MScanner: a classifier for retrieving Medline citations

BACKGROUND: Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains. RESULTS: MScanner is an implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by decreasing probability of relevance. For maximum speed it uses the Medical Subject Headings (MeSH) and journal of publication as a concise document representation, and takes roughly 90 seconds to return results against the 16 million records in Medline. The web interface provides interactive exploration of the results, and cross validated performance evaluation on the relevant input against a random subset of Medline. We describe the classifier implementation, cross validate it on three domain-specific topics, and compare its performance to that of an expert PubMed query for a complex topic. In cross validation on the three sample topics against 100,000 random articles, the classifier achieved excellent separation of relevant and irrelevant article score distributions, ROC areas between 0.97 and 0.99, and averaged precision between 0.69 and 0.92. CONCLUSION: MScanner is an effective non-domain-specific classifier that operates on the entire Medline database, and is suited to retrieving topics for which many features may indicate relevance. Its web interface simplifies the task of classifying Medline citations, compared to building a pre-filter and classifier specific to the topic. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material, and the web interface may be accessed at http://mscanner.stanford.edu

the relationship between alcohol consumption and vascular complications and mortality in individuals with type 2 diabetes

OBJECTIVE Moderate alcohol consumption has been associated with a reduced risk of mortality and coronary artery disease. The relationship between cardiovascular health and alcohol use in type 2 diabetes is less clear. The current study assesses the effects of alcohol use among participants in the Action in Diabetes and Vascular Disease: Preterax and Diamicron Modified-Release Controlled Evaluation (ADVANCE) trial. RESEARCH DESIGN AND METHODS The effects of alcohol use were explored using Cox regression models, adjusted for potential confounders. The study end points were cardiovascular events (cardiovascular death, myocardial infarction, and stroke), microvascular complications (new or worsening nephropathy or retinopathy), and all-cause mortality. RESULTS During a median of 5 years of follow-up, 1,031 (9%) patients died, 1,147 (10%) experienced a cardiovascular event, and 1,136 (10%) experienced a microvascular complication. Compared with patients who reported no alcohol consumption, those who reported moderate consumption had fewer cardiovascular events (adjusted hazard ratio [aHR] 0.83; 95% CI 0.72–0.95; P = 0.008), less microvascular complications (aHR 0.85; 95% CI 0.73–0.99; P = 0.03), and lower all-cause mortality (aHR 0.87; 96% CI 0.75–1.00; P = 0.05). The benefits were particularly evident in participants who drank predominantly wine (cardiovascular events aHR 0.78, 95% CI 0.63–0.95, P = 0.01; all-cause mortality aHR 0.77, 95% CI 0.62–0.95, P = 0.02). Compared with patients who reported no alcohol consumption, those who reported heavy consumption had dose-dependent higher risks of cardiovascular events and all-cause mortality. CONCLUSION In patients with type 2 diabetes, moderate alcohol use, particularly wine consumption, is associated with reduced risks of cardiovascular events and all-cause mortality

A comparison of variate pre-selection methods for use in partial least squares regression: a case study on NIR spectroscopy applied to monitoring beer fermentation

This work investigates four methods of selecting variates from near-infrared (NIR) spectra for use in partial least squares (PLS) regression models to predict biomass and chemical changes during beer fermentation. The fermentation parameters studied were ethanol concentration, specific gravity (SG), optical density (OD) and dry cell weight (DCW). The four selection methods investigated were: Simple, where a fingerprint region is chosen manually; CovProc, a covariance procedure where variates are introduced based on the magnitude of the 1st PLS vector coefficients; CovProc-SavGo, a modification to CovProc where the window size of a Savitzky-Golay filter applied to the spectra is also optimised; and Genetic Algorithm (GA), where variates are selected based on the frequency of appearance in 8-variate multiple linear regression models found from repeated execution of the GA routine. The analysis found that all four methods produced good predictive models. The GA approach produced the lowest standard error in prediction (SEP) based on leave-one-out cross validation (LOO-CV), although this advantage was not reflected in the standard error in validation values, SEV, where all four models performed comparably. From this work, we would recommend using the Simple approach if a suitable fingerprint region can be identified, and using CovProc otherwise

Regulation of Stress-Inducible Phosphoprotein 1 Nuclear Retention by Protein Inhibitor of Activated STAT PIAS1

Stress-inducible phosphoprotein 1 (STI1), a cochaperone for Hsp90, has been shown to regulate multiple pathways in astrocytes, but its contributions to cellular stress responses are not fully understood. We show that in response to irradiation-mediated DNA damage stress STI1 accumulates in the nucleus of astrocytes. Also, STI1 haploinsufficiency decreases astrocyte survival after irradiation. Using yeast two-hybrid screenings we identified several nuclear proteins as STI1 interactors. Overexpression of one of these interactors, PIAS1, seems to be specifically involved in STI1 nuclear retention and in directing STI1 and Hsp90 to specific sub-nuclear regions. PIAS1 and STI1 co-immunoprecipitate and PIAS1 can function as an E3 SUMO ligase for STI. Using mass spectrometry we identified five SUMOylation sites in STI1. A STI1 mutant lacking these five sites is not SUMOylated, but still accumulates in the nucleus in response to increased expression of PIAS1, suggesting the possibility that a direct interaction with PIAS1 could be responsible for STI1 nuclear retention. To test this possibility, we mapped the interaction sites between PIAS1 and STI1 using yeast-two hybrid assays and surface plasmon resonance and found that a large domain in the N-terminal region of STI1 interacts with high affinity with amino acids 450-480 of PIAS1. Knockdown of PIAS1 in astrocytes impairs the accumulation of nuclear STI1 in response to irradiation. Moreover, a PIAS1 mutant lacking the STI1 binding site is unable to increase STI1 nuclear retention. Interestingly, in human glioblastoma multiforme PIAS1 expression is increased and we found a significant correlation between increased PIAS1 expression and STI1 nuclear localization. These experiments provide evidence that direct interaction between STI1 and PIAS1 is involved in the accumulation of nuclear STI1. This retention mechanism could facilitate nuclear chaperone activity. Molecular & Cellular Proteomics 12: 10.1074/mcp.M113.031005, 3253-3270, 2013

Infestation of shore crab gills by a free-living mussel species

Parasitic and commensal species can impact the structure and function of ecological communities and are typically highly specialized to overcome host defences. Here, we report multiple instances of a normally free-living species, the blue mussel Mytilus edulis Linnaeus, 1758, inhabiting the branchial chamber of the shore crab Carcinus maenas (Linnaeus, 1758) collected from widely separated geographical locations. A total of 127 C. maenas were examined from four locations in the English Channel, one location in the Irish Sea and two locations at the entrance of the Baltic Sea. The branchial chambers of three crabs (one from the English Channel and two from Gullmar Fjord, Sweden) were infested with mussels resembling the genus Mytilus. Sequencing at the Me15/16 locus on the polyphenolic adhesive protein gene confirmed the identity as M. edulis. Bivalve infestation always occurred in larger red male individuals. Up to 16 mussels, ranging from 2 to 11 mm in shell length, were found in each individual, either wedged between gill lamellae or attached to the branchial chamber inner wall. This is one of the first reports of a bivalve inhabiting crustacean gills and is an intriguing case of a normally free-living prey species infesting its predato

The seeds of commerce: a network analysis-based approach to the Romano-British transport system

Communication routes are an important subject in the study of the human past. They allowed interactions between communities and the dispersal of goods and ideas. Their study, therefore, can shed light on the way in which communities inhabited the landscape, related to each other and were affected by macro-regional trends. Many methods, such as archaeomorphological analysis and Least Cost Route modelling (LCR), have been devised and are routinely employed for the reconstruction of ancient routes. Their analysis in terms of communication, trade or historical significance, however, has usually been left unexplored. This is probably due to the connected nature of routes, which form communication networks: these are shaped by interconnected nodes and extend over territories surpassing the regional scale in such a way that even a change in a single node or link can affect the whole network. Consequently, the partial reconstruction of communication networks provided by the aforementioned methods does not usually allow a holistic analysis. In this paper the relatively well understood British Roman road network is employed to explore the analytical possibilities offered by a combination of Social Network Analysis, Spatial Network Analysis and spatial interpolation-based distribution analysis. The British road network has been reconstructed using published data but also a variation of LCR in which cost surfaces are derived from cultural data obtained from large-scale cultural inventories. The distribution of introduced food plants during the Roman period serve as an excellent proxy for the study of trade along the network and its historical consequences. This multi-period archaeobotanical dataset has some evident advantages to other types of material remains: archaeobotanical remains are not reused as, for example, amphorae and, accordingly, they reflect a distribution pattern based on consumption or commerce. Some of them are imported (as they cannot be produced locally) and, consequently, their distribution would be applied through usage of the main routes. The results suggest a continuous inflow of exotics but highlight their changing transport routes, their differential access and the particular weight of certain nodal sites in the development of this commerce with direct impact on urbanisation and the overall economy of Britannia. The Roman road network acted as a major factor in the distribution of sites, their political and economic importance and their permanence or disappearance as global economic trends changed over time

Mutations in REEP6 Cause Autosomal-Recessive Retinitis Pigmentosa

Retinitis pigmentosa (RP) is the most frequent form of inherited retinal dystrophy. RP is genetically heterogeneous and the genes identified to date encode proteins involved in a wide range of functional pathways, including photoreceptor development, phototransduction, the retinoid cycle, cilia, and outer segment development. Here we report the identification of biallelic mutations in Receptor Expression Enhancer Protein 6 (REEP6) in seven individuals with autosomal-recessive RP from five unrelated families. REEP6 is a member of the REEP/Yop1 family of proteins that influence the structure of the endoplasmic reticulum but is relatively unstudied. The six variants identified include three frameshift variants, two missense variants, and a genomic rearrangement that disrupts exon 1. Human 3D organoid optic cups were used to investigate REEP6 expression and confirmed the expression of a retina-specific isoform REEP6.1, which is specifically affected by one of the frameshift mutations. Expression of the two missense variants (c.383C>T [p.Pro128Leu] and c.404T>C [p.Leu135Pro]) and the REEP6.1 frameshift mutant in cultured cells suggest that these changes destabilize the protein. Furthermore, CRISPR-Cas9-mediated gene editing was used to produce Reep6 knock-in mice with the p.Leu135Pro RP-associated variant identified in one RP-affected individual. The homozygous knock-in mice mimic the clinical phenotypes of RP, including progressive photoreceptor degeneration and dysfunction of the rod photoreceptors. Therefore, our study implicates REEP6 in retinal homeostasis and highlights a pathway previously uncharacterized in retinal dystrophy

A clinical and molecular characterisation of CRB1-associated maculopathy

To date, over 150 disease-associated variants in CRB1 have been described, resulting in a range of retinal disease phenotypes including Leber congenital amaurosis and retinitis pigmentosa. Despite this, no genotype–phenotype correlations are currently recognised. We performed a retrospective review of electronic patient records to identify patients with macular dystrophy due to bi-allelic variants in CRB1. In total, seven unrelated individuals were identified. The median age at presentation was 21 years, with a median acuity of 0.55 decimalised Snellen units (IQR = 0.43). The follow-up period ranged from 0 to 19 years (median = 2.0 years), with a median final decimalised Snellen acuity of 0.65 (IQR = 0.70). Fundoscopy revealed only a subtly altered foveal reflex, which evolved into a bull’s-eye pattern of outer retinal atrophy. Optical coherence tomography identified structural changes—intraretinal cysts in the early stages of disease, and later outer retinal atrophy. Genetic testing revealed that one rare allele (c.498_506del, p.(Ile167_Gly169del)) was present in all patients, with one patient being homozygous for the variant and six being heterozygous. In trans with this, one variant recurred twice (p.(Cys896Ter)), while the four remaining alleles were each observed once (p.(Pro1381Thr), p.(Ser478ProfsTer24), p.(Cys195Phe) and p.(Arg764Cys)). These findings show that the rare CRB1 variant, c.498_506del, is strongly associated with localised retinal dysfunction. The clinical findings are much milder than those observed with bi-allelic, loss-of-function variants in CRB1, suggesting this in-frame deletion acts as a hypomorphic allele. This is the most prevalent disease-causing CRB1 variant identified in the non-Asian population to date

Classical and Quantum Critical Phenomena in the Dipolar Antiferromagnet LiErF4

The collective behavior of systems consisting of interacting dipoles is a subject of considerable studies. The anisotropic nature of such interactions opens an arena to explore fundamental questions in correlated electron physics, ranging from quantum entanglement, phase transitions, spin glass states to disorder and fluctuations. LiHoF4 is a textbook example of a ferromagnetic Ising-dipolar model, offering a simple and well-understood Hamiltonian. The system undergoes a quantum phase transition (QPT) in a field transverse to the easy axis, which induces quantum fluctuations between the ground state doublet. Dilution of Ho sites with non-magnetic Yttrium ions lowers only the transition temperature (Tc), and eventually lead to spin-glass state. While Tc decreases in a linear fashion, as expected from simple mean-field (MF) calculation, critical field decreases much faster. The behavior upon dilution has been pointed out to be related to randomness and off-diagonal dipolar interactions. In chapter 5 of this thesis I quantify the deviation of experimental results from neutron scattering studies from MF prediction, with the aim that this analysis can be used in future theoretical efforts towards a quantitative description. The aim of this thesis, however, deals with LiErF4 which is an unexplored planar dipolar antiferromagnetic member of LiReF4 family, with TN ≃ 370 mK. The system undergoes a QPT in an applied field H∥c = 4.0±0.1 kOe, confirmed by a softening of the characteristic excitations at Hc. A combined neutron scattering, specific heat, and magnetic susceptibility study reveals a novel non-MF critical scaling of the classical phase transition, belonging to the 2DXY /h4 universality class. In accord with this, the quantum phase transition at Hc exhibits a three-dimensional classical behavior. The effective dimensional reduction may be a consequence of the intrinsic anisotropic nature of the dipolar interaction. Four-fold anisotropy and degeneracy breaking could be due to the "order-by-disorder" phenomena, which could open a gap in dispersion of the magnetic excitations