MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog

Negative Magnetoresistance in Dirac Semimetal Cd3As2

A large negative magnetoresistance is anticipated in topological semimetals in the parallel magnetic and electric field configuration as a consequence of the nontrivial topological properties. The negative magnetoresistance is believed to demonstrate the chiral anomaly, a long-sought high-energy physics effect, in solid-state systems. Recent experiments reveal that Cd3As2, a Dirac topological semimetal, has the record-high mobility and exhibits positive linear magnetoresistance in the orthogonal magnetic and electric field configuration. However, the negative magnetoresistance in the parallel magnetic and electric field configuration remains unveiled. Here, we report the observation of the negative magnetoresistance in Cd3As2 microribbons in the parallel magnetic and electric field configuration as large as 66% at 50 K and even visible at room temperatures. The observed negative magnetoresistance is sensitive to the angle between magnetic and electrical field, robust against temperature, and dependent on the carrier density. We have found that carrier densities of our Cd3As2 samples obey an Arrhenius's law, decreasing from 3.0x10^17 cm^-3 at 300 K to 2.2x10^16 cm^-3 below 50 K. The low carrier densities result in the large values of the negative magnetoresistance. We therefore attribute the observed negative magnetoresistance to the chiral anomaly. Furthermore, in the perpendicular magnetic and electric field configuration a positive non-saturating linear magnetoresistance up to 1670% at 14 T and 2 K is also observed. This work demonstrates potential applications of topological semimetals in magnetic devices

Addressing Parental Smoking in Pediatric Settings of Chinese Hospitals: A Qualitative Study of Parents

This study explored factors associated with SHS exposure from parental smoking in Chinese families and assessed nature of antismoking discussions parents had with their children's pediatricians and how pediatricians might best engage with parents in an effort to reduce children's exposure to SHS. Six focus group discussions (FGDs) were conducted among 33 Chinese parents attending six major hospitals in Guangxi province, China. Most participants (32/33) had family members who smoke, and only 21% had strict restriction on smoking at home. Some parents did not know about health consequences of smoking and effects of SHS exposure on children. Situations that made it especially hard to avoid the child's SHS exposure were having an elderly smoker at home and having a visitor who smoked. Only few parents were asked by pediatricians about child's exposure to SHS at home, but only when child's illness was related to smoking. Parents believed that suggestions coming from pediatricians about smoke-free home and parental quitting would be acceptable to parents and other household members. The findings provide insight into SHS exposure reduction effort among Chinese parents and underscore the demand for pediatrician's engagement in addressing parental tobacco use

Secondhand smoke exposure assessment and counseling in the Chinese pediatric setting: a qualitative study

Background: Assisting smoking parents to quit smoking and eliminating the secondhand smoke (SHS) exposure of their children is a global health priority. Engaging healthcare workers in developing countries to address this priority has been a challenge. This study intends to explore issues around current practice related to SHS exposure assessment and counseling and identify barriers to SHS exposure reduction counseling in the Chinese pediatric setting. Methods: We conducted qualitative interviews (11 focus groups discussions (FGDs) with pediatricians, 6 FGDs with pediatric nurses and 11 in-depth interviews (IDIs) with hospital administrators) among 101 health-care professionals (HCP) from 5 hospitals in four major cities of Guangxi Province, China. All FGDs/ IDIs were audio recorded and analysed thematically. Results: The findings suggest that few Chinese pediatricians routinely address the SHS exposure of children in their usual practice. All HCPs felt the need for clinical interventions to promote SHS exposure reduction for children. Primary barriers to SHS exposure reduction counseling in the Chinese pediatric setting included: lack of skills and training in tobacco use reduction and cessation counseling; time constraints and heavy workloads, uncertainty about the usefulness of smoking cessation interventions and lack of hospital-wide systems requiring pediatricians to record tobacco use or SHS exposure information. Ideas for overcoming these barriers were building capacity of pediatricians, collaboration with international organization to initiate training, engaging top level leaders in the effort and ensuring financial resources to support the program. Conclusions: This study among hospital administrators and service providers in China demonstrated a high level of interest in delivering SHS exposure reduction interventions in the pediatric setting. The findings can inform the creation and delivery of clinical interventions in China to promote SHS exposure reduction to children in the pediatric setting. Electronic supplementary material The online version of this article (doi:10.1186/1471-2431-14-266) contains supplementary material, which is available to authorized users

Global attractors for non-linear viscoelastic equation with strong damping

In this paper, we consider the long-time dynamical behavior of the viscoelastic equations with strong damping and further prove the existence of global attractors for this system