Emergent order in the kagome Ising magnet Dy3_3Mg2_2Sb3_3O14_{14}

The Ising model-in which degrees of freedom (spins) are binary valued (up/down)-is a cornerstone of statistical physics that shows rich behaviour when spins occupy a highly frustrated lattice such as kagome. Here we show that the layered Ising magnet Dy$_3$Mg$_2$Sb$_3$O$_{14}$ hosts an emergent order predicted theoretically for individual kagome layers of in-plane Ising spins. Neutron-scattering and bulk thermomagnetic measurements reveal a phase transition at ~0.3 K from a disordered spin-ice-like regime to an emergent charge ordered state, in which emergent magnetic charge degrees of freedom exhibit three-dimensional order while spins remain partially disordered. Monte Carlo simulations show that an interplay of inter-layer interactions, spin canting and chemical disorder stabilizes this state. Our results establish Dy$_3$Mg$_2$Sb$_3$O$_{14}$ as a tuneable system to study interacting emergent charges arising from kagome Ising frustration.Work at Cambridge was supported through the Winton Programme for the Physics of Sustainability. The work of J.A.M.P., X.B. and M.M. and facilities at Georgia Tech were supported by the College of Sciences through M.M. start-up funds. J.A.M.P. gratefully acknowledges Churchill College, Cambridge for the provision of a Junior Research Fellowship. H.S.O. acknowledges a Teaching Scholarship (Overseas) from the Ministry of Education, Singapore. J.O.H. is grateful to the Engineering and Physical Sciences Research Council (EPSRC) for funding. C.C. was supported by EPSRC Grant No. EP/G049394/1, and the EPSRC NetworkPlus on ‘Emergence and Physics far from Equilibrium’. Experiments at the ISIS Pulsed Neutron and Muon Source were supported by a beamtime allocation from the Science and Technology Facilities Council. This work utilized facilities at the NIST Center for Neutron Research. Monte Carlo simulations were performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/) and the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk/, for which access was provided by an ARCHER Instant Access scheme)

Experimental Animal Models in Periodontology: A Review

In periodontal research, animal studies are complementary to in vitro experiments prior to testing new treatments. Animal models should make possible the validation of hypotheses and prove the safety and efficacy of new regenerating approaches using biomaterials, growth factors or stem cells. A review of the literature was carried out by using electronic databases (PubMed, ISI Web of Science). Numerous animal models in different species such as rats, hamsters, rabbits, ferrets, canines and primates have been used for modeling human periodontal diseases and treatments. However, both the anatomy and physiopathology of animals are different from those of humans, making difficult the evaluation of new therapies. Experimental models have been developed in order to reproduce major periodontal diseases (gingivitis, periodontitis), their pathogenesis and to investigate new surgical techniques. The aim of this review is to define the most pertinent animal models for periodontal research depending on the hypothesis and expected results

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the ‘rare biosphere’. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature

Non-surgical instrumentation associated with povidone-iodine in the treatment of interproximal furcation involvements

OBJECTIVE: The aim of this controlled clinical trial was to evaluate the effect of topically applied povidone-iodine (PVP-I) used as an adjunct to non-surgical treatment of interproximal class II furcation involvements. MATERIAL AND METHODS: Thirty-two patients presenting at least one interproximal class II furcation involvement that bled on probing with probing pocket depth (PPD) ≥5 mm were recruited. Patients were randomly chosen to receive either subgingival instrumentation with an ultrasonic device using PVP-I (10%) as the cooling liquid (test group) or identical treatment using distilled water as the cooling liquid (control group). The following clinical outcomes were evaluated: visible plaque index, bleeding on probing (BOP), position of the gingival margin, relative attachment level (RAL), PPD and relative horizontal attachment level (RHAL). BAPNA (N-benzoyl-Larginine-p-nitroanilide) testing was used to analyze trypsin-like activity in dental biofilm. All parameters were evaluated at baseline and 1, 3 and 6 months after non-surgical subgingival instrumentation. RESULTS: Six months after treatment, both groups had similar means of PPD reduction, RAL and RHAL gain (p>0.05). These variables were, respectively, 2.20±1.10 mm, 1.27±1.02 mm and 1.33±0.85 mm in the control group and 2.67±1.21 mm, 1.50±1.09 mm and 1.56±0.93 mm in the test group. No difference was observed between groups at none of the posttreatment periods, regarding the number of sites showing clinical attachment gain ≥2 mm. However, at 6 months posttreatment, the test group presented fewer sites with PPD ≥5 mm than the control group. Also at 6 months the test group had lower BAPNA values than control group. CONCLUSION: The use of PVP-I as an adjunct in the non-surgical treatment of interproximal class II furcation involvements provided limited additional clinical benefits

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

Emergent Order in the Frustrated Kagome Magnet Dy3Mg2Sb3O14

Frustrated magnetic materials - in which the lattice occupied by spins prevents all their interactions from being satisfiedsimultaneously - can host exotic states of matter that are both disordered and strongly correlated, such as spin ices andquantum spin liquids. The magnetic diffuse scattering measured in neutron-scattering experiments is highly sensitive tosuch states, but data analysis is often challenging, especially when only powder samples are available. In my talk, I willdiscuss the information content of powder neutron-scattering data for frustrated magnets. In particular, I will address howsuch data can be converted into a magnetic-structure model without advance knowledge of the underlying magneticinteractions, using the atomistic method of reverse Monte Carlo refinemen