•We propose a new MILP formulation; it computes the global optimum for small cases.•Improvements over travel time of around 3% are obtained for a small real case.•We propose a metaheuristic to solve ...large-sized cases.•The metaheuristic is applied to a larger real case, comprising more than 130 lines.
We study the transit frequency optimization problem, which aims to determine the time interval between subsequent buses for a set of public transportation lines given by their itineraries, i.e., sequences of stops and street sections. The solution should satisfy a given origin–destination demand and a constraint on the available fleet of buses. We propose a new mixed integer linear programming (MILP) formulation for an already existing model, originally formulated as a nonlinear bilevel one. The proposed formulation is able to solve to optimality real small-sized instances of the problem using MILP techniques. For solving larger instances we propose a metaheuristic which accuracy is estimated by comparing against exact results (when possible). Both exact and approximated approaches are tested by using existing cases, including a real one related to a small-city which public transportation system comprises 13 lines. The magnitude of the improvement of that system obtained by applying the proposed methodologies, is comparable with the improvements reported in the literature, related to other real systems. Also, we investigate the applicability of the metaheuristic to a larger-sized real case, comprising more than 130 lines.
•We consider several aspects of transit systems, which have not been jointly modeled.•We review existing formulations, discussing the treatment of such aspects.•We propose a new mixed integer linear ...formulation.•We discuss the impact of adding new aspects, on the mathematical structure.•Numerical applications show the contribution of the proposal.
In this work, we study the transit network design problem from the perspective of mathematical programming. More precisely, we consider the problem of defining the number and itinerary of bus routes and their frequencies, for a public transportation system. In this problem, the routes should be defined in terms of a given infrastructure of streets and stops and should cover a given origin–destination demand. The solution (routes and frequencies) should be convenient for the users and the operators. We review existing mathematical programming formulations and propose a new one, paying attention to the following aspects of public transportation systems, that are identified as key elements in order to have a realistic model: (a) the interest of the users, (b) the interest of the operators, (c) the behavior of the users, and (d) constraints regarding transfer, infrastructure and bus capacity. First, we discuss the formulations existing on the literature, in terms of the aspects mentioned above. Second, we propose a mixed integer linear programming (MILP) formulation, that incorporates the waiting time and the existence of multiple lines in the behavior of the users. We validate the proposed formulation using several cases, including a real one. Also, we compare the obtained results against results from the existing literature. In order to include transfer, infrastructure and bus capacity constraints, we propose an extension to the formulation and we discuss its impact in the structure of the model, based on concepts of bi-level mathematical programming. The mathematical formulations developed contribute towards a more realistic modeling effort, taking into account important aspects of the real system which were not included in previous proposals in the literature.
The transit network design problem (TNDP) aims to determine a set of bus routes for a public transportation system, which must be convenient from the viewpoints of both users (people who use public ...transportation) and operators (companies who own the resources to give the service). This article presents a constructive algorithm for the TNDP. It is specially designed to produce a set of routes that fulfils demand covering constraints, while taking into account the interests of both users and operators. Its general structure is inspired in the Route Generation Algorithm (RGA) of Baaj and Mahmassani, where its original expansion of routes by inserting individual vertices is replaced by a strategy of insertion of pairs of vertices. The algorithm proposed, called Pair Insertion Algorithm (PIA) can be used to generate initial solutions for a local improvement or evolutionary algorithm, as well as to complete an unfeasible solution with respect to demand covering constraints. Numerical results comparing PIA with RGA over a real test case show that both algorithms produce solutions with similar quality from the users viewpoint (in terms of in-vehicle travel time), while the former produces better solutions from the operators viewpoint (in terms of number of routes and total route duration) and requires a higher execution time. Since the TNDP arises in a context of strategic planning, a solution that reduces the operation cost of the system is highly desirable, even though it takes more time to be computed. The experimental study of the proposed algorithm also shows its ability to produce diverse solutions in both decision and objective spaces; this is a useful property when looking at the use of PIA as a subroutine in the context of another algorithm such as metaheuristics, in particular for a multi-objective problem like TNDP.
Perrault syndrome is a genetically and clinically heterogeneous autosomal-recessive condition characterized by sensorineural hearing loss and ovarian failure. By a combination of linkage analysis, ...homozygosity mapping, and exome sequencing in three families, we identified mutations in CLPP as the likely cause of this phenotype. In each family, affected individuals were homozygous for a different pathogenic CLPP allele: c.433A>C (p.Thr145Pro), c.440G>C (p.Cys147Ser), or an experimentally demonstrated splice-donor-site mutation, c.270+4A>G. CLPP, a component of a mitochondrial ATP-dependent proteolytic complex, is a highly conserved endopeptidase encoded by CLPP and forms an element of the evolutionarily ancient mitochondrial unfolded-protein response (UPRmt) stress signaling pathway. Crystal-structure modeling suggests that both substitutions would alter the structure of the CLPP barrel chamber that captures unfolded proteins and exposes them to proteolysis. Together with the previous identification of mutations in HARS2, encoding mitochondrial histidyl-tRNA synthetase, mutations in CLPP expose dysfunction of mitochondrial protein homeostasis as a cause of Perrault syndrome.
We describe a distinct retinal disorder, autosomal-recessive bestrophinopathy (ARB), that is consequent upon biallelic mutation in
BEST1 and is associated with central visual loss, a characteristic ...retinopathy, an absent electro-oculogram light rise, and a reduced electroretinogram. Heterozygous mutations in
BEST1 have previously been found to cause the two dominantly inherited disorders, Best macular dystrophy and autosomal-dominant vitreoretinochoroidopathy. The transmembrane protein bestrophin-1, encoded by
BEST1, is located at the basolateral membrane of the retinal pigment epithelium in which it probably functions as a Cl
− channel. We sequenced
BEST1 in five families, identifying DNA variants in each of ten alleles. These encoded six different missense variants and one nonsense variant. The alleles segregated appropriately for a recessive disorder in each family. No clinical or electrophysiological abnormalities were identified in any heterozygotes. We conducted whole-cell patch-clamping of HEK293 cells transfected with bestrophin-1 to measure the Cl
− current. Two ARB missense isoforms severely reduced channel activity. However, unlike two other alleles previously associated with Best disease, cotransfection with wild-type bestrophin-1 did not impair the formation of active wild-type bestrophin-1 channels, consistent with the recessive nature of the condition. We propose that ARB is the null phenotype of bestrophin-1 in humans.
Heimler syndrome (HS) is a rare recessive disorder characterized by sensorineural hearing loss (SNHL), amelogenesis imperfecta, nail abnormalities, and occasional or late-onset retinal pigmentation. ...We ascertained eight families affected by HS and, by using a whole-exome sequencing approach, identified biallelic mutations in PEX1 or PEX6 in six of them. Loss-of-function mutations in both genes are known causes of a spectrum of autosomal-recessive peroxisome-biogenesis disorders (PBDs), including Zellweger syndrome. PBDs are characterized by leukodystrophy, hypotonia, SNHL, retinopathy, and skeletal, craniofacial, and liver abnormalities. We demonstrate that each HS-affected family has at least one hypomorphic allele that results in extremely mild peroxisomal dysfunction. Although individuals with HS share some subtle clinical features found in PBDs, the diagnosis was not suggested by routine blood and skin fibroblast analyses used to detect PBDs. In conclusion, our findings define HS as a mild PBD, expanding the pleiotropy of mutations in PEX1 and PEX6.
Biallelic inactivation of the NF2 gene occurs in the majority of schwannomas. This usually involves a combination of a point mutation or multiexon deletion, in conjunction with either a second point ...mutation or loss of heterozygosity (LOH). We have performed DNA sequence and dosage analysis of the NF2 gene in a panel of 239 schwannoma tumours: 97 neurofibromatosis type 2 (NF2)-related schwannomas, 104 sporadic vestibular schwannomas (VS) and 38 schwannomatosis-related schwannomas. In total, we identified germline NF2 mutations in 86 out of 97 (89%) NF2 patients and a second mutational event in 77 out of 97 (79%). LOH was by far the most common form of second hit. A combination of microsatellite analysis with either conventional comparative genomic hybridization (CGH) or multiplex ligation-dependent probe amplification (MLPA) identified mitotic recombination (MR) as the cause of LOH in 14 out of 72 (19%) total evaluable tumours. Among sporadic VS, at least one NF2 mutation was identified by sequence analysis or MLPA in 65 out of 98 (66%) tumours. LOH occurred in 54 out of 96 (56%) evaluable tumours, but MR only accounted for 5 out of 77 (6%) tested. LOH was present in 28 out of 34 (82%) schwannomatosis-related schwannomas. In all eight patients who had previously tested positive for a germline SMARCB1 mutation, this involved loss of the whole, or part of the long arm, of chromosome 22. In contrast, 5 out of 22 (23%) tumours from patients with no germline SMARCB1 mutation exhibited MR. High-resolution Affymetrix SNP6 genotyping and copy number (CN) analysis (Affymetrix, Santa Clara, CA, USA) were used to determine the chromosomal breakpoint locations in tumours with MR. A range of unique recombination sites, spanning approximately 11.4 Mb, were identified. This study shows that MR is a mechanism of LOH in NF2 and SMARCB1-negative schwannomatosis-related schwannomas, occurring less frequently in sporadic VS. We found no evidence of MR in SMARCB1-positive schwannomatosis, suggesting that susceptibility to MR varies according to the disease context.
Perrault syndrome is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) in both sexes and primary ovarian insufficiency in 46, XX karyotype females. Biallelic ...variants in five genes are reported to be causative: HSD17B4, HARS2, LARS2, CLPP and C10orf2. Here we present eight families affected by Perrault syndrome. In five families we identified novel or previously reported variants in HSD17B4, LARS2, CLPP and C10orf2. The proband from each family was whole exome sequenced and variants confirmed by Sanger sequencing. A female was compound heterozygous for a known, p.(Gly16Ser) and novel, p.(Val82Phe) variant in D‐bifunctional protein (HSD17B4). A family was homozygous for mitochondrial leucyl aminocyl tRNA synthetase (mtLeuRS) (LARS2) p.(Thr522Asn), previously associated with Perrault syndrome. A further family was compound heterozygous for mtLeuRS, p.(Thr522Asn) and a novel variant, p.(Met117Ile). Affected individuals with LARS2 variants had low frequency SNHL, a feature previously described in Perrault syndrome. A female with significant neurological disability was compound heterozygous for p.(Arg323Gln) and p.(Asn399Ser) variants in Twinkle (C10orf2). A male was homozygous for a novel variant in CLPP, p.(Cys144Arg). In three families there were no putative pathogenic variants in these genes confirming additional disease‐causing genes remain unidentified. We have expanded the spectrum of disease‐causing variants associated with Perrault syndrome.
Bestrophin-1 is preferentially expressed at the basolateral membrane of the retinal pigmented epithelium (RPE) of the retina. Mutations in the BEST1 gene cause the retinal dystrophies vitelliform ...macular dystrophy, autosomal-dominant vitreochoroidopathy, and autosomal-recessive bestrophinopathy. Here, we describe four missense mutations in bestrophin-1, three that we believe are previously unreported, in patients diagnosed with autosomal-dominant and -recessive forms of retinitis pigmentosa (RP). The physiological function of bestrophin-1 remains poorly understood although its heterologous expression induces a Cl−-specific current. We tested the effect of RP-causing variants on Cl− channel activity and cellular localization of bestrophin-1. Two (p.L140V and p.I205T) produced significantly decreased chloride-selective whole-cell currents in comparison to those of wild-type protein. In a model system of a polarized epithelium, two of three mutations (p.L140V and p.D228N) caused mislocalization of bestrophin-1 from the basolateral membrane to the cytoplasm. Mutations in bestrophin-1 are increasingly recognized as an important cause of inherited retinal dystrophy.
Amelogenesis imperfecta (AI) describes a clinically and genetically heterogeneous group of disorders of biomineralization resulting from failure of normal enamel formation. AI is found as an isolated ...entity or as part of a syndrome, and an autosomal-recessive syndrome associating AI and gingival hyperplasia was recently reported. Using whole-exome sequencing, we identified a homozygous nonsense mutation in exon 2 of FAM20A that was not present in the Single Nucleotide Polymorphism database (dbSNP), the 1000 Genomes database, or the Centre d'Etude du Polymorphisme Humain (CEPH) Diversity Panel. Expression analyses indicated that Fam20a is expressed in ameloblasts and gingivae, providing biological plausibility for mutations in FAM20A underlying the pathogenesis of this syndrome.
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