Extracting the time-dependent transmission rate from infection data via solution of an inverse ODE problem

The transmission rate of many acute infectious diseases varies significantly in time, but the underlying mechanisms are usually uncertain. They may include seasonal changes in the environment, contact rate, immune system response, etc. The transmission rate has been thought difficult to measure directly. We present a new algorithm to compute the time-dependent transmission rate directly from prevalence data, which makes no assumptions about the number of susceptible or vital rates. The algorithm follows our complete and explicit solution of a mathematical inverse problem for SIR-type transmission models. We prove that almost any infection profile can be perfectly fitted by an SIR model with variable transmission rate. This clearly shows a serious danger of overfitting such transmission models. We illustrate the algorithm with historic UK measles data and our observations support the common belief that measles transmission was predominantly driven by school contacts

Induced CNS expression of CXCL1 augments neurologic disease in a murine model of multiple sclerosis via enhanced neutrophil recruitment.

Increasing evidence points to an important role for neutrophils in participating in the pathogenesis of the human demyelinating disease MS and the animal model EAE. Therefore, a better understanding of the signals controlling migration of neutrophils as well as evaluating the role of these cells in demyelination is important to define cellular components that contribute to disease in MS patients. In this study, we examined the functional role of the chemokine CXCL1 in contributing to neuroinflammation and demyelination in EAE. Using transgenic mice in which expression of CXCL1 is under the control of a tetracycline-inducible promoter active within glial fibrillary acidic protein-positive cells, we have shown that sustained CXCL1 expression within the CNS increased the severity of clinical and histologic disease that was independent of an increase in the frequency of encephalitogenic Th1 and Th17 cells. Rather, disease was associated with enhanced recruitment of CD11b+ Ly6G+ neutrophils into the spinal cord. Targeting neutrophils resulted in a reduction in demyelination arguing for a role for these cells in myelin damage. Collectively, these findings emphasize that CXCL1-mediated attraction of neutrophils into the CNS augments demyelination suggesting that this signaling pathway may offer new targets for therapeutic intervention

Ca-substitution and O-doping effects in superconducting Cu(Ba0.8Sr0.2)2(Yb1-xCax)Cu2O6+z obtained from neutron diffraction refinements

Distinct calcium and oxygen doping effects were studied in the Cu(Ba0.8Sr0.2)2(Yb1−xCax)Cu2O6+z (Cu−1212:P) system by means of neutron diffraction and superconducting quantum interference device experiments in the wide substitution ranges of 0<~x<~0.35 and 0<z<1. The effectiveness of the two different ways to introduce holes into the CuO2 planes was compared both in respect to the capability to increase Tc and in terms of the hole production as estimated from neutron-diffraction data via bond-valence-sum calculation. Oxygen doping was found to increase the hole concentration less efficiently, and further, at a certain hole concentration value higher Tc values were obtained with calcium substitution than with oxygen doping. The two different hole-doping methods exhibited also different Tc vs Cu-O bond length relations. As a conclusion, the possible roles of the hole distribution in the in-plane Cu-O bond and the flatness of the CuO2 planes in determining the superconducting properties were recognized.Peer reviewe

How blebs and pseudopods cooperate during chemotaxis

Two motors can drive extension of the leading edge of motile cells: actin polymerization and myosin-driven contraction of the cortex, producing fluid pressure and the formation of blebs. Dictyostelium cells can move with both blebs and actin-driven pseudopods at the same time, and blebs, like pseudopods, can be orientated by chemotactic gradients. Here we ask how bleb sites are selected and how the two forms of projection cooperate. We show that membrane curvature is an important, yet overlooked, factor. Dictyostelium cells were observed moving under agarose, which efficiently induces blebbing, and the dynamics of membrane deformations were analyzed. Blebs preferentially originate from negatively curved regions, generated on the flanks of either extending pseudopods or blebs themselves. This is true of cells at different developmental stages, chemotaxing to either folate or cyclic AMP and moving with both blebs and pseudopods or with blebs only. A physical model of blebbing suggests that detachment of the cell membrane is facilitated in concave areas of the cell, where membrane tension produces an outward directed force, as opposed to pulling inward in convex regions. Our findings assign a role to membrane tension in spatially coupling blebs and pseudopods, thus contributing to clustering protrusions to the cell front

Drug Repurposing: A Systematic Approach to Evaluate Candidate Oral Neuroprotective Interventions for Secondary Progressive Multiple Sclerosis

Objective: To develop and implement an evidence based framework to select, from drugs already licenced, candidate oral neuroprotective drugs to be tested in secondary progressive multiple sclerosis. Design: Systematic review of clinical studies of oral putative neuroprotective therapies in MS and four other neurodegenerative diseases with shared pathological features, followed by systematic review and meta-analyses of the in vivo experimental data for those interventions. We presented summary data to an international multi-disciplinary committee, which assessed each drug in turn using pre-specified criteria including consideration of mechanism of action. Results: We identified a short list of fifty-two candidate interventions. After review of all clinical and pre-clinical evidence we identified ibudilast, riluzole, amiloride, pirfenidone, fluoxetine, oxcarbazepine, and the polyunsaturated fatty-acid class (Linoleic Acid, Lipoic acid; Omega-3 fatty acid, Max EPA oil) as lead candidates for clinical evaluation. Conclusions: We demonstrate a standardised and systematic approach to candidate identification for drug rescue and repurposing trials that can be applied widely to neurodegenerative disorders

Inherited cataracts: molecular genetics, clinical features, disease mechanisms and novel therapeutic approaches

Cataract is the most common cause of blindness in the world; during infancy and early childhood, it frequently results in visual impairment. Congenital cataracts are phenotypically and genotypically heterogeneous and can occur in isolation or in association with other systemic disorders. Significant progress has been made in identifying the molecular genetic basis of cataract; 115 genes to date have been found to be associated with syndromic and non-syndromic cataract and 38 disease-causing genes have been identified to date to be associated with isolated cataract. In this review, we briefly discuss lens development and cataractogenesis, detail the variable cataract phenotypes and molecular mechanisms, including genotype-phenotype correlations, and explore future novel therapeutic avenues including cellular therapies and pharmacological treatments

CERKL-associated retinal dystrophy: Genetics, Phenotype and Natural History

PURPOSE: To analyze the clinical characteristics, natural history, and genetics of CERKL-associated retinal dystrophy in the largest series to date. DESIGN: Multicenter retrospective cohort study. SUBJECTS: 47 patients (37 families) with likely disease-causing CERKL variants METHODS: Review of clinical notes, ophthalmic images, and molecular diagnosis from two international centres. MAIN OUTCOME MEASURES: Visual function, retinal imaging and characteristics were evaluated and correlated. RESULTS: The mean age at the first visit was 29.6 + 13.9 years and the mean follow-up time was 9.1 + 7.4 years. The most frequent initial symptom was central vision loss (40%) and the most common retinal feature was well-demarcated areas of macular atrophy (57%). Seventy percent of the participants had double-null genotypes and 64% had electrophysiological assessment. Amongst the latter, 53% showed similar severity of rod and cone dysfunction, 27% revealed a rod-cone, 10% a cone-rod, and 10% a macular dystrophy dysfunction pattern. Patients without double-null genotypes tended to have fewer pigment deposits and included a higher proportion of older patients with a relatively mild electrophysiological phenotype. Longitudinal analysis showed that over half of the cohort lost 15 ETDRS letters or more in at least one eye during the first 5 years of follow up. CONCLUSIONS: The phenotype of CERKL-retinal dystrophy is broad, encompassing isolated macular disease to severe retina-wide involvement, with a range of functional phenotypes, generally not fitting in the rod-cone/cone-rod dichotomy. Disease onset is often earlier, with more severe retinal degenerative changes and photoreceptor dysfunction, in nullizygous cases

CRB1-associated Retinal Dystrophies: Genetics, Clinical Characteristics and Natural History

PURPOSE: To analyse the clinical characteristics, natural history, and genetics of CRB1-associated retinal dystrophies. DESIGN: Multicenter international retrospective cohort study. METHODS: Review of clinical notes, ophthalmic images, and genetic testing results of 104 patients (91 probands) with disease-causing CRB1 variants. Macular optical coherence tomography (OCT) parameters, visual function, fundus characteristics, and associations between variables were our main outcome measures. RESULTS: The mean age of the cohort at the first visit was 19.8 ± 16.1 (median 15) years of age, with a mean follow-up of 9.6 ± 10 years. Based on history, imaging, and clinical examination, 26 individuals were diagnosed with retinitis pigmentosa (RP, 26%), 54 with early-onset severe retinal dystrophy/Leber Congenital Amaurosis (EOSRD/LCA, 51%), and 24 with macular dystrophy (MD, 23%). Severe visual impairment was most frequent after 40 years of age for patients with RP and after 20 years of age for EOSRD/LCA. Longitudinal analysis revealed a significant difference between baseline and follow up best corrected visual acuity in the three sub-cohorts. Macular thickness decreased in most patients with EOSRD/LCA and MD, whereas the majority of patients with RP had increased perifoveal thickness. CONCLUSIONS: A subset of individuals with CRB1 variants present with mild, adult-onset RP. EOSRD/LCA phenotype was significantly associated with null variants, and 167_169 deletion was exclusively present in the MD cohort. The poor OCT lamination may have a degenerative component, as well as being congenital. Disease symmetry and reasonable window for intervention highlight CRB1 retinal dystrophies as a promising target for trials of novel therapeutics

Best Vitelliform Macular Dystrophy Natural History Study Report 1: Clinical Features and Genetic Findings

PURPOSE: To analyze the genetic findings, clinical spectrum and natural history of Best vitelliform macular dystrophy (BVMD) in a cohort of 222 children and adults. DESIGN: Single-center retrospective, consecutive, observational study. PARTICIPANTS: Patients with a clinical diagnosis of BVMD, from pedigrees with a likely disease-causing monoallelic sequence variant in the BEST1 gene. METHODS: Data were extracted from electronic and physical case notes. Electrophysiologic assessment and molecular genetic testing were analyzed. MAIN OUTCOME MEASUREMENTS: Molecular genetic testing, clinical findings including best-corrected visual acuity (BCVA), choroidal neovascularization (CNV) rates, and electrophysiology parameters. RESULTS: 222 patients (127 males and 95 females) from 141 families were identified, harboring 69 BEST1 variants, including 22 novel variants. Mean age at presentation was 26.8 years (range 1.3-84.8 years) and most patients (61.5%) presented with a deterioration of central vision. Major funduscopic findings at presentation included: 128 eyes (30.6%) with yellow vitelliform lesions, 78 eyes (18.7%) with atrophic changes, 49 eyes (11.7%) with fibrotic changes, 48 eyes (11.5%) with mild pigmentary changes and 43 eyes (10.3%) showing a vitelliruptive appearance. Mean BCVA was 0.37 LogMAR (20/47) for the right eye and 0.33 LogMAR (20/43) for the left eye at presentation, with a mean annual loss rate of 0.013 LogMAR and 0.009 LogMAR respectively over a mean follow-up of 9.6 years. 37 patients (17.3%) were diagnosed with CNV over a mean follow-up period of 8.0 years (range 0-55 years). Eyes with CNV that received treatment with anti-VEGF had a better mean VA compared to eyes that were not treated with anti-VEGF (0.28 LogMAR (20/38) versus 0.62 LogMAR (20/83). The majority of eyes exhibited a hyperopic refractive error (185/235, 78.7%) and 13 patients (6.1%) were diagnosed with amblyopia. Among the three most common variants, p.A243V was associated with a later age of onset, a better age-adjusted VA and less advanced Gass stages compared to p.R218C and p.R218H. CONCLUSIONS: BVMD shows a wide spectrum of phenotypic variability. The disease is very slowly progressive, and the observed phenotype-genotype correlations allow for more accurate prognostication and counselling

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Background: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions. Results: We report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species. Conclusions:B. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems