•CECscreen is an annotation database for CECs in human biological samples.•CECscreen includes 70,397 structures, 306,071 simulated metabolites, and metadata.•CECscreen is openly accessible and is ...incorporated into Metfrag.•CECscreen facilitates large-scale detection of chemicals in exposome research.
Chemicals of Emerging Concern (CECs) include a very wide group of chemicals that are suspected to be responsible for adverse effects on health, but for which very limited information is available. Chromatographic techniques coupled with high-resolution mass spectrometry (HRMS) can be used for non-targeted screening and detection of CECs, by using comprehensive annotation databases. Establishing a database focused on the annotation of CECs in human samples will provide new insight into the distribution and extent of exposures to a wide range of CECs in humans.
This study describes an approach for the aggregation and curation of an annotation database (CECscreen) for the identification of CECs in human biological samples.
The approach consists of three main parts. First, CECs compound lists from various sources were aggregated and duplications and inorganic compounds were removed. Subsequently, the list was curated by standardization of structures to create “MS-ready” and “QSAR-ready” SMILES, as well as calculation of exact masses (monoisotopic and adducts) and molecular formulas. The second step included the simulation of Phase I metabolites. The third and final step included the calculation of QSAR predictions related to physicochemical properties, environmental fate, toxicity and Absorption, Distribution, Metabolism, Excretion (ADME) processes and the retrieval of information from the US EPA CompTox Chemicals Dashboard.
All CECscreen database and property files are publicly available (DOI: https://doi.org/10.5281/zenodo.3956586). In total, 145,284 entries were aggregated from various CECs data sources. After elimination of duplicates and curation, the pipeline produced 70,397 unique “MS-ready” structures and 66,071 unique QSAR-ready structures, corresponding with 69,526 CAS numbers. Simulation of Phase I metabolites resulted in 306,279 unique metabolites. QSAR predictions could be performed for 64,684 of the QSAR-ready structures, whereas information was retrieved from the CompTox Chemicals Dashboard for 59,739 CAS numbers out of 69,526 inquiries. CECscreen is incorporated in the in silico fragmentation approach MetFrag.
The CECscreen database can be used to prioritize annotation of CECs measured in non-targeted HRMS, facilitating the large-scale detection of CECs in human samples for exposome research. Large-scale detection of CECs can be further improved by integrating the present database with resources that contain CECs (metabolites) and meta-data measurements, further expansion towards in silico and experimental (e.g., MassBank) generation of MS/MS spectra, and development of bioinformatics approaches capable of using correlation patterns in the measured chemical features.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Purpose: To investigate changes in penetration depths and angles of EndoAnchor implants with initially good penetration after therapeutic use in endovascular aneurysm repair. Materials and Methods: ...Patients were selected from the Aneurysm Treatment Using the Heli-FX Aortic Securement System Global Registry (ANCHOR; ClinicalTrials.gov identifier NCT01534819). Inclusion criteria were (1) EndoAnchor implantation to treat intraoperative or late type Ia endoleak and (2) at least 2 postoperative computed tomography angiography (CTA) scans. Exclusion criteria were the use of adjunct procedures. Based on these criteria, 54 patients (44 men) with 360 EndoAnchor implants were eligible for this analysis. Penetration depth of each EndoAnchor implant into the aortic wall was judged as (1) good (≥2-mm penetration), (2) borderline (<2 mm or when there was a gap between the endograft and the aortic wall), or (3) no penetration. The penetration depth and longitudinal angles of EndoAnchors with good penetration were investigated on the last available postprocedure CTA scan. Endoleaks were also analyzed. Results: EndoAnchor penetration on the first postprocedure CTA scan was good in 187 (51.9%), borderline in 69 (19.2%), and missing in 104 (28.9%). On the last CTA scan, 182 (97.4%) of the 187 initially well-positioned EndoAnchors remained good. Five (2.6%) EndoAnchors in 4 patients changed configuration over time (4 became borderline and 1 became nonpenetrating), all without any clinical sequelae. The median orthogonal angles of the EndoAnchor implants with good penetration on the first and last CTA scans were 92° interquartile range (IQR) 85, 98 and 90° (IQR 84, 97), respectively (p=0.822); for longitudinal angles, medians of 85° (IQR 71, 96) and 84° (IQR 70, 96) were found (p=0.043). Of the 18 (33%) patients who had a type Ia endoleak on the first postprocedure CTA, 6 resolved over time. Median follow-up was 13 months, during which no new type Ia endoleak was found. Conclusion: Despite the small number of EndoAnchors analyzed, this study showed that the sustainability of EndoAnchor implants with initially good penetration is satisfactory at 1-year follow-up. The vast majority of EndoAnchor implants with good penetration initially remained in good position; <3% of implants became borderline or nonpenetrating, without any clinical consequence.
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NUK, OILJ, SAZU, UKNU, UL, UM, UPUK
Most metal‐organic frameworks (MOFs) possess anisotropic properties, the full exploitation of which necessitates a general strategy for the controllable orientation of such MOF crystals. Current ...methods largely rely upon layer‐by‐layer MOF epitaxy or tuning of MOF crystal growth on appropriate substrates, yielding MOFs with fixed crystal orientations. Here, the dynamic magnetic alignment of different MOF crystals (NH2‐MIL‐53(Al) and NU‐1000) is shown. The MOFs were magnetized by electrostatic adsorption of iron oxide nanoparticles, dispersed in curable polymer resins (Formlabs 1+ clear resin/ Sylgard 184), magnetically oriented, and fixed by resin curing. The importance of crystal orientation on MOF functionality was demonstrated whereby magnetically aligned NU‐1000/Sylgard 184 composite was excited with linearly polarized 405 nm light, affording an anisotropic fluorescence response dependent on the polarization angle of the excitation beam relative to NU‐1000 crystal orientation.
Magnetic attraction: Free‐standing NH2‐MIL‐53(Al) and NU‐1000 metal‐organic framework (MOF) crystals were magnetized by electrostatic adsorption of iron oxide nanoparticles onto their surfaces, and then magnetically aligned in different fluid matrices. MOF/polymer composites with aligned MOF crystals were prepared, and the importance of crystal orientation on MOF functionality was demonstrated using aligned NU‐1000/Sylgard 184, which showed anisotropic fluorescence response to linearly polarized excitation. This general strategy for controlling MOF crystal orientation will open up new avenues for exploiting anisotropic MOF properties.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
For a comprehensive overview of the genetic alterations of neuroblastoma, their association and clinical significance, we conducted a whole-genome DNA copy number analysis.
A series of 493 ...neuroblastoma (NB) samples was investigated by array-based comparative genomic hybridization in two consecutive steps (224, then 269 patients).
Genomic analysis identified several types of profiles. Tumors presenting exclusively whole-chromosome copy number variations were associated with excellent survival. No disease-related death was observed in this group. In contrast, tumors with any type of segmental chromosome alterations characterized patients with a high risk of relapse. Patients with both numerical and segmental abnormalities clearly shared the higher risk of relapse of segmental-only patients. In a multivariate analysis, taking into account the genomic profile, but also previously described individual genetic and clinical markers with prognostic significance, the presence of segmental alterations with (HR, 7.3; 95% CI, 3.7 to 14.5; P < .001) or without MYCN amplification (HR, 4.5; 95% CI, 2.4 to 8.4; P < .001) was the strongest predictor of relapse; the other significant variables were age older than 18 months (HR, 1.8; 95% CI, 1.2 to 2.8; P = .004) and stage 4 (HR, 1.8; 95% CI, 1.2 to 2.7; P = .005). Finally, within tumors showing segmental alterations, stage 4, age, MYCN amplification, 1p and 11q deletions, and 1q gain were independent predictors of decreased overall survival.
The analysis of the overall genomic pattern, which probably unravels particular genomic instability mechanisms rather than the analysis of individual markers, is essential to predict relapse in NB patients. It adds critical prognostic information to conventional markers and should be included in future treatment stratification.
Precipitous declines in Africa's native fauna and flora are recognized, but few comprehensive records of these changes have been compiled. Here, we present population trends for African elephants in ...the 6,213,000 km² Sudano-Sahelian range of West and Central Africa assessed through the analysis of aerial and ground surveys conducted over the past 4 decades. These surveys are focused on the best protected areas in the region, and therefore represent the best case scenario for the northern savanna elephants. A minimum of 7,745 elephants currently inhabit the entire region, representing a minimum decline of 50% from estimates four decades ago for these protected areas. Most of the historic range is now devoid of elephants and, therefore, was not surveyed. Of the 23 surveyed elephant populations, half are estimated to number less than 200 individuals. Historically, most populations numbering less than 200 individuals in the region were extirpated within a few decades. Declines differed by region, with Central African populations experiencing much higher declines (-76%) than those in West Africa (-33%). As a result, elephants in West Africa now account for 86% of the total surveyed. Range wide, two refuge zones retain elephants, one in West and the other in Central Africa. These zones are separated by a large distance (∼900 km) of high density human land use, suggesting connectivity between the regions is permanently cut. Within each zone, however, sporadic contacts between populations remain. Retaining such connectivity should be a high priority for conservation of elephants in this region. Specific corridors designed to reduce the isolation of the surveyed populations are proposed. The strong commitment of governments, effective law enforcement to control the illegal ivory trade and the involvement of local communities and private partners are all critical to securing the future of elephants inhabiting Africa's northern savannas.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•Seeds dispersed by duikers are orthodox pioneer colonisers.•No significant impact of selective logging on duiker occupancy.•Dispersal role of the duiker community is not altered by certified ...logging.•Studied frugivores play overlapping rather than complementary dispersal roles.•Duikers disperse species logged for timber production.
Seed dispersal by frugivores is a key process which is necessary for the regeneration of plant communities. The decrease in the abundance of fruit-eating mammals due to anthropogenic pressures impacts on the proper functioning of forest ecosystems.
In this study, for the first time we evaluate seed dispersal by duikers (Bovidae, frugivores and the most hunted animals of the rainforests of central Africa: Congo basin), using germination trials of seeds contained in their dung and rumen. The influence of selective timber harvesting on this dispersal was also examined by comparing duiker community occupancy between a logged and an unlogged site.
Our results revealed a community of four duiker species Cephalophus silvicultor, Philantomba congica and two species of ‘red’ duiker (C. callipygus and C. castaneus). A total of 79 plant species (5481 seedlings) were found in the dungs of all duikers and a total of 37 species (5225 seedlings) were observed in the rumens of red duikers and P. congica. Phyllanthus sp. and Musanga cecropioides were the dominant taxa in dung and rumen contents respectively. Taxa of high commercial value such as Erythrophleum suaveolens, Milicia excelsa and Nauclea diderrichii were also observed. The lack of a clear difference between the plant communities dispersed by the duiker species (assessed by β-diversity) showed that they play redundancy rather than complementary dispersal roles.
Duikers play an underestimated role in the restoration of environments disturbed by logging or shifting cultivation as most of the species observed are pioneer colonizing species. Furthermore duiker communities appear to be affected little by selective logging.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Objective: Aortic pulse-wave-velocity (aPWV) is a measure for arterial stiffness, which is associated with increased cardiovascular risk. Recent evidence suggests aPWV increases after ...endograft-placement for aortic aneurysms. The aim of this study was to investigate the influence of different aortic endoprostheses on aPWV and structural stiffness in vitro. Approach: Three different abdominal aortic endoprostheses (AFX, Endurant II, and Nellix) were implanted in identical silicone aneurysm models. One model was left untreated, and another model contained an aortic tube graft (Gelweave). The models were placed in an in vitro flow set-up that mimics physiological flow. aPWV was measured as the transit time of the pressure wave over the flow trajectory of the suprarenal to iliac segment. Structural stiffness corrected for lumen diameter was calculated for each model. Results: aPWV was significantly lower for the control compared to the AFX, Endurant, Nellix and tube graft models (13.00 ± 1.20, 13.40 ± 1.17, 18.18 ± 1.20, 16.19 ± 1.25 and 15.41 ± 0.87 m s−1, respectively (P < 0.05)). Structural stiffness of the AFX model was significant lower compared to the control model (4718 N m−1 versus 5115 N m−1 (P < 0.001), respectively), whereas all other models showed higher structural stiffness. Significance: Endograft placement resulted in a higher aPWV compared to a non-treated aortic flow model. All models showed increased structural stiffness over the flow trajectory compared to the control model, except for the AFX endoprosthesis. Future studies in patients treated with an endograft are needed to evaluate the current results in vivo.
A series of tetrasubstituted fluoroalkenes were synthesized in good yield and high E/Z selectivity (up to 96/4) by Wittig reaction between α-heterosubstituted ketones and α-fluorophosphonium ylides. ...A detailed study of factors that control stereoselectivity in these reactions shows that stereoselectivity is the result of stabilizing CH···F and N···CO interactions in the addition TS leading to the E isomer. This analysis provides a rationale for the observed decrease in selectivity for reactions of stabilized ylides with α-alkoxy aldehydes.
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IJS, KILJ, NUK, PNG, UL, UM
DOCK2 is a guanine-nucleotide-exchange factor for Rac proteins. Activated Rac serves various cellular functions including the reorganization of the actin cytoskeleton in lymphocytes and neutrophils ...and production of reactive oxygen species in neutrophils. Since 2015, six unrelated patients with combined immunodeficiency and early-onset severe viral infections caused by bi-allelic loss-of-function mutations in
DOCK2
have been described
.
Until now, the function of phagocytes, specifically neutrophils, has not been assessed in human DOCK2 deficiency. Here, we describe a new kindred with four affected siblings harboring a homozygous splice-site mutation (c.2704-2 A > C) in
DOCK2
. The mutation results in alternative splicing and a complete loss of DOCK2 protein expression. The patients presented with leaky severe combined immunodeficiency or Omenn syndrome. The novel mutation affects EBV-B cell migration and results in NK cell dysfunction similar to previous observations. Moreover, both cytoskeletal rearrangement and reactive oxygen species production are partially impaired in DOCK2-deficient neutrophils.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Summary Background Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are extremes of a clinically, pathologically, and genetically overlapping disease spectrum. A locus ...on chromosome 9p21 has been associated with both disorders, and we aimed to identify the causal gene within this region. Methods We studied 305 patients with FTLD, 137 with ALS, and 23 with concomitant FTLD and ALS (FTLD-ALS) and 856 controls from Flanders (Belgium); patients were identified from a hospital-based cohort and were negative for mutations in known FTLD and ALS genes. We also examined the family of one patient with FTLD-ALS previously linked to 9p21 (family DR14). We analysed 130 kbp at 9p21 in association and segregation studies, genomic sequencing, repeat genotyping, and expression studies to identify the causal mutation. We compared genotype-phenotype correlations between mutation carriers and non-carriers. Findings In the patient-control cohort, the single-nucleotide polymorphism rs28140707 within the 130 kbp region of 9p21 was associated with disease (odds ratio OR 2·6, 95% CI 1·5–4·7; p=0·001). A GGGGCC repeat expansion in C9orf72 completely co-segregated with disease in family DR14. The association of rs28140707 with disease in the patient-control cohort was abolished when we excluded GGGGCC repeat expansion carriers. In patients with familial disease, six (86%) of seven with FTLD-ALS, seven (47%) of 15 with ALS, and 12 (16%) of 75 with FTLD had the repeat expansion. In patients without known familial disease, one (6%) of 16 with FTLD-ALS, six (5%) of 122 with ALS, and nine (4%) of 230 with FTLD had the repeat expansion. Mutation carriers primarily presented with classic ALS (10 of 11 individuals) or behavioural variant FTLD (14 of 15 individuals). Mean age at onset of FTLD was 55·3 years (SD 8·4) in 21 mutation carriers and 63·2 years (9·6) in 284 non-carriers (p=0·001); mean age at onset of ALS was 54·5 years (9·9) in 13 carriers and 60·4 years (11·4) in 124 non-carriers. Postmortem neuropathological analysis of the brains of three mutation carriers with FTLD showed a notably low TDP-43 load. In brain at postmortem, C9orf72 expression was reduced by nearly 50% in two carriers compared with nine controls (p=0·034). In familial patients, 14% of FTLD-ALS, 50% of ALS, and 62% of FTLD was not accounted for by known disease genes. Interpretation We identified a pathogenic GGGGCC repeat expansion in C9orf72 on chromosome 9p21, as recently also reported in two other studies. The GGGGCC repeat expansion is highly penetrant, explaining all of the contribution of chromosome 9p21 to FTLD and ALS in the Flanders-Belgian cohort. Decreased expression of C9orf72 in brain suggests haploinsufficiency as an underlying disease mechanism. Unidentified genes probably also contribute to the FTLD-ALS disease spectrum. Funding Full funding sources listed at end of paper (see Acknowledgments).
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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