Locating binding poses in protein-ligand systems using reconnaissance metadynamics

A molecular dynamics-based protocol is proposed for finding and scoring protein-ligand binding poses. This protocol uses the recently developed reconnaissance metadynamics method, which employs a self-learning algorithm to construct a bias that pushes the system away from the kinetic traps where it would otherwise remain. The exploration of phase space with this algorithm is shown to be roughly six to eight times faster than unbiased molecular dynamics and is only limited by the time taken to diffuse about the surface of the protein. We apply this method to the well-studied trypsin-benzamidine system and show that we are able to refind all the poses obtained from a reference EADock blind docking calculation. These poses can be scored based on the length of time the system remains trapped in the pose. Alternatively, one can perform dimensionality reduction on the output trajectory and obtain a map of phase space that can be used in more expensive free-energy calculations.

Identification of Gene Expression-Based Prognostic Markers in the Hematopoietic Stem Cells of Patients With Myelodysplastic Syndromes

The diagnosis of patients with myelodysplastic syndromes (MDS) is largely dependent on morphologic examination of bone marrow aspirates. Several criteria that form the basis of the classifications and scoring systems most commonly used in clinical practice are affected by operator-dependent variation. To identify standardized molecular markers that would allow prediction of prognosis, we have used gene expression profiling (GEP) data on CD34+ cells from patients with MDS to determine the relationship between gene expression levels and prognosis.

Change of visual acuity recording methods in clinical studies across the years

Purpose: To report any differences in the visual acuity (VA) recording method used in peer-reviewed ophthalmology clinical studies over the past decade. Methods: We reviewed the method of assessing and reporting VA in 160 clinical studies from 2 UK and 2 US peer-reviewed journals, published in 1994 and 2004. Results: The method used to assess VA was specified in 62.5% of UK-published and 60% of US-published papers. In the results sections of the UK publications the VA measurements presented were Snellen acuity (n = 58), logMAR acuity (n = 20) and symbol acuity (n = 1). Similarly in the US publications the VA was recorded in the results section using Snellen acuity (n = 60) and logMAR acuity (n = 14). Overall 10% of the authors appeared to convert Snellen acuity measurements to logMAR format. Five studies (3%) chose to express Snellen-type acuities in decimal form, a method which can easily lead to confusion given the increased use of logMAR scoring systems. Conclusion: The authors recommend that to ensure comparable visual results between studies and different study populations it would be useful if clinical scientists worked to standardized VA testing protocols and reported results in a manner consistent with the way in which they are measured. Copyright © 2008 S. Karger AG.

Measuring the significance of inconsistency in the Viewpoints framework

Measuring inconsistency is crucial to effective inconsistency management in software development. A complete measurement of inconsistency should focus on not only the degree but also the significance of inconsistency. However, most of the approaches available only take the degree of inconsistency into account. The significance of inconsistency has not yet been given much needed consideration. This paper presents an approach for measuring the significance of inconsistency arising from different viewpoints in the Viewpoints framework. We call an individual set of requirements belonging to different viewpoints a combined requirements collection in this paper. We argue that the
significance of inconsistency arising in a combined requirements collection is closely associated with global priority levels of requirements involved in the inconsistency. Here we assume that the global priority level of an individual requirement captures the relative importance of every viewpoint including this requirement as well as the local priority level of the requirement within the viewpoint. Then we use the synthesis of global priority levels of all the requirements in a combined collection to measure the significance of the
collection. Following this, we present a scoring matrix function to measure the significance of inconsistency in an inconsistent combined requirements collection, which describes the contribution made by each subset of the requirements collection to the significance of the set of requirements involved in the inconsistency. An ordering relationship between inconsistencies of two combined requirements collections, termed more significant than, is also presented by comparing their significance scoring matrix functions. Finally, these techniques were implemented in a prototype tool called IncMeasurer, which we developed as a proof of concept.

The prognostic significance of the aberrant extremes of p53 immunophenotypes in breast cancer

Aims: The utility of p53 as a prognostic assay has been elusive. The aims of this study were to describe a novel, reproducible scoring system and assess the relationship between differential p53 immunohistochemistry (IHC) expression patterns, TP53 mutation status and patient outcomes in breast cancer.

Methods and Results: Tissue microarrays were used to study p53 IHC expression patterns: expression was defined as extreme positive (EP), extreme negative (EN), and non-extreme (NE; intermediate patterns). Overall survival (OS) was used to define patient outcome. A representative subgroup (n = 30) showing the various p53 immunophenotypes was analysed for TP53 hotspot mutation status (exons 4-9). Extreme expression of any type occurred in 176 of 288 (61%) cases. As compared with NE expression, EP expression was significantly associated (P = 0.039) with poorer OS. In addition, as compared with NE expression, EN expression was associated (P = 0.059) with poorer OS. Combining cases showing either EP or EN expression better predicted OS than either pattern alone (P = 0.028). This combination immunophenotype was significant in univariate but not multivariate analysis. In subgroup analysis, six substitution exon mutations were detected, all corresponding to extreme IHC phenotypes. Five missense mutations corresponded to EP staining, and the nonsense mutation corresponded to EN staining. No mutations were detected in the NE group.

Conclusions: Patients with extreme p53 IHC expression have a worse OS than those with NE expression. Accounting for EN as well as EP expression improves the prognostic impact. Extreme expression positively correlates with nodal stage and histological grade, and negatively with hormone receptor status. Extreme expression may relate to specific mutational status.

Venn I

Original composition for the animated graphic scoring environment, Venn. Performed by FAINT.

Mathematics and reading difficulty subtypes: Minor phonological influences on mathematics for 5-7 year olds

Linguistic influences in mathematics have previously been explored throughsubtyping methodology and by taking advantage of the componential nature ofmathematics and variations in language requirements that exist across tasks. Thepresent longitudinal investigation aimed to examine the language requirements of mathematical tasks in young children aged 5-7 years. Initially, 256 children were screened for mathematics and reading difficulties using standardised measures. Those scoring at or below the 35th percentile on either dimension were classified as having difficulty. From this screening, 115 children were allocated to each of the MD (n=26), MDRD (n=32), reading difficulty (RD, n=22) and typically achieving (TA, n=35) subtypes. These children were tested at four time points, separated by six monthly intervals, on a battery of seven mathematical tasks. Growth curve analysis indicated that, in contrast to previous research on older children, young children with MD and MDRD had very similar patterns of development on all mathematical tasks. Overall, the subtype comparisons suggested that language played only a minor mediating role in most tasks, and this was secondary in importance to non-verbal skills. Correlational evidence suggested that children from the different subtypescould have been using different mixes of verbal and non-verbal strategies to solve the mathematical problems.

Neuropeptides in Helminths: Occurrence and Distribution

Nematode neuropeptide systems comprise an exceptionally complex array of similar to 250 peptidic signaling molecules that operate within a structurally simple nervous system of similar to 300 neurons. A relatively complete picture of the neuropeptide complement is available for Caenorhabditis elegans, with 30 flp, 38 ins and 43 nlp genes having been documented; accumulating evidence indicates similar complexity in parasitic nematodes from clades I, III, IV and V. In contrast, the picture for parasitic platyhelminths is less clear, with the limited peptide sequence data available providing concrete evidence for only FMRFamide-like peptide (FLP) and neuropeptide F (NPF) signaling systems, each of which only comprises one or two peptides. With the completion of the Schmidtea meditteranea and Schistosoma mansoni genome projects and expressed sequence tag datasets for other flatworm parasites becoming available, the time is ripe for a detailed reanalysis of neuropeptide signaling in flatworms. Although the actual neuropeptides provide limited obvious value as targets for chemotherapeutic-based control strategies, they do highlight the signaling systems present in these helminths and provide tools for the discovery of more amenable targets such as neuropeptide receptors or neuropeptide processing enzymes. Also, they offer opportunities to evaluate the potential of their associated signaling pathways as targets through RNA interference (RNAi)-based, target validation strategies. Currently, within both helminth phyla, the flp signaling systems appear to merit further investigation as they are intrinsically linked with motor function, a proven target for successful anti-parasitics; it is clear that some nematode NLPs also play a role in motor function and could have similar appeal. At this time, it is unclear if flatworm NPF and nematode INS peptides operate in pathways that have utility for parasite control. Clearly, RNAi-based validation could be a starting point for scoring potential target pathways within neuropeptide signaling for parasiticide discovery programs. Also, recent successes in the application of in planta-based RNAi control strategies for plant parasitic nematodes reveal a strategy whereby neuropeptide encoding genes could become targets for parasite control. The possibility of developing these approaches for the control of animal and human parasites is intriguing, but will require significant advances in the delivery of RNAi-triggers.

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014

G-protein coupled receptors (GPCRs) are the targets of over half of all prescribed drugs today. The UniProt database has records for about 800 proteins classified as GPCRs, but drugs have only been developed against 50 of these. Thus, there is huge potential in terms of the number of targets for new therapies to be designed. Several breakthroughs in GPCRs biased pharmacology, structural biology, modelling and scoring have resulted in a resurgence of interest in GPCRs as drug targets. Therefore, an international conference, sponsored by the Royal Society, with world-renowned researchers from industry and academia was recently held to discuss recent progress and highlight key areas of future research needed to accelerate GPCR drug discovery. Several key points emerged. Firstly, structures for all three major classes of GPCRs have now been solved and there is increasing coverage across the GPCR phylogenetic tree. This is likely to be substantially enhanced with data from x-ray free electron sources as they move beyond proof of concept. Secondly, the concept of biased signalling or functional selectivity is likely to be prevalent in many GPCRs, and this presents exciting new opportunities for selectivity and the control of side effects, especially when combined with increasing data regarding allosteric modulation. Thirdly, there will almost certainly be some GPCRs that will remain difficult targets because they exhibit complex ligand dependencies and have many metastable states rendering them difficult to resolve by crystallographic methods. Subtle effects within the packing of the transmembrane helices are likely to mask and contribute to this aspect, which may play a role in species dependent behaviour. This is particularly important because it has ramifications for how we interpret pre-clinical data. In summary, collaborative efforts between industry and academia have delivered significant progress in terms of structure and understanding of GPCRs and will be essential for resolving problems associated with the more difficult targets in the future.

Alien aquatics in Europe: assessing the relative environmental and socio-economic impacts of invasive aquatic macroinvertebrates and other taxa

Invasive alien aquatic species, including marine and freshwater macroinvertebrates, have become increasingly important in terms of both environmental and socio-economic impacts. In order to assess their environmental and economic costs, we applied the Generic Impact Scoring System (GISS) and performed a comparison with other taxa of invaders in Europe. Impacts were scored into six environmental and six socio-economic categories, with each category containing five impact levels. Among 49 aquatic macroinvertebrates, the most impacting species were the Chinese mitten crab, Eriocheir sinensis (Milne-Edwards, 1853) and the zebra mussel, Dreissena polymorpha (Pallas, 1771). The highest impacts found per GISS impact category were, separately; on ecosystems, through predation, as competitors, and on animal production. Eleven species have an impact score > 10 (high impact) and seven reach impact level 5 in at least one impact category (EU blacklist candidates), the maximum score that can be given is 60 impact points. Comparisons were drawn between aquatic macroinvertebrates and vertebrate invaders such as fish, mammals and birds, as well as terrestrial arthropods, revealing invasive freshwater macroinvertebrates to be voracious predators of native prey and damaging to native ecosystems compared with other taxa. GISS can be used to compare these taxa and will aid policy making and targeting of invasive species for management by relevant agencies, or to assist in producing species blacklist candidates.

PTEN mRNA detection by chromogenic, RNA in situ technologies: a reliable alternative to PTEN immunohistochemistry

Immunohistochemical staining for phosphatase and tensin homolog (PTEN) does not have either an acceptable standard protocol or concordance of scoring between pathologists. Evaluation of PTEN mRNA with a unique and verified sequence probe may offer a realistic alternative providing a robust and reproducible protocol. In this study, we have evaluated an in situ hybridization (ISH) protocol for PTEN mRNA using RNAScope technology and compared it with a standard protocol for PTEN immunohistochemistry (IHC). PTEN mRNA expression by ISH was consistently more sensitive than PTEN IHC, with 56% of samples on a mixed-tumor tissue microarray (TMA) showing high expression by ISH compared with 42% by IHC. On a prostate TMA, 49% of cases showed high expression by ISH compared with 43% by IHC. Variations in PTEN mRNA expression within malignant epithelium were quantifiable using image analysis on the prostate TMAs. Within tumors, clear overexpression of PTEN mRNA on malignant epithelium compared with benign epithelium was frequently observed and quantified. The use of SpotStudio software in the mixed-tumor TMA allowed for clear demonstration of varying levels of PTEN mRNA between tumor samples by the mRNA methodology. This was evident by the quantifiable differences between distinct oropharyngeal tumors (up to 3-fold increase in average number of spots per cell between 2 cases). mRNA detection of PTEN or other biomarkers, for which optimal or standardized immunohistochemical techniques are not available, represents a means by which heterogeneity of expression within focal regions of tumor can be explored with more confidence.

Effects of scalding and dehairing of pig carcasses at abattoirs on the visibility of welfare-related lesions

There is increasing interest in developing abattoir-based welfare measures for pigs.The primary aim of this study was to determine the most appropriate place on theslaughter line to conduct assessments of welfare-related lesions, namely apparentaggression-related skin lesions (hereafter referred to as 'skin lesions'), loin bruising andapparent tail biting damage. The study also lent itself to an assessment of theprevalence of these lesions, and the extent to which they were linked with productionparameters. Finishing pigs processed at two abattoirs on the Island of Ireland (n =1950 in abattoir A, and n = 1939 in abattoir B) were used. Data were collected over 6days in each abattoir in July 2014. Lesion scoring took place at two points on theslaughter line: (1) at exsanguination (Slaughter Stage 1 [SS1]), and (2) followingscalding and dehairing of carcasses (Slaughter Stage 2 [SS2]). At both points, eachcarcass was assigned a skin and tail lesion score ranging from 0 (lesion absent) to 3 or4 (severe lesions), respectively. Loin bruising was recorded as present or absent.Differences in the percentage of pigs with observable lesions of each type werecompared between SS1 and SS2 using McNemar/McNemar-Bowker tests. Theassociations between each lesion type, and both cold carcass weight andcondemnations, were examined at batch level using Pearson's correlations. Batch wasdefined as the group of animals with a particular farm identification code on a givenday. The overall percentage of pigs with a visible skin lesion (i.e. score > 0) decreasedbetween SS1 and SS2 (P<0.001). However, the percentage of pigs with a severe skinlesion increased numerically from SS1 to SS2. The percentage of pigs with a visible taillesion and with loin bruising also increased between SS1 and SS2 (P<0.001). Therewas a positive correlation between the percentage of carcasses that were partiallycondemned, and the percentage of pigs with skin lesions, tail lesions and loin bruising(P<0.05). Additionally, as the batch-level frequency of each lesion type increased,average cold carcass weight decreased (P<0.001). These findings suggest that severeskin lesions, tail lesions and loin bruising are more visible on pig carcasses after theyhave been scalded and dehaired, and that this is when abattoir-based lesion scoringshould take place. The high prevalence of all three lesion types, and the links witheconomically important production parameters, suggests more research into identifying key risk factors is warranted.

Research Methods in Psychology For Dummies

Your hands-on introduction to research methods in psychology.  
Looking for an easily accessible overview of research methods in psychology? This is the book for you! Whether you need to get ahead in class, you're pressed for time, or you just want a take on a topic that's not covered in your textbook, Research Methods in Psychology For Dummies has you covered. 
Written in plain English and packed with easy-to-follow instruction, this friendly guide takes the intimidation out of the subject and tackles the fundamentals of psychology research in a way that makes it approachable and comprehensible, no matter your background. Inside, you'll find expert coverage of qualitative and quantitative research methods, including surveys, case studies, laboratory observations, tests and experiments—and much more. 
- Serves as an excellent supplement to course textbooks - Provides a clear introduction to the scientific method - Presents the methodologies and techniques used in psychology research- Written by the authors of Psychology Statistics For Dummies 
If you're a first or second year psychology student and want to supplement your doorstop-sized psychology textbook—and boost your chances of scoring higher at exam time—this hands-on guide breaks down the subject into easily digestible bits and propels you towards success.

Fast Mining of Interesting Phrases from Subsets of Text Corpora

We address the problem of mining interesting phrases from subsets of a text corpus where the subset is specified using a set of features such as keywords that form a query. Previous algorithms for the problem have proposed solutions that involve sifting through a phrase dictionary based index or a document-based index where the solution is linear in either the phrase dictionary size or the size of the document subset. We propose the usage of an independence assumption between query keywords given the top correlated phrases, wherein the pre-processing could be reduced to discovering phrases from among the top phrases per each feature in the query. We then outline an indexing mechanism where per-keyword phrase lists are stored either in disk or memory, so that popular aggregation algorithms such as No Random Access and Sort-merge Join may be adapted to do the scoring at real-time to identify the top interesting phrases. Though such an approach is expected to be approximate, we empirically illustrate that very high accuracies (of over 90%) are achieved against the results of exact algorithms. Due to the simplified list-aggregation, we are also able to provide response times that are orders of magnitude better than state-of-the-art algorithms. Interestingly, our disk-based approach outperforms the in-memory baselines by up to hundred times and sometimes more, confirming the superiority of the proposed method.

Finding Relevant Tweets

When a user of a microblogging site authors a microblog
post or browses through a microblog post, it provides cues as to what
topic she is interested in at that point in time. Example-based search
that retrieves similar tweets given one exemplary tweet, such as the one
just authored, can help provide the user with relevant content. We investigate
various components of microblog posts, such as the associated
timestamp, author’s social network, and the content of the post, and
develop approaches that harness such factors in finding relevant tweets
given a query tweet. An empirical analysis of such techniques on real
world twitter-data is then presented to quantify the utility of the various
factors in assessing tweet relevance. We observe that content-wise similar
tweets that also contain extra information not already present in the
query, are perceived as useful. We then develop a composite technique
that combines the various approaches by scoring tweets using a dynamic
query-specific linear combination of separate techniques. An empirical
evaluation establishes the effectiveness of the composite technique, and
that it outperforms each of its constituents.