Search

Patients with atrial septal defects (ASDs) have increased mortality and morbidity. This can only partly be explained by hemodynamic changes caused by the ASD, suggesting additional underlying causes. Patients with an ASD have an increased burden of pathogenic gene variants in ASD-related genes, indicating genetics as an important factor in etiology. Inheritance of genetic variants with high impact can cause ASD in relatives (familial ASD). This study aimed to investigate whether lifelong outcomes were different in patients with familial ASD compared with patients with sporadic ASD. We used health registries and a nationwide cohort of 2,151 patients with ASD to compare the incidences of atrial fibrillation or flutter (together abbreviated as AF), heart failure, and mortality between patients with familial and sporadic ASD using Cox proportional hazard ratio and Fine and Gray analysis. Patients with familial ASD experienced AF and heart failure earlier in life than patients with sporadic ASD, with hazard ratios of 1.6 and 1.7, respectively. Subdistribution hazard ratios showed an increased risk of AF and heart failure in patients with familial ASD compared with patients with sporadic ASDs (2.3 and 3.1, respectively). Our results suggest that genetic variants with high impact may influence the outcomes of patients with ASD. In conclusion, patients with familial ASD have an increased risk and an earlier onset of AF and heart failure compared with patients with sporadic ASD, hence clinical awareness of arrhythmias and heart failure in patients with familial ASD may lead to timely treatment.

Designing a public transport timetable that maximizes passenger service, measured in weighted travel time, is an intricate problem. The weighted travel time depends on the free route choice of passengers. Passenger route choice depends on the timetable. In turn, the timetable that minimizes weighted travel time depends on the route choice of passengers—and therefore requires passenger route choice information. Consequently, a sequential approach where timetables are designed provided pre-fixed passenger assignment to routes may not find the optimal timetable. This paper aims to integrate passenger route choice and timetabling. It addresses the problem of designing maximal passenger service public transport timetables in systems with free route choice within a budget for operating costs. Operating costs are defined by the minimal cost vehicle schedule required to operate the timetable. The proposed methodology integrates a matheuristic for timetabling and vehicle scheduling with a passenger assignment model in an iterative framework, where different forms of integration are evaluated. Focus is on long- to medium-term timetabling, provided an initial timetable. The results for a realistic case study in the Greater Copenhagen area indicate that our approach consistently leads, at no additional cost, to timetables that represent a reduction in passenger weighted travel time in comparison with both an initial timetable and a non-integrated timetabling method that receives a single-passenger assignment as input.

Primary microcephaly (MCPH) is characterized by reduced brain size and intellectual disability. The exact pathophysiological mechanism underlying MCPH remains to be elucidated, but dysfunction of neuronal progenitors in the developing neocortex plays a major role. We identified a homozygous missense mutation (p.W155C) in Ribosomal RNA Processing 7 Homolog A, RRP7A, segregating with MCPH in a consanguineous family with 10 affected individuals. RRP7A is highly expressed in neural stem cells in developing human forebrain, and targeted mutation of Rrp7a leads to defects in neurogenesis and proliferation in a mouse stem cell model. RRP7A localizes to centrosomes, cilia and nucleoli, and patient-derived fibroblasts display defects in ribosomal RNA processing, primary cilia resorption, and cell cycle progression. Analysis of zebrafish embryos supported that the patient mutation in RRP7A causes reduced brain size, impaired neurogenesis and cell proliferation, and defective ribosomal RNA processing. These findings provide novel insight into human brain development and MCPH., The RRP7A a gene is involved in ribosome biogenesis. Here the authors report a homozygous missense mutation segregating with primary microcephaly, and show that this occurs via functional defects in both nucleoli and primary cilia disrupting cell proliferation and neurogenesis.

Microcephaly primary hereditary (MCPH) is a congenital disease characterized by nonsyndromic reduction in brain size due to impaired neurogenesis, often associated with a variable degree of intellectual disability (ID). The genetic etiology of MCPH is heterogeneous and comprises more than 20 loci, nearly all following a recessive inheritance pattern. The first causative gene identified, MCPH1 or Microcephalin, encodes a centrosomal protein that modulates chromosome condensation and cell cycle progression. It is also involved in DNA damage response and telomere maintenance in the nucleus. Despite numerous studies on MCPH1 function, MCPH1-affected individuals are rare and the available clinical reports are not sufficient to define the natural history of the disease. Here, we present a novel patient with congenital microcephaly, ID, language delay, short stature, and other minor features such as strabismus. magnetic resonance imaging revealed ventriculomegaly, simplified gyral pattern in the frontal lobes, and a neuronal migration defect. Genetic testing detected a homozygous deletion of exons 1–8 of MCPH1. We compare the patients’ characteristics with a list of features from MCPH1 cases described in the literature, in an effort to provide additional clues for a comprehensive definition of disease presentation and evolution.

Urban consolidation centers (UCCs) have a key role in many initiatives in urban logistics, yet few of them are successful in the long run. The high costs often prevent attracting a sufficient number of UCC users. In this paper, we study sustainable business models and the supporting role of administrative policies. We perform an agent-based simulation applied to the city of Copenhagen and collect data from a variety of sources to model the agents. Both the data and case setup are validated by means of expert interviews. We test 1,458 schemes that combine several administrative measures and cost settings. Most schemes yield significant environmental benefits; many of them reduce the truck kilometers driven by about 65% and emissions by about 70%. The key challenge is to identify schemes that are also financially sustainable. We show the importance of committing carriers to the UCC as soon as possible, as carriers potentially generate the bulk of the revenue. Subsequent revenues may be generated by offering value-adding services to receivers. Based on the numerical experiments, we pose various propositions that aid in providing favorable conditions for a UCC, improving its chances of long-term success.

BackgroundIn a recent nationwide cohort study, we have discovered that patients living with an atrial septal defect (ASD) have a shorter life expectancy, increased risk of atrial fibrillation, pneumonia, and psychiatric issues compared to the general population. The pathophysiological mechanisms are still unknown. The objective of this study is to investigate if this group of patients is burdened by mutations in genes associated with ASD.MethodsWe included 147 patients with an unrepaired ASD. We curated a list of ASD candidate genes, and patients were analyzed for genetic variants in these genes, using targeted next generation sequencing. We filtered for protein altering variants (PAVs) and protein truncating variants (PTVs) with minor allele frequency (MAF) ResultsWe identified 384 rare (MAFConclusionsPatients with a small, unrepaired ASD were enriched for rare PAVs within 59 ASD candidate disease genes. Our results suggest that recurrence risk of congenital heart defects in offspring may be increased for this group of patients and warrants further investigations.

Congenital Heart Disease (CHD) affects approximately 7-9 children per 1000 live births. Numerous genetic studies have established a role for rare genomic variants at the copy number variation (CNV) and single nucleotide variant level. In particular, the role of de novo mutations (DNM) has been highlighted in syndromic and non-syndromic CHD. To identify novel haploinsufficient CHD disease genes we performed an integrative analysis of CNVs and DNMs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm (TAA). We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed mutation rate testing for DNMs identified in 2,489 parent-offspring trios. Our combined analysis revealed 21 genes which were significantly affected by rare genomic deletions and/or constrained non-synonymous de novo mutations in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in singletons and small cases series, or show new associations with CHD. In addition, a systems level analysis revealed shared contribution of CNV deletions and DNMs in CHD probands, affecting protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes.

In this paper, we study the problem of optimizing the size and mix of a mixed fleet of electric and conventional vehicles owned by firms providing urban freight logistics services. Uncertain customer requests are considered at the strategic planning stage. These requests are revealed before operations commence in each operational period. At the operational level, a new model for vehicle power consumption is suggested. In addition to mechanical power consumption, this model accounts for cabin climate control power, which is dependent on ambient temperature, and auxiliary power, which accounts for energy drawn by external devices. We formulate the problem of stochastic fleet size and mix optimization as a two-stage stochastic program and propose a sample average approximation based heuristic method to solve it. For each operational period, an adaptive large neighborhood search algorithm is used to determine the operational decisions and associated costs. The applicability of the approach is demonstrated through two case studies within urban logistics services.

BackgroundCongenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease aetiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD.MethodsWe used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model.ResultsWe identified 1,785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes and 218 of the genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signalling. Replication confirmed increased mutation burden of calcium-signalling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1, PLCB2 and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes.ConclusionsThe study identifies abnormal calcium signalling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD.

Smad ubiquitin regulatory factor 1 (SMURF1) is a HECT-type E3 ubiquitin ligase that plays a critical role in vertebrate development by regulating planar cell polarity (PCP) signaling and convergent extension (CE). Here we show that SMURF1 is involved in mammalian heart development. We find that SMURF1 is highly expressed in outflow tract cushion mesenchyme and Smurf1−/− mouse embryos show delayed outflow tract septation. SMURF1 is expressed in smooth muscle cells of the coronary arteries and great vessels. Thickness of the aortic smooth muscle cell layer is reduced in Smurf1−/− mouse embryos. We show that SMURF1 is a negative regulator of cardiomyogenesis and a positive regulator of smooth muscle cell and cardiac fibroblast differentiation, indicating that SMURF1 is important for cell-type specification during heart development. Finally, we provide evidence that SMURF1 localizes at the primary cilium where it may regulate bone morphogenetic protein (BMP) signaling, which controls the initial phase of cardiomyocyte differentiation. In summary, our results demonstrate that SMURF1 is a critical regulator of outflow tract septation and cell-type specification during heart development, and that these effects may in part be mediated via control of cilium-associated BMP signaling.

Long transfer times often add unnecessary inconvenience to journeys in public transport systems. Synchronizing relevant arrival and departure times through small timetable modifications could reduce excess transfer times, but may also directly affect the operational costs, as the timetable defines the set of feasible vehicle schedules. Therefore better results in terms of passenger service, operational costs, or both, could be obtained by solving these problems simultaneously. This paper addresses the tactical level of the integrated timetabling and vehicle scheduling problem as a bi-objective mixed integer programming problem that minimizes transfer costs and operational costs. Given an initial non-cyclical timetable, and time-dependent service times and passenger demand, the weighted sum of transfer time cost and operational costs is minimized by allowing modifications to the timetable that respect a set of headway constraints. Timetable modifications consist of shifts in departure time and addition of dwell time at intermediate stops with transfer opportunities. A matheuristic is proposed that iteratively solves the mathematical formulation of the integrated timetabling and vehicle scheduling problem allowing timetable modifications for a subset of timetabled trips only, while solving the full vehicle scheduling problem. We compare different selection strategies for defining the sub-problems. Results for a realistic case study of the Greater Copenhagen area indicate that the matheuristic is able to find better feasible solutions faster than a commercial solver and that allowing the addition of dwell time creates a larger potential for reducing transfer costs.

Battery electric buses are seen as a well-suited technology for the electrification of road-based public transport. However, the transition process from conventional diesel to electric buses faces major hurdles caused by range limitations and required charging times of battery buses. This work addresses these constraints and provides a methodology for the cost-optimized planning of depot charging battery bus fleets and their corresponding charging infrastructure. The defined problem covers the scheduling of battery buses, the fleet composition, and the optimization of charging infrastructure in a joint process. Vehicle schedule adjustments are monetized and evaluated together with the investment and operational costs of the bus system. The resulting total cost of ownership enables a comparison of technical alternatives on a system level, which makes this approach especially promising for feasibility studies comprising a wide range of technical concepts. Two scenarios of European cities are analyzed and discussed in a case study, revealing that the cost structure is influenced significantly by the considered bus type and its technical specifications. For example, the total energy consumption of the considered lightweight bus is up to 32% lower than the total consumption of the high range bus, although the deadheading mileage increases. However, the total costs of ownership for operating both bus types are relatively close, due to the increased fleet size and driver expenses required for the lightweight bus system. The case study furthermore reveals that a mixed fleet of different bus types could be advantageous depending on the operational characteristics of the bus route.

Aims: Congenital heart defects (CHD) affect almost 1% of all live born children and the number of adults with CHD is increasing. In families where CHD has occurred previously, estimates of recurrence risk, and the type of recurring malformation are important for counselling and clinical decision-making, but the recurrence patterns in families are poorly understood. We aimed to determine recurrence patterns, by investigating the co-occurrences of CHD in 1163 families with known malformations, comprising 3080 individuals with clinically confirmed diagnosis.Methods and results: We calculated rates of concordance and discordance for 41 specific types of malformations, observing a high variability in the rates of concordance and discordance. By calculating odds ratios for each of 1640 pairs of discordant lesions observed between affected family members, we were able to identify 178 pairs of malformations that co-occurred significantly more or less often than expected in families. The data show that distinct groups of cardiac malformations co-occur in families, suggesting influence from underlying developmental mechanisms. Analysis of human and mouse susceptibility genes showed that they were shared in 19% and 20% of pairs of co-occurring discordant malformations, respectively, but none of malformations that rarely co-occur, suggesting that a significant proportion of co-occurring lesions in families is caused by overlapping susceptibility genes.Conclusion: Familial CHD follow specific patterns of recurrence, suggesting a strong influence from genetically regulated developmental mechanisms. Co-occurrence of malformations in families is caused by shared susceptibility genes.

CDK5RAP2 gene encodes a centrosomal protein, highly expressed in fetal brain and essentially indispensable for its normal development, as biallelic mutations in it lead to primary microcephaly (MCPH). Despite being known as MCPH linked gene for more than a decade, the phenotypic spectrum of CDK5RAP2 mutations is still under explored as only eleven families have been reported worldwide. Here, we analyzed a consanguineous Pakistani MCPH family, characterized by moderate to severe intellectual disability, speech impairment, moderately short stature and sparse eyebrows. Whole exome sequencing of the proband identified a 2bp duplication in exon 34 of CDK5RAP2 that causes frame-shift, leading to a premature stop codon. The resultant transcript is resistant to nonsense mediated decay, suggesting that the mutation leads to a truncated protein lacking C-terminal domains; CDK5R1, and Cnn motif 2 (CM2), required for its localization to centrosome and Golgi Apparatus. Clinical variability observed in the family highlights the importance of further detailed clinical description of patients with CDK5RAP2 mutations.

Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways., Author summary Congenital heart disease (CHD) is the most common congenital anomaly and represents a major global health burden. Multiple studies have identified a key genetic component contributing to the aetiology of CHD. However, despite the advances in the field of CHD within the last three decades, the genetic causes underlying CHD are still not fully understood. Herein we have assembled a large patient CHD cohort and performed a data-driven meta-analysis of genomic variants in CHD. This analysis has allowed us to strengthen the disease association of known CHD genes, as well as identifying novel haploinsufficient CHD candidate genes.

Objective Atrial septal defect (ASD) is the second most common congenital heart defect (CHD) and is observed in families as an autosomal dominant trait as well as in nonfamilial CHD. Mutations in the NKX2-5 gene, located on chromosome 5, are associated with ASD, often combined with conduction disturbances, cardiomyopathies, complex CHD, and sudden cardiac death as well. Here, we show that NKX2-5 mutations primarily occur in ASD patients with conduction disturbances and heritable ASD. Furthermore, these families are at increased risk of sudden cardiac death. Results We screened 39 probands with familial CHD for mutations in NKX2-5 and discovered a novel mutation in one family (2.5%) with ASD and atrioventricular block. A review of the literature revealed 59 different NKX2-5 mutations in 202 patients. Mutations were significantly more common in familial cases compared to nonfamilial cases (P = 7.1 × 10−9). The majority of patients (74%) had ASD with conduction disturbance. Nineteen patients (15%) of 120 with familial ASD and conduction disturbance died from sudden cardiac death of which nine (8%) were confirmed mutation carriers, and 10 were possible carriers. Conclusions NKX2-5 mutations mainly occur in familial CHD, the signature phenotype is ASD with conduction disturbances and mutation carriers are at increased risk of sudden cardiac death. We suggest that familial ASD patients should be screened for NKX2-5 mutations and, if they are mutation carriers, implantation of an implantable cardioverter-defibrillator should be considered in these patients.

Disasters such as fires, earthquakes, and floods cause severe casualties and enormous economic losses. One effective method to reduce these losses is to construct a disaster relief network to deliver disaster supplies as quickly as possible. This method requires solutions to the following problems. 1) Given the established distribution centers, which center(s) should be open after a disaster? 2) Given a set of vehicles, how should these vehicles be assigned to each open distribution center? 3) How can the vehicles be routed from the open distribution center(s) to demand points as efficiently as possible? 4) How many supplies can be delivered to each demand point on the condition that the relief allocation plan is made a priority before the actual demands are realized? This study proposes a model for risk-averse optimization of disaster relief facility location and vehicle routing under stochastic demand that solves the four problems simultaneously. The novel contribution of this study is its presentation of a new model that includes conditional value at risk with regret (CVaR-R)—defined as the expected regret of worst-case scenarios—as a risk measure that considers both the reliability and unreliability aspects of demand variability in the disaster relief facility location and vehicle routing problem. Two objectives are proposed: the CVaR-R of the waiting time and the CVaR-R of the system cost. Due to the nonlinear capacity constraints for vehicles and distribution centers, the proposed problem is formulated as a bi-objective mixed-integer nonlinear programming model and is solved with a hybrid genetic algorithm that integrates a genetic algorithm to determine the satisfactory solution for each demand scenario and a non-dominated sorting genetic algorithm II (NSGA-II) to obtain the non-dominated Pareto solution that considers all demand scenarios. Moreover, the Nash bargaining solution is introduced to capture the decision-maker’s interests of the two objectives. Numerical examples demonstrate the trade-off between the waiting time and system cost and the effects of various parameters, including the confidence level and distance parameter, on the solution. It is found that the Pareto solutions are distributed unevenly on the Pareto frontier due to the difference in the number of the distribution centers opened. The Pareto frontier and Nash bargaining solution change along with the confidence level and distance parameter, respectively.

Family studies have established that the heritability of blood pressure is significant and genome-wide association studies (GWAS) have identified numerous susceptibility loci, including one within the non-coding part of Rho GTPase-activating protein 42 gene (ARHGAP42) on chromosome 11q22.1. Arhgap42-deficient mice have significantly elevated blood pressure, but the phenotypic effects of human variants in the coding part of the gene are unknown. In a Danish cohort of carriers with apparently balanced chromosomal rearrangements, we identified a family where a reciprocal translocation t(11;18)(q22.1;q12.2) segregated with hypertension and obesity. Clinical re-examination revealed that four carriers (age 50–77 years) have had hypertension for several years along with an increased body mass index (34–43 kg/m(2)). A younger carrier (age 23 years) had normal blood pressure and body mass index. Mapping of the chromosomal breakpoints with mate-pair and Sanger sequencing revealed truncation of ARHGAP42. A decreased expression level of ARHGAP42 mRNA in the blood was found in the translocation carriers relative to controls and allele-specific expression analysis showed monoallelic expression in the translocation carriers, confirming that the truncated allele of ARHGAP42 was not expressed. These findings support that haploinsufficiency of ARHGAP42 leads to an age-dependent hypertension. The other breakpoint truncated a regulatory domain of the CUGBP Elav-like family member 4 (CELF4) gene on chromosome 18q12.2 that harbours several GWAS signals for obesity. We thereby provide additional support for an obesity locus in the CELF4 domain.

PDGFRα signals from cilia to control development and tumorigenesis. Schmid et al. now show that intraflagellar transport protein 20 (IFT20) interacts with and stabilizes the E3 ubiquitin ligases c-Cbl and Cbl-b to promote feedback inhibition of PDGFRα signaling at the primary cilium., Primary cilia have pivotal roles as organizers of many different signaling pathways, including platelet-derived growth factor receptor α (PDGFRα) signaling, which, when aberrantly regulated, is associated with developmental disorders, tumorigenesis, and cancer. PDGFRα is up-regulated during ciliogenesis, and ciliary localization of the receptor is required for its appropriate ligand-mediated activation by PDGF-AA. However, the mechanisms regulating sorting of PDGFRα and feedback inhibition of PDGFRα signaling at the cilium are unknown. Here, we provide evidence that intraflagellar transport protein 20 (IFT20) interacts with E3 ubiquitin ligases c-Cbl and Cbl-b and is required for Cbl-mediated ubiquitination and internalization of PDGFRα for feedback inhibition of receptor signaling. In wild-type cells treated with PDGF-AA, c-Cbl becomes enriched in the cilium, and the receptor is subsequently ubiquitinated and internalized. In contrast, in IFT20-depleted cells, PDGFRα localizes aberrantly to the plasma membrane and is overactivated after ligand stimulation because of destabilization and degradation of c-Cbl and Cbl-b.

Most university biobanks begin like other university research projects, that is, with an idea conceived by an individual researcher in pursuit of his/her own research interests, publications, funding, and career. Some biobanks, however, come to have scientific value that goes beyond the projects that were initially responsible for the collection of the samples and data they contain. Such value may derive from among other things the uniqueness of the samples in terms of their sheer volume, the quality of the samples, the ability to link the samples with information retrieved in disease registries, or the fact that the samples represent very rare diseases. This article focuses on biobanks of this kind, and the special obligations that publicly funded universities have to ensure the sustainability of biobanks with continued scientific value. We argue that universities should adopt policies to deal with the various, diverse issues which may arise during the lifecycle of a biobank. The policies should be flexible, accommodate the freedoms of individual researchers, and reflect the multifaceted nature of biobanks. Yet they should be specific enough to provide guidance and robust enough to safeguard legal norms and ethical values. The article sets out concrete recommendations which universities should consider and act upon.

Most of the operational problems in container terminals are strongly interconnected. In this paper, we study the integrated Berth Allocation and Quay Crane Assignment Problem in seaport container terminals. We will extend the current state-of-the-art by proposing novel set partitioning models. To improve the performance of the set partitioning formulations, a number of variable reduction techniques are proposed. Furthermore, we analyze the effects of different discretization schemes and the impact of using a time-variant/invariant quay crane allocation policy. Computational experiments show that the proposed models significantly improve the benchmark solutions of the current state-of-art optimal approaches.

A novel splice site mutation in CEP135 is associated with primary microcephaly in a Pakistani family

Summary: The centrosome is the main microtubule-organizing center in animal cells and comprises a mother and daughter centriole surrounded by pericentriolar material. During formation of primary cilia, the mother centriole transforms into a basal body that templates the ciliary axoneme. Ciliogenesis depends on mother centriole-specific distal appendages, whereas the role of subdistal appendages in ciliary function is unclear. Here, we identify CEP128 as a centriole subdistal appendage protein required for regulating ciliary signaling. Loss of CEP128 did not grossly affect centrosomal or ciliary structure but caused impaired transforming growth factor-β/bone morphogenetic protein (TGF-β/BMP) signaling in zebrafish and at the primary cilium in cultured mammalian cells. This phenotype is likely the result of defective vesicle trafficking at the cilium as ciliary localization of RAB11 was impaired upon loss of CEP128, and quantitative phosphoproteomics revealed that CEP128 loss affects TGF-β1-induced phosphorylation of multiple proteins that regulate cilium-associated vesicle trafficking. : Mönnich et al. show that CEP128 localizes to the subdistal appendages of the mother centriole and basal body of the primary cilium. CEP128 regulates vesicular trafficking and targeting of RAB11 to the primary cilium. CEP128 loss leads to impaired TGF-β/BMP signaling, which, in zebrafish, is associated with defective organ development. Keywords: primary cilium, basal body, centriole, subdistal appendage, centrosome, transforming growth factor β, TGF-β, bone morphogenetic protein, BMP, zebrafish, phosphoproteomics, CEP128

Background Three-dimensional explant spheroid formation is an ex vivo technique previously used in studies of airway epithelial ion and water transport. Explanted cells and sheets of nasal epithelium form fully differentiated spheroids enclosing a partly fluid-filled lumen with the ciliated apical surface facing the outside and accessible for analysis of ciliary function. Methods We performed a two-group comparison study of ciliary beat pattern and ciliary beat frequency in spheroids derived from nasal airway epithelium in patients with primary ciliary dyskinesia (PCD) and in healthy controls. Nasal ciliary cells and sheets were removed on day 1 by nasal brush biopsy and analyzed with regard to ciliary beat pattern—and frequency using high-speed video imaging for standard reference values. Three-dimensional explant spheroid formation was initiated in the same individual on the same day by incubation of cells and sheets from a separate brush biopsy. Harvested spheroids were analyzed earliest possible and values of spheroid ciliary beat pattern and frequency were compared to the corresponding reference values from day 1. Results Spheroids formed fast in serum-free culture medium. Formation was successful in 15 out of 18 (82%) sampled individuals. Thus, formation was successful in seven healthy controls and eight PCD patients, while unsuccessful in 3 with PCD due to infection. Median (range) number of days in culture before harvesting of spheroids was 4 (1–5) in healthy versus 2 (1–5) in PCD. Spheroid ciliary beat pattern and frequency were unchanged compared to their corresponding day 1 standard reference values. Spheroid ciliary beat frequency discriminated highly significant between healthy controls (9.3 Hz) and PCD patients (2.4 Hz) (P

The Integrated Timetabling and Vehicle Scheduling Problem (IT-VSP) is a generalization of the well-known Vehicle Scheduling Problem (VSP). In the IT-VSP the trips in the original timetables may be modified in terms of arrival and departure times in order to minimize a new objective function that considers both operational costs and passenger transfer costs. Starting from a base timetable, the allowed modifications include shifting the departure time from the first station of each trip and also the extension of dwell times at important stops where large flows of passengers are expected to transfer between different trips. We consider transfers between bus trips scheduled by the model, but also transfers to other fixed lines that intersect the lines considered in the IT-VSP. We present a MIP formulation of the IT-VSP able to solve small instances of the problem, and a matheuristic approach that uses the compact MIP to solve larger instances of the problem. The idea is to iteratively solve restricted versions of the MIP selecting at each step a subset of trips where modifications are allowed, while all other trips remain fixed. The performance of the proposed matheuristic is shown on a case studywith real-life instances provided by the main service provider in the greater Copenhagen area. The effect of allowing dwell times is compared to previous approaches to the problem where trips are only allowed to be shifted in time.

The molecular mechanisms by whichEntamoeba histolyticacauses amebic liver abscess (ALA) are still not fully understood. Amebic mechanisms of adherence and cytotoxic activity are pivotal for amebic survival but apparently do not directly cause liver abscess. Abundant evidence indicates that chronic inflammation (resulting from an inadequate immune response) is probably the main cause of ALA. Reports referring to inflammatory mechanisms of liver damage mention a repertoire of toxic molecules by the immune response (especially nitric oxide and reactive oxygen intermediates) and cytotoxic substances released by neutrophils and macrophages after being lysed by amoebas (e.g., defensins, complement, and proteases). Nevertheless, recent evidence downplays these mechanisms in abscess formation and emphasizes the importance of peroxynitrite (ONOO−). It seems that the defense mechanism of amoebas against ONOO−, namely, the amebic thioredoxin system (including peroxiredoxin), is superior to that of mammals. The aim of the present text is to define the importance of ONOO−as the main agent of liver abscess formation during amebic invasion, and to explain the superior capacity of amoebas to defend themselves against this toxic agent through the peroxiredoxin and thioredoxin system.

Passengers using public transport systems often experience waiting times when transferring between two scheduled services. In this paper we propose a planning approach that seeks to obtain a favourable trade-off between the two contrasting objectives, passenger service and operating cost, by modifying the timetable. The planning approach is referred to as the simultaneous vehicle scheduling and passenger service problem (SVSPSP). The SVSPSP is modelled as an integer programming problem and solved using a large neighborhood search metaheuristic. The proposed framework is tested on data inspired by the express-bus network in the Greater Copenhagen area. The results are encouraging and indicate a potential decrease of passenger transfer waiting times in the network of up to 20%, with the vehicle scheduling costs remaining mostly unaffected.

Congenital heart disease (CHD) affects nearly 1 % of the population. It is a complex disease, which may be caused by multiple genetic and environmental factors. Studies in human genetics have led to the identification of more than 50 human genes, involved in isolated CHD or genetic syndromes, where CHD is part of the phenotype. Furthermore, mapping of genomic copy number variants and exome sequencing of CHD patients have led to the identification of a large number of candidate disease genes. Experiments in animal models, particularly in mice, have been used to verify human disease genes and to gain further insight into the molecular pathology behind CHD. The picture emerging from these studies suggest that genetic lesions associated with CHD affect a broad range of cellular signaling components, from ligands and receptors, across down-stream effector molecules to transcription factors and co-factors, including chromatin modifiers.

SummaryTransforming growth factor β (TGF-β) signaling is regulated by clathrin-dependent endocytosis (CDE) for the control of cellular processes during development and in tissue homeostasis. The primary cilium coordinates several signaling pathways, and the pocket surrounding the base and proximal part of the cilium is a site for CDE. We report here that TGF-β receptors localize to the ciliary tip and endocytic vesicles at the ciliary base in fibroblasts and that TGF-β stimulation increases receptor localization and activation of SMAD2/3 and ERK1/2 at the ciliary base. Inhibition of CDE reduced TGF-β-mediated signaling at the cilium, and TGF-β signaling and CDE activity are reduced at stunted primary cilia in Tg737orpk fibroblasts. Similarly, TGF-β signaling during cardiomyogenesis correlated with accumulation of TGF-β receptors and activation of SMAD2/3 at the ciliary base. Our results indicate that the primary cilium regulates TGF-β signaling and that the ciliary pocket is a compartment for CDE-dependent regulation of signal transduction.Video Abstract

This paper addresses the Electric Vehicle Scheduling Problem (E-VSP), in which a set of timetabled bus trips, each starting from and ending at specific locations and at specific times, should be carried out by a set of electric buses or vehicles based at a number of depots with limited driving ranges. The electric vehicles are allowed to be recharged fully or partially at any of the given recharging stations. The objective is to firstly minimize the number of vehicles needed to cover all the timetabled trips, and secondly to minimize the total traveling distance, which is equivalent to minimizing the total deadheading distance. A mixed integer programming formulation as well as an Adaptive Large Neighborhood Search (ALNS) heuristic for the E-VSP are presented. ALNS is tested on newly generated E-VSP benchmark instances. Result shows that the proposed heuristic can provide good solutions to large E-VSP instances and optimal or near-optimal solutions to small E-VSP instances. HighlightsThe electric vehicle scheduling with partial charging is addressed.A mixed integer programming model based on a directed acyclic graph is presented.An adaptive large neighborhood search heuristic is developed and tested on generated data.The model can solve instances with up to 30 trips and the heuristic up to 500 trips.

Bridge hanger vibrations have been reported under icy conditions. In this paper, the results from a series of static and dynamic wind tunnel tests on a circular cylinder representing a bridge hanger with simulated thin ice accretions are presented. The experiments focus on ice accretions produced for wind perpendicular to the cylinder at velocities below 30 m/s and for temperatures between -5C and -1C. Aerodynamic drag, lift and moment coefficients are obtained from the static tests, whilst mean and fluctuating responses are obtained from the dynamic tests. The influence of varying surface roughness is also examined. The static force coefficients are used to predict parameter regions where aerodynamic instability of the iced bridge hanger might be expected to occur, through use of an adapted theoretical 3- DOF quasi-steady galloping instability model, which accounts for sectional axial rotation. A comparison between the 3-DOF model and the instabilities found through two degree-of-freedom (2-DOF) dynamic tests is presented. It is shown that, although there is good agreement between the instabilities found through use of the quasi-steady theory and the dynamic tests, discrepancies exist-indicating the possible inability of quasi-steady theory to fully predict these vibrational instabilities.

Congenital heart disease (CHD) occurs in ∼1% of newborns. CHD arises from many distinct etiologies, ranging from genetic or genomic variation to exposure to teratogens, which elicit diverse cell and molecular responses during cardiac development. To systematically explore the relationships between CHD risk factors and responses, we compiled and integrated comprehensive datasets from studies of CHD in humans and model organisms. We examined two alternative models of potential functional relationships between genes in these datasets: direct convergence, in which CHD risk factors significantly and directly impact the same genes and molecules and functional convergence, in which risk factors significantly impact different molecules that participate in a discrete heart development network. We observed no evidence for direct convergence. In contrast, we show that CHD risk factors functionally converge in protein networks driving the development of specific anatomical structures (e.g., outflow tract, ventricular septum, and atrial septum) that are malformed by CHD. This integrative analysis of CHD risk factors and responses suggests a complex pattern of functional interactions between genomic variation and environmental exposures that modulate critical biological systems during heart development.

This paper provides a thorough review of the current state-of-the-art within airline disruption management of resources, including aircraft, crew, passenger and integrated recovery. An overview of model formulations of the aircraft and crew scheduling problems is presented in order to emphasize similarities between solution approaches applied to the planning and recovery problems. A brief overview of research within schedule robustness in airline scheduling is included in the review, since this proactive measure is a natural complement to disruption management.

The 22q11 deletion syndrome, which is caused by a 1.5- to 3.0-megabase hemizygous deletion in chromosome 22q11.2, has a prevalence of 1/2000 to 1/4000. However, the syndrome presents with highly variable phenotypes and thus may be underestimated among Danish newborns. To establish a true incidence of 22q11.2 deletions among certain manifestations, eg, congenital heart disease, on selected Danes, a multiplex ligation-dependant probe amplification (MLPA) analysis was designed. The analysis was planned to be performed on DNA extracted from dried blood spot samples (DBSS) obtained from Guthrie cards collected during neonatal screening programs. However, the DNA concentration necessary for a standard MLPA analysis (20 ng) could not be attained from DBSS, and a novel MLPA design was developed to permit for analysis on limited amounts of DNA (2 ng). A pilot study is reported here that validates the new MLPA design using nine patients diagnosed with the 22q11.2 deletion and 101 controls. All deletions were identified using DNA extracted from DBSS, and no copy number variations were detected in the controls, resulting in a specificity and sensitivity of 100%. It is thereby concluded that the novel MLPA probe design is successful and reliable using minimal amounts of DNA. This allows for use of DBSS samples in a retrospective study of 22q11.2 deletion among certain manifestations associated with DiGeorge Syndrome.

Defects in the assembly or function of primary cilia, which are sensory organelles, are tightly coupled to developmental defects and diseases in mammals. Here, we investigated the function of the primary cilium in regulating hedgehog signaling and early cardiogenesis. We report that the pluripotent P19.CL6 mouse stem cell line, which can differentiate into beating cardiomyocytes, forms primary cilia that contain essential components of the hedgehog pathway, including Smoothened, Patched-1 and Gli2. Knockdown of the primary cilium by Ift88 and Ift20 siRNA or treatment with cyclopamine, an inhibitor of Smoothened, blocks hedgehog signaling in P19.CL6 cells, as well as differentiation of the cells into beating cardiomyocytes. E11.5 embryos of the Ift88tm1Rpw (Ift88-null) mice, which form no cilia, have ventricular dilation, decreased myocardial trabeculation and abnormal outflow tract development. These data support the conclusion that cardiac primary cilia are crucial in early heart development, where they partly coordinate hedgehog signaling.

The chromosome break points of the t(8;21)(q21.3;q22.12) translocation associated with acute myeloid leukemia disrupt the RUNX1 gene (also known as AML1) and the RUNX1T1 gene (also known as CBFA2T3, MTG8 and ETO) and generate a RUNX1–RUNX1T1 fusion protein. Molecular characterization of the translocation break points in a t(5;8)(q32;q21.3) patient with mild-to-moderate mental retardation and congenital heart disease revealed that one of the break points was within the RUNX1T1 gene. Analysis of RUNX1T1 expression in human embryonic and fetal tissues suggests a role of RUNX1T1 in brain and heart development and support the notion that disruption of the RUNX1T1 gene is associated with the patient's phenotype.

In this study we report a female patient with an interstitial duplication of a region (10q22-q23) which is rarely reported in the literature. We fine mapped the aberration with array CGH, which revealed an 18.6-Mb duplication, covering 89 annotated genes, at 10q22.2-q23.33. There were no other deletions or duplications elsewhere in the genome. The main clinical features of the patient are microcephaly and congenital heart disease, which are likely to be caused by dosage effect of one or several genes in the duplicated region. Similar phenotypes have been found in other patients with 10q11-q22 duplications and in two out of three patients with 10q22-q25 duplications. However, most of the duplication cases were investigated only by conventional chromosome analyses, and fine mapping of these and other duplications of 10q22-q23 are warranted for genotype-phenotype comparisons.

Over the past decade, airlines have become more concerned with developing an optimal flight schedule, with very little slack left to accommodate for any form of variation from the optimal solution. During operation the planned schedules often have to be revised due to disruptions caused by for example severe weather, technical problems and crew sickness. Thus, the field of Airline Disruption Management has emerged within the past few years. The increased focus on cutting cost at the major airlines has intensified the interest in the development of new and cost efficient methods to handle airline disruptions. The purpose of this paper is twofold. In the first part it offers an introduction to airline disruption management, provides the readers with a description of the planning processes and delivers a detailed overview of the numerous aspects of airline disruption management. In the second part we report on experiences from a large research and development project on airline disruption management. Within the project the first prototype of a multiple resource decision support system at the operations control center in a major airline, has been implemented.

Background: The Pierre Robin sequence (PRS), consisting of cleft palate, micrognathia and glossoptosis, can be seen as part of the phenotype in other Mendelian syndromes—for instance, campomelic dysplasia (CD) which is caused by SOX9 mutations—but the aetiology of non-syndromic PRS has not yet been unravelled. Objective: To gain more insight into the aetiology of PRS by studying patients with PRS using genetic and cytogenetic methods. Methods: 10 unrelated patients with PRS were investigated by chromosome analyses and bacterial artificial chromosome arrays. A balanced translocation was found in one patient, and the breakpoints were mapped with fluorescence in situ hybridisation and Southern blot analysis. All patients were screened for SOX9 and KCNJ2 mutations, and in five of the patients expression analysis of SOX9 and KCNJ2 was carried out by quantitative real-time PCR. Results: An abnormal balanced karyotype 46,XX, t(2;17)(q23.3;q24.3) was identified in one patient with PRS and the 17q breakpoint was mapped to 1.13 Mb upstream of the transcription factor SOX9 and 800 kb downstream of the gene KCNJ2 . Furthermore, a significantly reduced SOX9 and KCNJ2 mRNA expression was observed in patients with PRS. Conclusion: Our findings suggest that non-syndromic PRS may be caused by both SOX9 and KCNJ2 dysregulation.

We previously showed that canonical TGFβ signaling is regulated in part by the primary cilium, and that ciliary TGFβ signaling is upregulated in stem cells differentiating into cardiomyocytes [1]. Ciliary signaling was shown to be associated with clathrin-dependent endocytosis at the ciliary pocket for activation of SMAD2/3 transcription factors that associate with and promote SMAD4 translocation to the nucleus for target gene expression. Here we investigated whether other receptor types of the TGFβ/BMP superfamily are associated with the primary cilium and whether ciliary TGFβ/BMP signaling regulates the commitment of stem cells to different lineages. Using retinal pigment epithelium cells, we demonstrate that multiple receptor systems within the TGFβ/BMP superfamily localize to the cilium and the ciliary pocket region, including TGFβ receptors I and II (TGF-RI/II), BMP receptors I and II (BMP-RI/II) as well as two isoforms of Activin II receptors (AcRIIa/b) that can be activated by their corresponding ligands to phosphorylate SMAD2/3, SMAD1/5, ERK1/2, AKT and TAK1 at the ciliary base. Further, knockdown of the feedback inhibitor of SMAD signaling, SMURF1, leads to increased SMAD1/5 phosphorylation at the ciliary base, indicating a major role of the primary cilium in balancing the cellular level of TGFβ/BMP signaling to control cellular processes during development and in tissue homeostasis. Indeed, the level of ciliary TGFβ/BMP signaling was shown to be associated with the ability to commit stem cells to either neurogenesis or cardiomyogenesis, such that downregulation of ciliary signaling promotes neurogenesis and inhibits cardiomyogenesis. Current studies focus on the mechanisms for targeting of TGFβ/BMP superfamily receptors to the primary cilium, trafficking and activation of the receptors within the ciliary compartment, and how these processes contribute to differential cross-talking with other signaling pathways in the cilium and at the pocket region to control cellular processes during development.

The purpose of the current study was to investigate the potential effect of intraoperative fluoroscopy on the accuracy of femoral tunnel placement in anatomic ACL reconstruction, using an ideal anatomic point as reference and evaluating postoperative tunnel placement based on 3D CT.An experienced ACL surgeon, using the anatomic approach for femoral tunnel placement, relying on intraarticular landmarks and remnants of the torn ACL-and novel to the fluoroscopic assist-was introduced to its use. A prospective series of patients was included where group 1 (without fluoroscopy) and group 2 (with fluoroscopy) both had postoperative CT scans so that femoral tunnel position could be evaluated and compared to an ideal tunnel centre based on anatomic studies by using the Bernard and Hertel grid.Group 2, where fluoroscopy was used, had a mean femoral tunnel that was closer to the ideal anatomic centre than group 1. In the Bernard and Hertel grid, the distance in the high-low axis (y-axis) was found significantly closer (P = 0.001), whilst the deep-shallow axis (x-axis) and a total absolute distance were not significantly closer to the ideal described anatomic centre.Intraoperative fluoroscopy was found effective as an aid for placing the femoral tunnel in a more accurate position, as compared to a desired anatomic centre. Although the concept of the "one-size-fits-all" approach for tunnel placement is debatable, the avoidance of grossly misplaced tunnels is the benefit of using fluoroscopy during ACL reconstruction. The authors hold that fluoroscopy is readily available, safe and easy to use and therefore a good aid in the anatomic approach for graft tunnel placement, for example, in a learning situation, in revision cases and when performing low volumes of such surgery.III.

Familial hypertrophic cardiomyopathy (FHC) is, in most cases, a disease of the sarcomere, caused by a mutation in one of 10 known sarcomere disease genes. More than 266 mutations have been identified since 1989. The FHC disease gene first characterized MYH7, encodes the cardiac beta-myosin heavy chain, and contains more than 115 of these mutations. However, in most studies, only the region encoding the globular head and the hinge region of the mature cardiac beta-myosin heavy chain have been investigated. Furthermore, most studies carries out screening for mutations in the most prevalent disease genes, and discontinues screening when an apparent disease-associated mutation has been identified. The aim of the present study was to screen for mutations in the rod region of the MYH7 gene in all probands of the cohort, regardless of the known genetic status of the proband. Three disease-causing mutations were identified in the rod region in four probands using capillary electrophoresis single-strand conformation polymorphism as a screening method. All mutations were novel: N1327K, R1712W, and E1753K. Two of the probands had already been shown to carry other FHC-associated mutations. In conclusion, we show that in the Danish cohort we find one third of all MYH7 mutations in the rod-encoding region and we find that two of the patients carrying these mutations also carry mutations in other FHC disease genes stressing the need for a complete screening of all known disease genes in FHC-patients.