Unified framework for hybrid percolation transitions based on microscopic dynamics

A hybrid percolation transition (HPT) exhibits both discontinuity of the order parameter and critical behavior at the transition point. Such dynamic transitions can occur in two ways: by cluster pruning with suppression of loop formation of cut links or by cluster merging with suppression of the creation of large clusters. While the microscopic mechanism of the former is understood in detail, a similar framework is missing for the latter. By studying two distinct cluster merging models, we uncover the universal mechanism of the features of HPT-s at a microscopic level. We find that these features occur in three steps: (i) medium-sized clusters accumulate due to the suppression rule hindering the growth of large clusters, (ii) those medium size clusters eventually merge and a giant cluster increases rapidly, and (iii) the suppression effect becomes obsolete and the kinetics is governed by the Erd\H{o}s-R\'enyi type of dynamics. We show that during the second and third period, the growth of the largest component must proceed in the form of a Devil's staircase. We characterize the critical behavior by two sets of exponents associated with the order parameter and cluster size distribution, which are related to each other by a scaling relation. Extensive numerical simulations are carried out to support the theory where a specific method is applied for finite-size scaling analysis to enable handling the large fluctuations of the transition point. Our results provide a unified theoretical framework for the HPT.Comment: 15 pages, 14 figures, 4 table

Imaging Cerenkov emission as a quality assurance tool in electron radiotherapy

A new potential quality assurance (QA) method is explored (including assessment of depth dose, dose linearity, dose rate linearity and beam profile) for clinical electron beams based on imaging Cerenkov light. The potential of using a standard commercial camera to image Cerenkov light generated from electrons in water for fast QA measurement of a clinical electron beam was explored and compared to ionization chamber measurements. The new method was found to be linear with dose and independent of dose rate (to within 3%). The uncorrected practical range measured in Cerenkov images was found to overestimate the actual value by 3 mm in the worst case. The field size measurements underestimated the dose at the edges by 5% without applying any correction factor. Still, the measured field size could be used to monitor relative changes in the beam profile. Finally, the beam-direction profile measurements were independent of the field size within 2%. A simulation was also performed of the deposited energy and of Cerenkov production in water using GEANT4. Monte Carlo simulation was used to predict the measured light distribution around the water phantom, to reproduce Cerenkov images and to find the relation between deposited energy and Cerenkov production. The camera was modelled as a pinhole camera in GEANT4, to attempt to reproduce Cerenkov images. Simulations of the deposited energy and the Cerenkov light production agreed with each other for a pencil beam of electrons, while for a realistic field size, Cerenkov production in the build-up region overestimated the dose by +8%

Sentra: a database of signal transduction proteins for comparative genome analysis

Sentra (), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to reflect recent advances in understanding signal transduction events on a whole-genome scale. Sentra consists of two principal components, a manually curated list of signal transduction proteins in 202 completely sequenced prokaryotic genomes and an automatically generated listing of predicted signaling proteins in 235 sequenced genomes that are awaiting manual curation. In addition to two-component histidine kinases and response regulators, the database now lists manually curated Ser/Thr/Tyr protein kinases and protein phosphatases, as well as adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases, as defined in several recent reviews. All entries in Sentra are extensively annotated with relevant information from public databases (e.g. UniProt, KEGG, PDB and NCBI). Sentra's infrastructure was redesigned to support interactive cross-genome comparisons of signal transduction capabilities of prokaryotic organisms from a taxonomic and phenotypic perspective and in the framework of signal transduction pathways from KEGG. Sentra leverages the PUMA2 system to support interactive analysis and annotation of signal transduction proteins by the users

A multi-level developmental approach to exploring individual differences in Down syndrome: genes, brain, behaviour, and environment.

In this article, we focus on the causes of individual differences in Down syndrome (DS), exemplifying the multi-level, multi-method, lifespan developmental approach advocated by Karmiloff-Smith (1998, 2009, 2012, 2016). We evaluate the possibility of linking variations in infant and child development with variations in the (elevated) risk for Alzheimer's disease (AD) in adults with DS. We review the theoretical basis for this argument, considering genetics, epigenetics, brain, behaviour and environment. In studies 1 and 2, we focus on variation in language development. We utilise data from the MacArthur-Bates Communicative Development Inventories (CDI; Fenson et al., 2007), and Mullen Scales of Early Learning (MSEL) receptive and productive language subscales (Mullen, 1995) from 84 infants and children with DS (mean age 2;3, range 0;7 to 5;3). As expected, there was developmental delay in both receptive and expressive vocabulary and wide individual differences. Study 1 examined the influence of an environmental measure (socio-economic status as measured by parental occupation) on the observed variability. SES did not predict a reliable amount of the variation. Study 2 examined the predictive power of a specific genetic measure (apolipoprotein APOE genotype) which modulates risk for AD in adulthood. There was no reliable effect of APOE genotype, though weak evidence that development was faster for the genotype conferring greater AD risk (ε4 carriers), consistent with recent observations in infant attention (D'Souza, Mason et al., 2020). Study 3 considered the concerted effect of the DS genotype on early brain development. We describe new magnetic resonance imaging methods for measuring prenatal and neonatal brain structure in DS (e.g., volumes of supratentorial brain, cortex, cerebellar volume; Patkee et al., 2019). We establish the methodological viability of linking differences in early brain structure to measures of infant cognitive development, measured by the MSEL, as a potential early marker of clinical relevance. Five case studies are presented as proof of concept, but these are as yet too few to discern a pattern

Adaptive modulation in Ni2Mn1.4In0.6 magnetic shape memory Heusler alloy

The origin of incommensurate structural modulation in Ni-Mn based Heusler type magnetic shape memory alloys (MSMAs) is still an unresolved issue inspite of intense focus on this due to its role in the magnetic field induced ultra-high strains. In the archetypal MSMA Ni2MnGa, the observation of non-uniform displacement of atoms from their mean positions in the modulated martensite phase, premartensite phase and charge density wave as well as the presence of phason broadening of satellite peaks have been taken in support of the electronic instability model linked with a soft acoustic phonon. We present here results of a combined high resolution synchrotron x-ray powder diffraction (SXRPD) and neutron powder diffraction (NPD) study on Ni2Mn1.4In0.6 using (3+1)D superspace group approach, which reveal not only uniform atomic displacements in the modulated structure of the martensite phase with physically acceptable ordered magnetic moments in the antiferromagnetic phase at low temperatures but also the absence of any premartensite phase and phason broadening of the satellite peaks. Our HRTEM studies and first principles calculations of the ground state also support uniform atomic displacements predicted by powder diffraction studies. All these observations suggest that the structural modulation in the martensite phase of Ni2Mn1.4In0.6 MSMA can be explained in terms of the adaptive phase model. The present study underlines the importance of superspace group analysis using complimentary SXRPD and NPD in understanding the physics of the origin of modulation as well as the magnetic and the modulated ground states of the Heusler type MSMAs. Our work also highlights the fact that the mechanism responsible for the origin of modulated structure in different Ni-Mn based MSMAs may not be universal and it must be investigated thoroughly in different alloy compositions

Ultrafaint Dwarf Galaxy Candidates in the M81 Group: Signatures of Group Accretion

The faint and ultrafaint dwarf galaxies in the Local Group form the observational bedrock upon which our understanding of small-scale cosmology rests. In order to understand whether this insight generalizes, it is imperative to use resolved-star techniques to discover similarly faint satellites in nearby galaxy groups. We describe our search for ultrafaint galaxies in the M81 group using deep ground-based resolved-star data sets from Subaru's Hyper Suprime-Cam. We present one new ultrafaint dwarf galaxy in the M81 group and identify five additional extremely low surface brightness candidate ultrafaint dwarfs that reach deep into the ultrafaint regime to $M_V \sim -6$ (similar to current limits for Andromeda satellites). These candidates' luminosities and sizes are similar to known Local Group dwarf galaxies Tucana B, Canes Venatici I, Hercules, and Bo\"otes I. Most of these candidates are likely to be real, based on tests of our techniques on blank fields. Intriguingly, all of these candidates are spatially clustered around NGC 3077, which is itself an M81 group satellite in an advanced state of tidal disruption. This is somewhat surprising, as M81 itself and its largest satellite M82 are both substantially more massive than NGC 3077 and by virtue of their greater masses, would have been expected to host as many or more ultrafaint candidates. These results lend considerable support to the idea that satellites of satellites are an important contribution to the growth of satellite populations around Milky Way-mass galaxies.Comment: The Astrophysical Journal Letters; in press. 11 pages, 4 figures, 1 tabl

Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes

Non-healing chronic ulcers are a serious complication of diabetes and are a major healthcare problem. While a host of treatments have been explored to heal or prevent these ulcers from forming, these treatments have not been found to be consistently effective in clinical trials. An understanding of the changes in gene expression in the skin of diabetic patients may provide insight into the processes and mechanisms that precede the formation of non-healing ulcers. In this study, we investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic). This information may be useful in identifying the causal factors and potential therapeutic targets for the prevention and treatment of diabetic related diseases

Vitamin D to prevent lung injury following esophagectomy: A randomized, placebo-controlled trial

Objectives: Observational studies suggest an association between vitamin D deficiency and adverse outcomes of critical illness and identify it as a potential risk factor for the development of lung injury. To determine whether pre-operative administration of oral high-dose cholecalciferol ameliorates early acute lung injury post-operatively in adults undergoing elective esophagectomy. Design: A double-blind, randomized, placebo-controlled trial. Setting: Three large UK university hospitals. Patients: Seventy-nine adult patients undergoing elective esophagectomy were randomized. Intervention: A single oral preoperative (3-14 days) dose of 7.5mg (300,000IU; 15mls) cholecalciferol or matched placebo. Measurements and Main Results: Primary outcome was change in extravascular lung water index (EVLWI) at the end of esophagectomy. Secondary outcomes included PaO2:FiO2 ratio, development of lung injury, ventilator and organ-failure free days, 28 and 90 day survival, safety of cholecalciferol supplementation, plasma vitamin D status (25(OH)D, 1,25(OH)2D and vitamin D binding protein), pulmonary vascular permeability index (PVPI) and EVLWI day 1 postoperatively. An exploratory study measured biomarkers of alveolar-capillary inflammation and injury. Forty patients were randomized to cholecalciferol and 39 to placebo. There was no significant change in EVLWI at the end of the operation between treatment groups (placebo median 1.0[IQR 0.4 – 1.8] vs cholecalciferol median 0.4[IQR 0.4 – 1.2] ml/kg, p=0.059). Median PVPI values were significantly lower in the cholecalciferol treatment group (placebo 0.4[IQR 0 – 0.7] vs cholecalciferol 0.1[IQR -0.15 -0.35], p=0.027). Cholecalciferol treatment effectively increased 25(OH)D concentrations but surgery resulted in a decrease in 25(OH)D concentrations at day 3 in both arms. There was no difference in clinical outcomes. Conclusions: High-dose preoperative treatment with oral cholecalciferol was effective at increasing 25(OH)D concentrations, and reduced changes in postoperative PVPI but not EVLWI

Small-molecule Wnt agonists correct cleft palates in Pax9 mutant mice in utero.

Clefts of the palate and/or lip are among the most common human craniofacial malformations and involve multiple genetic and environmental factors. Defects can only be corrected surgically and require complex life-long treatments. Our studies utilized the well-characterized Pax9(-/-) mouse model with a consistent cleft palate phenotype to test small-molecule Wnt agonist therapies. We show that the absence of Pax9 alters the expression of Wnt pathway genes including Dkk1 and Dkk2, proven antagonists of Wnt signaling. The functional interactions between Pax9 and Dkk1 are shown by the genetic rescue of secondary palate clefts in Pax9(-/-)Dkk1(f/+);Wnt1Cre embryos. The controlled intravenous delivery of small-molecule Wnt agonists (Dkk inhibitors) into pregnant Pax9(+/-) mice restored Wnt signaling and led to the growth and fusion of palatal shelves, as marked by an increase in cell proliferation and osteogenesis in utero, while other organ defects were not corrected. This work underscores the importance of Pax9-dependent Wnt signaling in palatogenesis and suggests that this functional upstream molecular relationship can be exploited for the development of therapies for human cleft palates that arise from single-gene disorders