Search

In the middle of the night on September 2, 2011, the Dutch Minister of the Interior and Kingdom Relations held an emergency press conference. DigiNotar, a Certificate Authority (CA), had been electronically ‘broken into’ and as a result intruders had managed to generate falsified certificates. As a CA, DigiNotar issued digital certificates to secure digital communication, but as a result of the breach the authenticity of such certificates could no longer be verified. The Dutch government subsequently revoked its trust in all certificates issued by DigiNotar. This was the beginning of the first digital disaster in the Netherlands. As a pioneering disaster, this article focuses on the implications of DigiNotar as a vital case study for future scenarios of digital disaster management. The main focus of this article is on the underlying ‘weaknesses’ of the DigiNotar incident, which allowed the situation to evolve from a problem into a disaster. These include lack of oversight, lack of security attention and risk awareness and the absence of an effective mitigation strategy. By identifying and subsequently analyzing the underlying problems, this article aims to demonstrate how future situations can be better contained if sufficient attention is granted to these factors and subsequent changes are introduced.

Systemic lupus erythematosus (SLE) is marked by excessive complement activation, contributing to tissue damage. Complement activation can be detected in many organs including the skin, kidney, and brain. The involvement of the central nervous system is particularly relevant to understanding neuropsychiatric SLE (NPSLE), one of the poorest understood manifestations of SLE for which no biomarkers are available. We studied the levels of complement inhibitors in SLE in relation to disease activity and as possible biomarkers to identify NPSLE. Serum levels of complement inhibitors C1-inhibitor (C1-INH), C4b-binding protein (C4BP), Factor I, and Factor H were measured in 345 SLE patients (including 102 with NPSLE) and 108 healthy controls. Compared with controls, SLE patients had higher C1-INH and C4BP but lower Factor I and H levels. All inhibitors positively correlated with total C3 and C4 levels. While correlating with the SLE Disease Activity Index (SLEDAI), no distinction in inhibitor levels was found between SLE and NPSLE patients. Over time, C1-INH and Factor H levels normalized, but no significant changes were observed for C4BP and Factor I. In SLE the levels of circulating complement inhibitors are inversely correlated to complement consumption but do not serve as biomarkers for NPSLE., (© 2024 The Author(s). European Journal of Immunology published by Wiley‐VCH GmbH.)

Competing Interests: Competing interests: LAT is mentioned as inventor on a patent describing the methods to detect anti-CarP antibodies.

Competing Interests: LT is listed as an inventor on a patent on the detection of anti-CarP autoantibodies. The remaining 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.

Background: (Auto)immune mediated and cholestatic liver disease (AILD) includes autoimmune hepatitis (AIH), primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). Especially AIH is characterized by the presence of autoantibodies and elevated serum immunoglobulins. In rheumatoid arthritis, autoantibodies against post-translational modifications (PTMs) such as citrullination (Cit) and carbamylation (CarP) are used as diagnostic and prognostic markers, respectively. We studied the presence of six anti-PTM antibodies in patients with the three AILDs and non-AILD., Methods: Antibodies against six PTMs (malondialdehyde-acetaldehyde adducts (MAA), advanced glycation end-products (AGE), CarP, acetylation (AL), Cit, and nitration (NT)) were tested in sera of patients with AILD ( n  = 106), non-AILD ( n  = 101) and compared with healthy controls (HC) ( n  = 100). Levels and positivity were correlated with clinical and biochemical features in a well-defined cohort of untreated AIH patients., Results: Anti-PTM antibodies were more often detectable in sera from AILD patients compared with HCs (anti-MAA: 67.9% vs. 2.0%, anti-AGE: 36.8% vs. 4.0%, anti-CarP: 47.2% vs. 5.0% and anti-AL: 18.9% vs. 5.0%). In untreated AIH, time to complete biochemical response (CBR) was associated with anti-MAA, anti-AGE, anti-CarP and anti-AL antibodies. Significantly more patients with at least three anti-PTM antibodies attained CBR at 12  months of treatment (13 vs. 3 p  = 0.01)., Conclusion: Anti-PTM antibodies are frequently present in AILD. The presence of anti-MAA, anti-AGE and anti-CarP antibodies correlates with the presence of AIH within this cohort. In AIH, harboring at least three anti-PTM antibody responses is positively associated with CBR. Determination of anti-PTM antibodies in liver disease may have diagnostic and prognostic value., 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 © 2023 van den Beukel, Stoelinga, van der Meer, van der Meulen, Zhang, Tushuizen, van Hoek and Trouw.)

Previous RNA sequencing has allowed the identification of 129 long 5' untranslated regions (UTRs) in the Lactococcus lactis MG1363 transcriptome. These sequences potentially harbor cis -acting riboswitches. One of the identified extended 5' UTRs is a putative thiamine pyrophosphate (TPP) riboswitch. It is located immediately upstream of the thiamine transporter gene thiT ( llmg_0334 ). To confirm this assumption, the 5'-UTR sequence was placed upstream of the gene encoding the superfolder green fluorescent protein (sfGFP), sfgfp , allowing the examination of the expression of sfGFP in the presence or absence of thiamine in the medium. The results show that this sequence indeed represents a thiamine-responsive TPP riboswitch. This RNA-based genetic control device was used to successfully restore the mutant phenotype of an L. lactis strain lacking the major autolysin gene, acmA . The L. lactis thiT TPP riboswitch (RS thiT ) is a useful molecular genetic tool enabling the gradual downregulation of the expression of genes under its control by adjusting the thiamine concentration. IMPORTANCE The capacity of microbes with biotechnological importance to adapt to and survive under quickly changing industrial conditions depends on their ability to adequately control gene expression. Riboswitches are important RNA-based elements involved in rapid and precise gene regulation. Here, we present the identification of a natural thiamine-responsive riboswitch of Lactococcus lactis, a bacterium used worldwide in the production of dairy products. We used it to restore a genetic defect in an L. lactis mutant and show that it is a valuable addition to the ever-expanding L. lactis genetic toolbox.

Introduction: Urgent or emergency treatment of patients with abdominal aortic aneurysms that are anatomically unsuitable for conventional repair because of short proximal necks, small diameters and access vessel calcification, and high risk for open repair can be performed with commercially available branched or fenestrated aortic endografts or physician modified stent grafts., Report: A technique is described for modification and successful implantation of a commercially available standard aortic stent graft with a low profile main body in two patients at high risk for open repair, with small access vessels and requiring uni- or bilateral renal artery fenestration for juxtarenal aneurysm repair., Discussion: Based on two case experiences, the use of physician modified off the shelf endografts appears to be a feasible and effective alternative to fenestrated endovascular repair in patients with juxtarenal abdominal aortic aneurysms at high risk for open surgical repair. Studies comparing effectiveness of the different options, including chimney/snorkel technique and debranching, are warranted., (© 2021 The Authors.)

Background: Remodeling of the aortoiliac anatomy is a challenge to the long-term performance of stent grafts for endovascular aneurysm repair. Changes in vessel diameter and length can result in loss of seal at attachment sites, limb disunion, or kinking, with the development of high-pressure endoleaks, migration, or limb occlusion. The aim of this study was to assess the durability and conformability of the ultralow-profile INCRAFT AAA endograft (Cordis Corporation, Milpitas, Calif) during 5-year follow-up., Methods: From 2010 to 2011, there were 60 patients (median age, 74 years; range, 60-94 years) with intact abdominal aortic aneurysms who were enrolled in the INNOVATION trial to evaluate the safety, effectiveness, and durability of the INCRAFT AAA device. Clinical and technical success was assessed with protocol-specified, monitored follow-up clinic visits and core laboratory-assessed computed tomography (CT) at 1 month, 6 months, and 12 months after implantation and annually through 5 years thereafter. Diameter and angulation changes at the proximal aortic neck and diameter changes at the iliac attachment zones were measured in addition to the standard CT assessments., Results: Significant aortoiliac remodeling was observed throughout long-term follow-up after endovascular aneurysm repair. Proximal aortic neck diameter 15 mm below the lowest main renal artery increased from 23.5 ± 2.5 mm at 1 month to 27.3 ± 2.8 mm at 5 years (P = .002). Neck dilation >5 mm was observed in 8 of 38 patients with 5-year CT studies (21%). The aortic neck straightened, with angulation decreasing from 34 ± 14 degrees preoperatively to 31 ± 11 degrees at 1 month (P < .001) and to 20 ± 12 degrees at 5 years (P = .018). Straightening of the neck was most prominent in patients who presented with a high degree of preoperative angulation (r = 0.61; P < .001). Between 1 month and 5 years, iliac attachment zone diameter increased from 13.5 ± 1.9 mm to 15.0 ± 2.4 mm on the right (P = .002) and from 13.9 ± 2.3 mm to 16.8 ± 2.7 mm on the left (P < .001). During 5 years, 9 of 72 (13%) iliac arteries enlarged >5 mm. There was a significant relationship between main body oversizing and aortic neck enlargement (r = 0.42; P = .009). No similar association was observed between iliac limb oversizing and iliac dilation over time (r = 0.10 and P = .549, right side; r = 0.14 and P = .400, left side). There were no aneurysm-related deaths in the series. There were two type IA endoleaks, both of which were present on the 1-month CT scan and associated with challenging aortic neck anatomy. No patient experienced endograft migration or rupture through 5 years. Type IB endoleaks occurred in two patients, both accompanied by iliac artery dilation and loss of seal. Stent fracture occurred in two struts of the bare transrenal stent of one patient, without loss of fixation or seal. One patient experienced graft limb occlusion and was observed without intervention. There were three patients (5%) with aneurysm sac enlargement (>5 mm) through 5 years, each of whom had type II endoleak., Conclusions: Significant aortoiliac remodeling occurs after endograft implantation, including proximal aortic neck dilation, straightening of the neck, and iliac artery enlargement. The ultralow-profile INCRAFT device adapted well to these changes, with acceptably low 5-year rates of device-related endoleaks, endograft migration, and limb occlusion., (Copyright © 2018 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.)

Background: This paper reports the 4-year safety and effectiveness of the INCRAFT® AAA Stent-Graft System (Cordis Corp., Milpitas, CA, USA), an ultra-low-profile device for the treatment of abdominal aortic aneurysms., Methods: The INNOVATION Trial is the prospective, first-in-human, multicenter trial to evaluate the safety and effectiveness of the INCRAFT® System. Patients underwent annual clinical and computed tomography angiography examination as part of the study protocol. The INCRAFT® AAA Stent-Graft System is a customizable tri-modular design, with an ultra-low profile (14-Fr) delivery system. Patient were treated under approved protocol, the prescribed clinical and imaging follow-up at annually through 5 years. Results analyzed and adjudicated by a clinical events committee, independent core laboratory, and a data safety and monitoring board. This manuscript reports results through 4 years of follow-up., Results: A total of 60 patients were enrolled in the trial, all of whom were successfully treated. Follow-up rates at 1 and 4 years were 93% (56/60) and 85% (51/60), respectively. All-cause mortality at 4 years was 17.6% and no death was AAA-, device-, or procedure-related. The secondary reintervention rate at 1 year was 4.6%, primarily the result of stent thrombosis. In total, 10 patients required 13 post-procedure interventions within 4-years of follow-up (2 to repair a type I endoleak, 4 to repair a type II endoleak, 1 for stent thrombosis, 1 for renal stenosis, 1 for aneurysm enlargement, 2 for limb migration and 2 for prosthesis stenosis or occlusion). There were 4 cases (10%) of aneurysm enlargement reported at the 4 year follow-up. At 4 years, 38 out of 39 patients were free from type I and III endoleaks. There were no proximal type I or type III endoleaks at 4-year follow-up. Core laboratory evaluation of the postoperative imaging studies indicated absence of endograft migration while a single fracture was demonstrated without any clinical sequelae., Conclusions: The INCRAFT® AAA Stent-Graft System provides a minimally invasive and durable solution for patients undergoing EVAR that has been associated with a low frequency of device-related events through 4 years of follow-up.

Background: The use of Apps running on smartphones and tablets profoundly affects medicine. The MASK-rhinitis (MACVIA-ARIA Sentinel NetworK for allergic rhinitis) App (Allergy Diary) assesses allergic rhinitis symptoms, disease control and impact on patients' lives. It is freely available in 20 countries (iOS and Android platforms)., Aims: To assess in a pilot study whether (i) Allergy Diary users were able to properly provide baseline characteristics (ii) simple phenotypic characteristics based upon data captured by the Allergy Diary could be identified and (iii) information gathered by this study could suggest novel research questions., Methods: The Allergy Diary users were classified into six groups according to the baseline data that they entered into the App: (i) asymptomatic; (ii) nasal symptoms excluding rhinorrhea; (iii) rhinorrhea; (iv) rhinorrhea plus 1-2 nasal/ocular symptoms; (v) rhinorrhea plus ≥3 nasal/ocular symptoms; and (vi) rhinorrhea plus all nasal/ocular symptoms., Results: By 1 June 2016, 3260 users had registered with the Allergy Diary and 2710 had completed the baseline questionnaire. Troublesome symptoms were found mainly in the users with the most symptoms. Around 50% of users with troublesome rhinitis and/or ocular symptoms suffered work impairment. Sleep was impaired by troublesome symptoms and nasal obstruction., Conclusions: This is the first App (iOS and Android) to have tested for allergic rhinitis and conjunctivitis. A simple questionnaire administered by cell phones enables the identification of phenotypic differences between a priori defined rhinitis groups. The results suggest novel concepts and research questions in allergic rhinitis that may not be identified using classical methods., (© 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Lactococcus lactis MG1363 is an important gram-positive model organism. It is a plasmid-free and phage-cured derivative of strain NCDO712. Plasmid-cured strains facilitate studies on molecular biological aspects, but many properties which make L. lactis an important organism in the dairy industry are plasmid encoded. We sequenced the total DNA of strain NCDO712 and, contrary to earlier reports, revealed that the strain carries 6 rather than 5 plasmids. A new 50-kb plasmid, designated pNZ712, encodes functional nisin immunity (nisCIP) and copper resistance (lcoRSABC). The copper resistance could be used as a marker for the conjugation of pNZ712 to L. lactis MG1614. A genome comparison with the plasmid cured daughter strain MG1363 showed that the number of single nucleotide polymorphisms that accumulated in the laboratory since the strains diverted more than 30 years ago is limited to 11 of which only 5 lead to amino acid changes. The 16-kb plasmid pSH74 was found to contain a novel 8-kb pilus gene cluster spaCB-spaA-srtC1-srtC2, which is predicted to encode a pilin tip protein SpaC, a pilus basal subunit SpaB, and a pilus backbone protein SpaA. The sortases SrtC1/SrtC2 are most likely involved in pilus polymerization while the chromosomally encoded SrtA could act to anchor the pilus to peptidoglycan in the cell wall. Overexpression of the pilus gene cluster from a multi-copy plasmid in L. lactis MG1363 resulted in cell chaining, aggregation, rapid sedimentation and increased conjugation efficiency of the cells. Electron microscopy showed that the over-expression of the pilus gene cluster leads to appendices on the cell surfaces. A deletion of the gene encoding the putative basal protein spaB, by truncating spaCB, led to more pilus-like structures on the cell surface, but cell aggregation and cell chaining were no longer observed. This is consistent with the prediction that spaB is involved in the anchoring of the pili to the cell., Competing Interests: A patent pertaining to the use of strains expressing lactococcal pili was filed by TIFN. The affiliations to TIFN and NIZO food research do not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: Transcriptomics analyses of bacteria (and other organisms) provide global as well as detailed information on gene expression levels and, consequently, on other processes in the cell. RNA sequencing (RNA-seq) has over the past few years become the most accurate method for global transcriptome measurements and for the identification of novel RNAs. This development has been accompanied by advances in the bioinformatics methods, tools and software packages that deal with the analysis of the large data sets resulting from RNA-seq efforts., Results: Based on years of experience in analyzing transcriptome data, we developed a user-friendly webserver that performs the statistical analysis on the gene expression values generated by RNA-seq. It also provides the user with a whole range of data plots. We benchmarked our RNA-seq pipeline, T-REx, using a case study of CodY mutants of Bacillus subtilis and show that it could easily and automatically reproduce the statistical analysis of the cognate publication. Furthermore, by mining the correlation matrices, k-means clusters and heatmaps generated by T-REx we observed interesting gene-behavior and identified sub-groups in the CodY regulon., Conclusion: T-REx is a parameter-free statistical analysis pipeline for RNA-seq gene expression data that is dedicated for use by biologists and bioinformaticians alike. The tables and figures produced by T-REx are in most cases sufficient to accurately mine the statistical results. In addition to the stand-alone version, we offer a user-friendly webserver that only needs basic input ( http://genome2d.molgenrug.nl ).

Here, we developed a cell-based biosensor that can assess meat freshness using the Gram-positive model bacterium Bacillus subtilis as a chassis. Using transcriptome analysis, we identified promoters that are specifically activated by volatiles released from spoiled meat. The most strongly activated promoter was PsboA, which drives expression of the genes required for the bacteriocin subtilosin. Next, we created a novel BioBrick compatible integration plasmid for B. subtilis and cloned PsboA as a BioBrick in front of the gene encoding the chromoprotein amilGFP inside this vector. We show that the newly identified promoter could efficiently drive fluorescent protein production in B. subtilis in response to spoiled meat and thus can be used as a biosensor to detect meat spoilage.

Vasodilator-stimulated phosphoprotein (Ena/VASP) is an actin binding protein, important for actin dynamics in motile cells and developing organisms. Though VASP's main activity is the promotion of barbed end growth, it has an F-actin binding site and can form tetramers, and so could additionally play a role in actin crosslinking and bundling in the cell. To test this activity, we performed rheology of reconstituted actin networks in the presence of wild-type VASP or mutants lacking the ability to tetramerize or to bind G-actin and/or F-actin. We show that increasing amounts of wild-type VASP increase network stiffness up to a certain point, beyond which stiffness actually decreases with increasing VASP concentration. The maximum stiffness is 10-fold higher than for pure actin networks. Confocal microscopy shows that VASP forms clustered actin filament bundles, explaining the reduction in network elasticity at high VASP concentration. Removal of the tetramerization site results in significantly reduced bundling and bundle clustering, indicating that VASP's flexible tetrameric structure causes clustering. Removing either the F-actin or the G-actin binding site diminishes VASP's effect on elasticity, but does not eliminate it. Mutating the F-actin and G-actin binding site together, or mutating the F-actin binding site and saturating the G-actin binding site with monomeric actin, eliminates VASP's ability to increase network stiffness. We propose that, in the cell, VASP crosslinking confers only moderate increases in linear network elasticity, and unlike other crosslinkers, VASP's network stiffening activity may be tuned by the local concentration of monomeric actin.

In this study the hypothesis of motor programming involvement in developmental apraxia of speech (DAS) was investigated by studying articulatory compensation. Five children with DAS and 5 normally speaking children (age 5;0 [years;months] to 6;10), and 6 adult women produced utterances in a normal speaking condition and in a bite-block condition in which the mandible was kept in a fixed position. Throughout the utterances, the course of the second formant was used to determine articulatory compensation and the effect of the bite block on anticipatory coarticulation. Results showed that the bite-block condition in normally speaking children, like in adult women, did not affect the extent of anticipatory coarticulation. In the speech of children with DAS, the bite block had large effects on coarticulatory patterns and on vowel quality, which, contrary to expectations, had improved. These results are interpreted as a clear demonstration of deficient motor programming in DAS.

The aim of the present study was to investigate whether children with developmental apraxia of speech (DAS) show a deficit in planning syllables in speech production. Six children with DAS and six normally speaking (NS) children produced high- and low-frequency of occurrence syllable utterances, in which the syllable structure was systematically manipulated in an otherwise unchanging phoneme sequence. Anticipatory coarticulation, using second formant trajectories, and durational structure were analysed. The results showed stronger coarticulation in the children with DAS when compared to the normally speaking children. but in contrast to our expectations, in neither group was a systematic effect of syllable structure on the second format trajectory found. Effects of syllable structure did emerge for durational structure in that durational adjustments were found in the segments of the second syllable. These adjustments were less systematic in children with DAS when compared to normally speaking children. Furthermore, at the prosodic level, normally speaking children showed metrical contrasts that were not realized by the children with DAS. The latter results are interpreted as evidence for a problem in the planning of syllables in speech production of children with DAS, in particular concerning prosodic aspects, which is discussed in relation to the automation of speech production.

The aim of this study was to enhance our insight into the underlying deficit in developmental apraxia of speech (DAS). In particular, the involvement of planning and/or programming of speech movements in context was tested by analysing coarticulatory cohesion. For this purpose, second formant frequency measurements were conducted in repetitions of nonsense utterances ([[symbol: see text]] C = /s,x,b,d/; V = /i.a.u/), and compared across nine children with DAS, six normally speaking (NS) children and six adult women. The results showed both intra- and intersyllabic anticipatory coarticulation in NS children and adult women, in which the intersyllabic coarticulation was stronger in NS children than in adult women. The children with DAS showed more variability as compared to NS children, made, on average, less distinction between the vowels, and showed individually idiosyncratic coarticulation patterns. These results are discussed in the light of a delay as well as a deviance of speech development in children with DAS.