Anomalous transport in disordered exclusion processes with coupled particles

We consider one-dimensional asymmetric exclusion processes with a simple attractive interaction, where the distance between consecutive particles is not allowed to exceed a certain limit and investigate the consequences of this coupling on the transport properties in the presence of random-force type disorder by means of a phenomenological random trap picture. In the phase-separated steady state of the model defined on a finite ring, the properties of the density profile are studied and the exponent governing the decay of the current with the system size in the biased phase is derived. In case all consecutive particles are coupled with each other and form a closed string, the current is found to be enhanced compared to the model without coupling, while if groups of consecutive particles form finite strings, the current is reduced. The motion of a semi-infinite string entering an initially empty lattice is also studied. Here, the diffusion of the head of the string is found to be anomalous, and two phases can be distinguished, which are characterised by different functional dependences of the diffusion exponent on the bias. The obtained results are checked by numerical simulation.Comment: 20 pages, 11 figure

Identification of candidate tumour suppressor genes frequently methylated in renal cell carcinoma

Promoter region hyermethylation and transcriptional silencing is a frequent cause of tumour suppressor gene (TSG) inactivation in many types of human cancers. Functional epigenetic studies, in which gene expression is induced by treatment with demethylating agents, may identify novel genes with tumour-specific methylation. We used high-density gene expression microarrays in a functional epigenetic study of 11 renal cell carcinoma (RCC) cell lines. Twenty-eight genes were then selected for analysis of promoter methylation status in cell lines and primary RCC. Eight genes (BNC1, PDLIM4, RPRM, CST6, SFRP1, GREM1, COL14A1 and COL15A1) showed frequent (30% of RCC tested) tumour-specific promoter region methylation. Hypermethylation was associated with transcriptional silencing. Re-expression of BNC1, CST6, RPRM and SFRP1 suppressed the growth of RCC cell lines and RNA interference knock-down of BNC1, SFRP1 and COL14A1 increased the growth of RCC cell lines. Methylation of BNC1 or COL14A1 was associated with a poorer prognosis independent of tumour size, stage or grade. The identification of these epigenetically inactivated candidate RCC TSGs can provide insights into renal tumourigenesis and a basis for developing novel therapies and biomarkers for prognosis and detection. © 2010 Macmillan Publishers Limited.Published versio

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Nanomedicine Approaches for Autophagy Modulation in Cancer Therapy

Cancer is a daunting global health problem with a steadily rising incidence. Despite the wide arsenal of current anticancer therapies, challenges such as drug resistance, tumor heterogeneity, poor targeting, and severe side effects often lead to suboptimal efficacy and poor patient outcomes, highlighting the&nbsp;need for innovative therapies. Autophagy modulation has emerged as an attractive approach to complement existing therapies. The dual role of autophagy in cancer promotion and suppression has inspired the development of new drugs and therapeutic strategies focusing on both inhibition and induction. Despite the promising results of current autophagy modulators in preclinical studies, challenges such as the lack of selectivity and potency, toxicity, poor pharmacokinetics, and inadequate tumor targeting continue to limit their successful clinical translation. Many of these challenges could be overcome using nanomedicine. This review explores recent advancements in nanomedicine strategies for autophagy modulation. Successful combination strategies leveraging nanoparticles and autophagy modulators in synergy with chemotherapy, immunotherapy, phototherapy, gene therapy, and other modalities are presented. Additionally, nanomaterials with intrinsic autophagy-modulating capabilities, such as&nbsp;self-assembling autophagy inhibitors, are discussed. Finally, limitations of&nbsp;autophagy modulators currently in clinical trials are discussed, and future perspectives on designing nanomedicine for successful clinical implementation are explored

Computational solutions for omics data

High-throughput experimental technologies are generating increasingly massive and complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to make the arising problems computationally infeasible. Fortunately, powerful algorithmic techniques lead to software that can answer important biomedical questions in practice. In this Review, we sample the algorithmic landscape, focusing on state-of-the-art techniques, the understanding of which will aid the bench biologist in analysing omics data. We spotlight specific examples that have facilitated and enriched analyses of sequence, transcriptomic and network data sets.National Institutes of Health (U.S.) (Grant GM081871

Strong interlayer interactions in bilayer and trilayer moiré superlattices

Moiré superlattices constructed from transition metal dichalcogenides have demonstrated a series of emergent phenomena, including moiré excitons, flat bands, and correlated insulating states. All of these phenomena depend crucially on the presence of strong moiré potentials, yet the properties of these moiré potentials, and the mechanisms by which they can be generated, remain largely open questions. Here, we use angle-resolved photoemission spectroscopy with submicron spatial resolution to investigate an aligned WS2/WSe2 moiré superlattice and graphene/WS2/WSe2 trilayer heterostructure. Our experiments reveal that the hybridization between moiré bands in WS2/WSe2 exhibits an unusually large momentum dependence, with the splitting between moiré bands at the Γ point more than an order of magnitude larger than that at K point. In addition, we discover that the same WS2/WSe2 superlattice can imprint an unexpectedly large moiré potential on a third, separate layer of graphene (g/WS2/WSe2), suggesting new avenues for engineering two-dimensional moiré superlattices

A note on the Hawking radiation calculated by the quasi-classical tunneling method

Since Parikh and Wilczek's tunneling method was proposed, there have been many generalizations, such as its application to massive charged particles' tunneling and other spacetimes. Moreover, a variant tunneling method was also recently proposed by Angheben et al that it was independent of coordinates. However, there are some subtleties in the calculation of Hawking radiation, and particularly is the so-called factor of 2 problem during calculating the Hawking temperature. The most popular opinion on this problem is that it is just a problem of the choice of coordinates. However, following other treatments we show that we can also consider this problem as a problem that we do not consider the contribution from P(absorption). Moreover, we also give some subtleties in the balance method and some comparisons with other treatments. In addition, as Parikh and Wilczek's original works have showed that if one takes the tunneling particles' back-reaction into account, the Hawking radiation would be modified, and this modification is underlying consistent with the unitary theory, we further find that this modification is also underlying correlated with the laws of black hole thermodynamics. Furthermore, we show that this tunneling method may be valid just when the tunneling process is reversible.Comment: version to appear in MPL

Dynamics of mechanical waves in periodic grapheme nanoribbon assemblies

We simulate the natural frequencies and the acoustic wave propagation characteristics of graphene nanoribbons (GNRs) of the type (8,0) and (0,8) using an equivalent atomistic-continuum FE model previously developed by some of the authors, where the C-C bonds thickness and average equilibrium lengths during the dynamic loading are identified through the minimisation of the system Hamiltonian. A molecular mechanics model based on the UFF potential is used to benchmark the hybrid FE models developed. The acoustic wave dispersion characteristics of the GNRs are simulated using a Floquet-based wave technique used to predict the pass-stop bands of periodic mechanical structures. We show that the thickness and equilibrium lengths do depend on the specific vibration and dispersion mode considered, and that they are in general different from the classical constant values used in open literature (0.34 nm for thickness and 0.142 nm for equilibrium length). We also show the dependence of the wave dispersion characteristics versus the aspect ratio and edge configurations of the nanoribbons, with widening band-gaps that depend on the chirality of the configurations. The thickness, average equilibrium length and edge type have to be taken into account when nanoribbons are used to design nano-oscillators and novel types of mass sensors based on periodic arrangements of nanostructures

Structural basis for the recognition and cleavage of histone H3 by cathepsin L

Proteolysis of eukaryotic histone tails has emerged as an important factor in the modulation of cell-cycle progression and cellular differentiation. The recruitment of lysosomal cathepsin L to the nucleus where it mediates proteolysis of the mouse histone H3 tail has been described recently. Here, we report the three-dimensional crystal structures of a mature, inactive mutant of human cathepsin L alone and in complex with a peptide derived from histone H3. Canonical substrate–cathepsin L interactions are observed in the complex between the protease and the histone H3 peptide. Systematic analysis of the impact of posttranslational modifications at histone H3 on substrate selectivity suggests cathepsin L to be highly accommodating of all modified peptides. This is the first report of cathepsin L–histone H3 interaction and the first structural description of cathepsin L in complex with a substrate