from 0.59 to 0.94 cm/s), whereas cerebral oxygenation showed a reverse pattern with a decrease after the emergence of the infant (85% to 68%, p < 0.001)., Conclusion: It is possible to quantify cortical blood flow velocity during general anesthesia using conventional and ultrafast spectral Doppler cerebral ultrasound. Cerebral blood flow velocity and blood pressure decreased, while regional cerebral oxygenation increased during general anesthesia. Ultrafast spectral Doppler ultrasound offers novel insights into perfusion within the cerebral cortex, unattainable through conventional spectral ultrasound. Yet, ultrafast Doppler is curtailed by a lower success rate and a more rigorous learning curve compared to conventional method., Competing Interests: Declaration of Competing Interest The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (Copyright © 2023. Published by Elsevier Inc.)

Aim: To investigate the association between early brain magnetic resonance imaging (MRI) findings and neurodevelopmental outcome (NDO) in children with congenital heart disease (CHD)., Method: A search for studies was conducted in Embase, Medline, Web of Science, Cochrane Central, PsycINFO, and Google Scholar. Observational and interventional studies were included, in which patients with CHD underwent surgery before 2 months of age, a brain MRI scan in the first year of life, and neurodevelopmental assessment beyond the age of 1 year., Results: Eighteen studies were included. Thirteen found an association between either quantitative or qualitative brain metrics and NDO: 5 out of 7 studies showed decreased brain volume was significantly associated with worse NDO, as did 7 out of 10 studies on brain injury. Scanning protocols and neurodevelopmental tests varied strongly., Interpretation: Reduced brain volume and brain injury in patients with CHD can be associated with impaired NDO, yet standardized scanning protocols and neurodevelopmental assessment are needed to further unravel trajectories of impaired brain development and its effects on outcome., (© 2023 The Authors. Developmental Medicine & Child Neurology published by John Wiley & Sons Ltd on behalf of Mac Keith Press.)

Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the augmentation of energy-based protein binder design using deep learning. We find that using AlphaFold2 or RoseTTAFold to assess the probability that a designed sequence adopts the designed monomer structure, and the probability that this structure binds the target as designed, increases design success rates nearly 10-fold. We find further that sequence design using ProteinMPNN rather than Rosetta considerably increases computational efficiency., (© 2023. The Author(s).)

Previous studies have frequently reported neurocognitive deficits in children born with congenital diaphragmatic hernia (CDH) at school age, which may contribute to academic difficulties. Yet, age at onset of these deficits is currently unknown. We evaluated neurocognitive skills with possible determinants in preschool children born with CDH. Eligible 5-year-old children born with CDH (2010-2015) who participated in our prospective structural follow-up program were included. We used the WPPSI-III to assess intelligence, subtests of the Kaufman-ABC for memory, and NEPSY-II to assess inhibition and attention. We included 63 children. Their test scores generally were within or significantly above normal range: total IQ = 103.4 (15.7) (p = 0.13); Verbal memory = 10.2 (2.8) (p = 0.61); Visuospatial memory = 11.4 (2.6) (p < 0.01); Inhibition = 10.5 (2.2), (p = 0.10). In univariable analyses, length of ICU-stay was negatively associated with IQ, and maximum vasoactive inotropic score and open repair were negatively associated with inhibition skills. In multivariable regression analysis, the latter association remained (B = 5.52, p = 0.04 (CI 0.32-10.72)).   Conclusions: In these tested 5-year-old children born with CDH, neuropsychological outcome was normal on average. While problems in 8-year-olds are common, we did not detect onset of these problems at age 5. Yet, we cannot rule out that this cohort had a relatively mild level of disease severity; therefore, conclusions should be interpreted with caution. However, given the growing-into-deficit hypothesis, meaning that deviant brain development in early life is revealed once higher cognitive brain functions are demanded, follow-up should be conducted up to school age, and preferably beyond. What is Known: • Children born with CDH are at risk for academic difficulties at school age. • Whether these difficulties can be detected already before school age is unknown. What is New: • At age 5 years, intelligence, inhibition, attention, and memory skills were all within normal range, or even above, in children with CDH. This is supportive of the growing-into-deficit hypothesis in this patient population. • Those who underwent open surgical correction had poorer inhibition skills than those who were corrected with minimal access surgery., (© 2022. The Author(s).)

Anaplastic lymphoma kinase (ALK) 1 and the related leukocyte tyrosine kinase (LTK) 2 are recently deorphanized receptor tyrosine kinases 3 . Together with their activating cytokines, ALKAL1 and ALKAL2 4-6 (also called FAM150A and FAM150B or AUGβ and AUGα, respectively), they are involved in neural development 7 , cancer 7-9 and autoimmune diseases 10 . Furthermore, mammalian ALK recently emerged as a key regulator of energy expenditure and weight gain 11 , consistent with a metabolic role for Drosophila ALK 12 . Despite such functional pleiotropy and growing therapeutic relevance 13,14 , structural insights into ALK and LTK and their complexes with cognate cytokines have remained scarce. Here we show that the cytokine-binding segments of human ALK and LTK comprise a novel architectural chimera of a permuted TNF-like module that braces a glycine-rich subdomain featuring a hexagonal lattice of long polyglycine type II helices. The cognate cytokines ALKAL1 and ALKAL2 are monomeric three-helix bundles, yet their binding to ALK and LTK elicits similar dimeric assemblies with two-fold symmetry, that tent a single cytokine molecule proximal to the cell membrane. We show that the membrane-proximal EGF-like domain dictates the apparent cytokine preference of ALK. Assisted by these diverse structure-function findings, we propose a structural and mechanistic blueprint for complexes of ALK family receptors, and thereby extend the repertoire of ligand-mediated dimerization mechanisms adopted by receptor tyrosine kinases., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Background and Objectives: Children born with congenital diaphragmatic hernia (CDH) and treated with extracorporeal membrane oxygenation (ECMO), are at risk for motor function impairment during childhood. We hypothesized that all children born with CDH are at risk for persistent motor function impairment, irrespective of ECMO-treatment. We longitudinally assessed these children's motor function. Methods: Children with CDH with and without ECMO-treatment, born 1999-2007, who joined our structural prospective follow-up program were assessed with the Movement Assessment Battery for Children (M-ABC) at 5, 8, 12 years. Z-scores were used in a general linear model for longitudinal analysis. Results: We included 55 children, of whom 25 had been treated with ECMO. Forty-three (78%) were evaluated at three ages. Estimated mean (95% CI) z-scores from the general linear model were -0.67 (-0.96 to -0.39) at 5 years of age, -0.35 (-0.65 to -0.05) at 8 years, and -0.46 (-0.76 to -0.17) at 12 years. The 5- and 8-years scores differed significantly ( p = 0.02). Motor development was significantly below the norm in non-ECMO treated patients at five years; -0.44 (-0.83 to -0.05), and at all ages in the ECMO-treated-patients: -0.90 (-1.32 to -0.49), -0.45 (-0.90 to -0.02) and -0.75 (-1.2 to -0.34) at 5, 8, and 12 years, respectively. Length of hospital stay was negatively associated with estimated total z-score M-ABC ( p = 0.004 multivariate analysis). Conclusion: School-age children born with CDH are at risk for motor function impairment, which persists in those who received ECMO-treatment. Especially for them long-term follow up is recommended., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 de Munck, van der Cammen-van Zijp, Zanen-van den Adel, Wijnen, Cochius-den Otter, van Haren, Gischler, van Rosmalen and IJsselstijn.)

Clathrin-mediated endocytosis (CME) is the gatekeeper of the plasma membrane. In contrast to animals and yeasts, CME in plants depends on the TPLATE complex (TPC), an evolutionary ancient adaptor complex. However, the mechanistic contribution of the individual TPC subunits to plant CME remains elusive. In this study, we used a multidisciplinary approach to elucidate the structural and functional roles of the evolutionary conserved N-terminal Eps15 homology (EH) domains of the TPC subunit AtEH1/Pan1. By integrating high-resolution structural information obtained by X-ray crystallography and NMR spectroscopy with all-atom molecular dynamics simulations, we provide structural insight into the function of both EH domains. Both domains bind phosphatidic acid with a different strength, and only the second domain binds phosphatidylinositol 4,5-bisphosphate. Unbiased peptidome profiling by mass-spectrometry revealed that the first EH domain preferentially interacts with the double N-terminal NPF motif of a previously unidentified TPC interactor, the integral membrane protein Secretory Carrier Membrane Protein 5 (SCAMP5). Furthermore, we show that AtEH/Pan1 proteins control the internalization of SCAMP5 via this double NPF peptide interaction motif. Collectively, our structural and functional studies reveal distinct but complementary roles of the EH domains of AtEH/Pan1 in plant CME and connect the internalization of SCAMP5 to the TPLATE complex.

Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy., (open access.)

As the last enzyme in nucleotide synthesis as precursors for DNA replication, thymidylate kinase of M. tuberculosis (MtbTMPK) attracts significant interest as a target in the discovery of new anti-tuberculosis agents. Earlier, we discovered potent MtbTMPK inhibitors, but these generally suffered from poor antimycobacterial activity, which we hypothesize is due to poor bacterial uptake. To address this, we herein describe our efforts to equip previously reported MtbTMPK inhibitors with targeting moieties to increase the whole cell activity of the hybrid analogues. Introduction of a simplified Fe-chelating siderophore motif gave rise to analogue 17 that combined favorable enzyme inhibitory activity with significant activity against M. tuberculosis (MIC of 12.5 μM). Conjugation of MtbTMPK inhibitors with an imidazo[1,2-a]pyridine or 3,5-dinitrobenzamide scaffold afforded analogues 26, 27 and 28, with moderate MtbTMPK enzyme inhibitory potency, but sub-micromolar activity against mycobacteria without significant cytotoxicity. These results indicate that conjugation with structural motifs known to favor mycobacterial uptake may be a valid approach for discovering new antimycobacterial agents., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)

Histiocytoses are clonal hematopoietic disorders frequently driven by mutations mapping to the BRAF and MEK1 and MEK2 kinases. Currently, however, the developmental origins of histiocytoses in patients are not well understood, and clinically meaningful therapeutic targets outside of BRAF and MEK are undefined. In this study, we uncovered activating mutations in CSF1R and rearrangements in RET and ALK that conferred dramatic responses to selective inhibition of RET (selpercatinib) and crizotinib, respectively, in patients with histiocytosis.

Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems.

Small GTP-binding proteins from the ADP-ribosylation factor (ARF) family are important regulators of vesicle formation and cellular trafficking in all eukaryotes. ARF activation is accomplished by a protein family of guanine nucleotide exchange factors (GEFs) that contain a conserved catalytic Sec7 domain. Here, we identified and characterized Secdin, a small-molecule inhibitor of Arabidopsis thaliana ARF-GEFs. Secdin application caused aberrant retention of plasma membrane (PM) proteins in late endosomal compartments, enhanced vacuolar degradation, impaired protein recycling, and delayed secretion and endocytosis. Combined treatments with Secdin and the known ARF-GEF inhibitor Brefeldin A (BFA) prevented the BFA-induced PM stabilization of the ARF-GEF GNOM, impaired its translocation from the Golgi to the trans -Golgi network/early endosomes, and led to the formation of hybrid endomembrane compartments reminiscent of those in ARF-GEF-deficient mutants. Drug affinity-responsive target stability assays revealed that Secdin, unlike BFA, targeted all examined Arabidopsis ARF-GEFs, but that the interaction was probably not mediated by the Sec7 domain because Secdin did not interfere with the Sec7 domain-mediated ARF activation. These results show that Secdin and BFA affect their protein targets through distinct mechanisms, in turn showing the usefulness of Secdin in studies in which ARF-GEF-dependent endomembrane transport cannot be manipulated with BFA., (© 2018 American Society of Plant Biologists. All rights reserved.)

Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen parapox Orf virus deploys GIF, a member of the poxvirus immune evasion superfamily, to antagonize GM-CSF (granulocyte macrophage colony-stimulating factor) and IL-2 (interleukin-2), two pleiotropic cytokines of the mammalian immune system. However, structural and mechanistic insights into the unprecedented functional duality of GIF have remained elusive. Here we reveal that GIF employs a dimeric binding platform that sequesters two copies of its target cytokines with high affinity and slow dissociation kinetics to yield distinct complexes featuring mutually exclusive interaction footprints. We illustrate how GIF serves as a competitive decoy receptor by leveraging binding hotspots underlying the cognate receptor interactions of GM-CSF and IL-2, without sharing any structural similarity with the cytokine receptors. Our findings contribute to the tracing of novel molecular mimicry mechanisms employed by pathogenic viruses.

Human colony-stimulating factor 1 receptor (hCSF-1R) is unique among the hematopoietic receptors because it is activated by two distinct cytokines, CSF-1 and interleukin-34 (IL-34). Despite ever-growing insights into the central role of hCSF-1R signaling in innate and adaptive immunity, inflammatory diseases, and cancer, the structural basis of the functional dichotomy of hCSF-1R has remained elusive. Here, we report crystal structures of ternary complexes between hCSF-1 and hCSF-1R, including their complete extracellular assembly, and propose a mechanism for the cooperative human CSF-1:CSF-1R complex that relies on the adoption by dimeric hCSF-1 of an active conformational state and homotypic receptor interactions. Furthermore, we trace the cytokine-binding duality of hCSF-1R to a limited set of conserved interactions mediated by functionally equivalent residues on CSF-1 and IL-34 that play into the geometric requirements of hCSF-1R activation, and map the possible mechanistic consequences of somatic mutations in hCSF-1R associated with cancer., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Purpose: Chronic pain, posttraumatic stress disorder (PTSD), and depression are common outcomes following traumatic injury. Yet, screening and early intervention to prevent the onset of these disorders do not occur routinely in acute trauma settings. This pilot study examined the clinical utility of screening and early multidisciplinary intervention for reducing disability following traumatic injury., Method: 142 non-severe head injured trauma inpatients (26% female, Injury Severity Score M = 9.65, M age = 36 years) were assessed for injury-related factors, pain, and psychological function within 4 weeks post injury. Patients were randomly allocated to a Multidisciplinary Intervention (MI) or Usual Care (UC) group. MI patients received assessment and treatment at one and 3 months post injury from pain and rehabilitation medicine doctors, physiotherapists, occupational therapists, and clinical psychologists. Outcomes at 6 months were then compared., Results: Acute pain intensity, posttraumatic adjustment, depression and acute trauma symptoms, and alcohol use predicted a significant 26%, 49%, 56%, and 30% of the variance in pain, depressive, and PTSD severity, and physical mobility respectively at 6 months. Despite MI group patients reporting no improvement in the severity of pain and psychological symptoms, these patients reported significantly improved relief from pain symptoms as a result of treatment at 6 months. Twenty four per cent of the UC group initially below the cut-off for being at risk of developing PTSD/Depression received new clinical diagnoses at 6 months compared with none of the 'not at risk' MI group attendees who remained asymptomatic., Conclusions: Early findings point to the value of early screening to identify patients at risk of treatable pain, physical, and psychological impairments. Moreover, early multidisciplinary intervention models following traumatic injury show promise for protecting against the onset of posttraumatic psychological disorders.

This comparative longitudinal study investigated aftercare and compliance of attempted suicide patients after standardized psychosocial assessment. Structured interviews were conducted 1 month (FU1) and 6 months (FU2) after an index suicide attempt. Assessment was associated with more frequent discussion of treatment options with the patient at the hospital and a shorter interval between discharge and contacting the general practitioner (GP). A near significant effect was found for discussing the suicide attempt with the GP more frequently and with start or change of the medication scheme after the index attempt. The current findings support the use of a standardized tool for the assessment of suicide attempters and are in line with the chain of care model for suicide attempters.

Background: Notwithstanding the epidemiological studies indicating an increased risk of attempted suicide among adolescents and young adults, there is a scarcity of international studies that examine long-term epidemiological trends in rates and characteristics of this vulnerable group., Aims: This article describes the results of a 9-year monitoring study of suicide attempts in adolescents and young adults referred to the Accident and Emergency Department of the Gent University Hospital (Belgium)., Methods: Between January 1996 and December 2004, trends, sociodemographic, and methodrelated characteristics of suicide attempts were assessed by a psychiatrist on data sheets., Results: Attempted suicide rates declined from 1996 to 2001 and then rose until 2004, but did not exceed previous rates. During the 9 years of monitoring, there was a preponderance of female suicide attempters, except for 1997. Rates of attempts and of fatal suicide were negatively correlated. Significantly more males than females deliberately injured themselves. Younger attempters, especially females, significantly more often poisoned themselves with analgesics. In nearly one in five attempts, alcohol was used in combination with other methods, and alcohol intake was more commonly observed in older suicide attempters. Nearly half of the adolescents were identified as repeaters., Conclusions: The results of this study warrant further monitoring of trends and characteristics of young suicide attempters.