Domainoid: domain-oriented orthology inference

BACKGROUND: Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains. RESULTS: This domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories. In addition to domain level analysis, protein level orthology based on the fraction of domains that are orthologous can be inferred. Domainoid orthology assignments were compared to those yielded by the conventional full-length approach InParanoid, and were validated in a standard benchmark. CONCLUSIONS: Our results show that domain-based orthology inference can reveal many orthologous relationships that are not found by full-length sequence approaches. AVAILABILITY: https://bitbucket.org/sonnhammergroup/domainoid/

Cross-cultural adaptation and validation of the “spinal cord injury-falls concern scale” in the Italian population

Study design: Psychometrics study. Objective: The objective of this study was to develop an Italian version of the Spinal Cord Injury-Falls Concern Scale (SCI-FCS) and examine its reliability and validity. Setting: Multicenter study in spinal units in Northern and Southern Italy. The scale also was administered to non-hospitalized outpatient clinic patients. Methods: The original scale was translated from English to Italian using the “Translation and Cultural Adaptation of Patient-Reported Outcomes Measures” guidelines. The reliability and validity of the culturally adapted scale were assessed following the “Consensus-Based Standards for the Selection of Health Status Measurement Instruments” checklist. The SCI-FCS-I internal consistency, inter-rater, and intra-rater reliability were examined using Cronbach’s alpha coefficient and the intraclass correlation coefficient, respectively. Concurrent validity was evaluated using Pearson’s correlation coefficient with the Italian version of the short form of the Wheelchair Use Confidence Scale for Manual Wheelchair Users (WheelCon-M-I-short form). Results: The Italian version of the SCI-FCS-I was administered to 124 participants from 1 June to 30 September 2017. The mean ± SD of the SCI-FCS-I score was 16.73 ± 5.88. All SCI-FCS items were either identical or similar in meaning to the original version’s items. Cronbach’s α was 0.827 (p < 0.01), the inter-rater reliability was 0.972 (p < 0.01), and the intra-rater reliability was 0.973 (p < 0.01). Pearson’s correlation coefficient of the SCI-FCS-I scores with the WheelCon-M-I-short form was 0.56 (p < 0.01). Conclusions: The SCI-FCS-I was found to be reliable and a valid outcome measure for assessing manual wheelchair concerns about falling in the Italian population

Negative muon spin rotation and relaxation on superconducting MgB2

The internal nuclear magnetic field in a superconducting MgB2 powder sample was studied with a μ- SR technique. Although the past μ +SR study on MgB2 reported the appearance of a dynamic behavior even below Tc due to μ + diffusion, μ- SR shows a static behavior in the whole temperature range measured, as expected. The ZF-μ- SR spectra do not suggest any appearance of additional magnetic field below Tc within the experimental accuracy. Considering the small asymmetry of the μ- SR signal, it is a challenge to detect the appearance of an internal magnetic field below Tc caused by the time reversal symmetry breaking

Confirming the high pressure phase diagram of the Shastry-Sutherland model

A Muon Spin Rotation (μ + SR) study was conducted to investigate the magnetic properties of SrCu2(BO3)2 (SCBO) as a function of temperature/pressure. Measurements in zero field and transverse field confirm the absence of long range magnetic order at high pressures and low temperatures. These measurements suggest changes in the Cu spin fluctuations characteristics above 21 kbar, consistent with the formation of a plaquette phase as previously suggested by inelastic neutron scattering measurements. SCBO is the only known realisation of the Shatry-Sutherland model, thus the ground state mediating the dimer and antiferromagnetic phase is likekly to be a plaquette state

Computational 3-D inversion for seismic exploration

This is the final report of a four-month, Laboratory Directed Research and Development (LDRD) project carried out at the Los Alamos National Laboratory (LANL). There is a great need for a new and effective technology with a wide scope of industrial applications to investigate media internal properties of which can be explored only from the backscattered data. The project was dedicated to the development of a three-dimensional computational inversion tool for seismic exploration. The new computational concept of the inversion algorithm was suggested. The goal of the project was to prove the concept and the practical validity of the algorithm for petroleum exploration

Three-Dimensional Fermi Surface of Overdoped La-Based Cuprates

We present a soft x-ray angle-resolved photoemission spectroscopy study of the overdoped high-temperature superconductors La$_{2-x}$Sr$_x$CuO$_4$ and La$_{1.8-x}$Eu$_{0.2}$Sr$_x$CuO$_4$. In-plane and out-of-plane components of the Fermi surface are mapped by varying the photoemission angle and the incident photon energy. No $k_z$ dispersion is observed along the nodal direction, whereas a significant antinodal $k_z$ dispersion is identified. Based on a tight-binding parametrization, we discuss the implications for the density of states near the van-Hove singularity. Our results suggest that the large electronic specific heat found in overdoped La$_{2-x}$Sr$_x$CuO$_4$ can not be assigned to the van-Hove singularity alone. We therefore propose quantum criticality induced by a collapsing pseudogap phase as a plausible explanation for observed enhancement of electronic specific heat

Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance

Conjugative transposition drives the emergence of multidrug resistance in diverse bacterial pathogens, yet the mechanisms are poorly characterized. The Tn1549 conjugative transposon propagates resistance to the antibiotic vancomycin used for severe drug-resistant infections. Here, we present four high-resolution structures of the conserved Y-transposase of Tn1549 complexed with circular transposon DNA intermediates. The structures reveal individual transposition steps and explain how specific DNA distortion and cleavage mechanisms enable DNA strand exchange with an absolute minimum homology requirement. This appears to uniquely allow Tn916-like conjugative transposons to bypass DNA homology and insert into diverse genomic sites, expanding gene transfer. We further uncover a structural regulatory mechanism that prevents premature cleavage of the transposon DNA before a suitable target DNA is found and generate a peptide antagonist that interferes with the transposase-DNA structure to block transposition. Our results reveal mechanistic principles of conjugative transposition that could help control the spread of antibiotic resistance genes

Modeling emergency department visit patterns for infectious disease complaints: results and application to disease surveillance

BACKGROUND: Concern over bio-terrorism has led to recognition that traditional public health surveillance for specific conditions is unlikely to provide timely indication of some disease outbreaks, either naturally occurring or induced by a bioweapon. In non-traditional surveillance, the use of health care resources are monitored in "near real" time for the first signs of an outbreak, such as increases in emergency department (ED) visits for respiratory, gastrointestinal or neurological chief complaints (CC). METHODS: We collected ED CCs from 2/1/94 – 5/31/02 as a training set. A first-order model was developed for each of seven CC categories by accounting for long-term, day-of-week, and seasonal effects. We assessed predictive performance on subsequent data from 6/1/02 – 5/31/03, compared CC counts to predictions and confidence limits, and identified anomalies (simulated and real). RESULTS: Each CC category exhibited significant day-of-week differences. For most categories, counts peaked on Monday. There were seasonal cycles in both respiratory and undifferentiated infection complaints and the season-to-season variability in peak date was summarized using a hierarchical model. For example, the average peak date for respiratory complaints was January 22, with a season-to-season standard deviation of 12 days. This season-to-season variation makes it challenging to predict respiratory CCs so we focused our effort and discussion on prediction performance for this difficult category. Total ED visits increased over the study period by 4%, but respiratory complaints decreased by roughly 20%, illustrating that long-term averages in the data set need not reflect future behavior in data subsets. CONCLUSION: We found that ED CCs provided timely indicators for outbreaks. Our approach led to successful identification of a respiratory outbreak one-to-two weeks in advance of reports from the state-wide sentinel flu surveillance and of a reported increase in positive laboratory test results