Evidence for high gene flow, nonrandom mating, and genetic bottlenecks of Ganoderma boninense infecting oil palm (Elaeis guineensis Jacq.) plantations in Malaysia and Indonesia

Ganoderma boninense, the causal agent of basal stem rot (BSR) disease, has been recognized as a major economic threat to commercial plantings of oil palm (Elaeis guineensis Jacq.) in Southeast Asia, which supplies 86% of the world's palm oil. High genetic diversity and gene flow among regional populations of 417 G. boninense isolates collected from Sabah, Sarawak, and Peninsular Malaysia (Malaysia) and Sumatra (Indonesia) were demonstrated using 16 microsatellite loci. Three genetic clusters and different admixed populations of G. boninense across regions were detected, and they appeared to follow the spread of the fungus from the oldest (Peninsular Malaysia and Sumatra) to younger generations of oil palm plantings (Sabah and Sarawak). Low spatial genetic differentiation of G. boninense (F_ST = 0.05) among the sampling regions revealed geographically nonrestricted gene dispersal, but isolation by distance was still evident. Analysis of molecular variance (AMOVA) confirmed the little to no genetic differentiation among the pathogen populations and the three genetic clusters defined by STRUCTURE and minimum spanning network. Despite G. boninense being highly outcrossing and spread by sexual spores, linkage disequilibrium was detected in 7 of the 14 populations. Linkage disequilibrium indicated that the reproduction of the fungus was not entirely by random mating and genetic drift could be an important structuring factor. Furthermore, evidence of population bottleneck was indicated in the oldest oil palm plantations as detected in genetic clusters 2 and 3, which consisted mainly of Peninsular Malaysia and Sumatra isolates. The population bottleneck or founding event could have arisen from either new planting or replanting after the removal of large number of palm hosts. The present study also demonstrated that migration and nonrandom mating of G. boninense could be important for survival and adaptation to new palm hosts.

Genetic diversity and gene flow amongst admixed populations of Ganoderma boninense, causal agent of basal stem rot in African oil palm (Elaeis guineensis Jacq.) in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia)

In 1911 and 1917, the first commercial plantings of African oil palm (Elaeis guineensis Jacq.) were made in Indonesia and Malaysia in Southeast Asia. In less than 15 years, basal stem rot (BSR) was reported in Malaysia. It took nearly another seven decades to identify the main causal agent of BSR as the fungus, Ganoderma boninense. Since then, research efforts have focused on understanding G. boninense disease epidemiology, biology, and etiology, but limited progress was made to characterize pathogen genetic diversity, spatial structure, pathogenicity, and virulence. This study describes pathogen variability, gene flow, population differentiation, and genetic structure of G. boninense in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia) inferred by 16 highly polymorphic cDNA-SSR (simple sequence repeat) markers. Marker-inferred genotypic diversity indicated a high level of pathogen variability among individuals within a population and among different populations. This genetic variability is clearly the result of outcrossing between basidiospores to produce recombinant genotypes. Although our results indicated high gene flow among the populations, there was no significant genetic differentiation among G. boninense populations on a regional scale. It suggested that G. boninense genetic makeup is similar across a wide region. Furthermore, our results revealed the existence of three admixed genetic clusters of G. boninense associated with BSR-diseased oil palms sampled throughout Sarawak, Peninsular Malaysia, and Sumatra. We postulate that the population structure is likely a reflection of the high genetic variability of G. boninense populations. This, in turn, could be explained by highly successful outcrossing between basidiospores of G. boninense from Southeast Asia and introduced genetic sources from various regions of the world, as well as regional adaptation of various pathogen genotypes to different palm hosts. Pathogen variability and population structure could be employed to deduce the epidemiology of G. boninense, as well as the implications of plantation cultural practices on BSR disease control in different regions.

Hypocrisy Around Medical Patient Data: Issues of Access for Biomedical Research, Data Quality, Usefulness for the Purpose and Omics Data as Game Changer

Whether due to simplicity or hypocrisy, the question of access to patient data for biomedical research is widely seen in the public discourse only from the angle of patient privacy. At the same time, the desire to live and to live without disability is of much higher value to the patients. This goal can only be achieved by extracting research insight from patient data in addition to working on model organisms, something that is well understood by many patients. Yet, most biomedical researchers working outside of clinics and hospitals are denied access to patient records when, at the same time, clinicians who guard the patient data are not optimally prepared for the data’s analysis. Medical data collection is a time- and cost-intensive process that is most of all tedious, with few elements of intellectual and emotional satisfaction on its own. In this process, clinicians and bioinformaticians, each group with their own interests, have to join forces with the goal to generate medical data sets both from clinical trials and from routinely collected electronic health records that are, as much as possible, free from errors and obvious inconsistencies. The data cleansing effort as we have learned during curation of Singaporean clinical trial data is not a trivial task. The introduction of omics and sophisticated imaging modalities into clinical practice that are only partially interpreted in terms of diagnosis and therapy with today’s level of knowledge warrant the creation of clinical databases with full patient history. This opens up opportunities for re-analyses and cross-trial studies at future time points with more sophisticated analyses of the same data, the collection of which is very expensive.

Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z

Distant homology relationships among proteins with many transmembrane regions (TMs) are difficult to detect as they are clouded by the TMs’ hydrophobic compositional bias and mutational divergence in connecting loops. In the case of several GPI lipid anchor biosynthesis pathway components, the hidden evolutionary signal can be revealed with dissectHMMER, a sequence similarity search tool focusing on fold-critical, high complexity sequence segments. We find that a sequence module with 10 TMs in PIG-W, described as acyl transferase, is homologous to PIG-U, a transamidase subunit without characterized molecular function, and to mannosyltransferases PIG-B, PIG-M, PIG-V and PIG-Z. We conclude that this new, membrane-embedded domain named BindGPILA functions as the unit for recognizing, binding and stabilizing the GPI lipid anchor in a modification-competent form as this appears the only functional aspect shared among all proteins. Thus, PIG-U's likely molecular function is shuttling/presenting the anchor in a productive conformation to the transamidase complex.

Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis

BACKGROUND

Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i.e., varying exponent values) in a log-log plot. If transcript abundance is truly power-law distributed, the varying exponent signifies changing mathematical moments (e.g., mean, variance) and creates heteroskedasticity which compromises statistical rigor in analysis. The impact of this deviation from the asymptotic power-law on sequencing count data has never truly been examined and quantified.

RESULTS

The anecdotal description of transcript abundance being almost Zipf's law-like distributed can be conceptualized as the imperfect mathematical rendition of the Pareto power-law distribution when subjected to the finite-size effects in the real world; This is regardless of the advancement in sequencing technology since sampling is finite in practice. Our conceptualization agrees well with our empirical analysis of two modern day NGS (Next-generation sequencing) datasets: an in-house generated dilution miRNA study of two gastric cancer cell lines (NUGC3 and AGS) and a publicly available spike-in miRNA data; Firstly, the finite-size effects causes the deviations of sequencing count data from Zipf's law and issues of reproducibility in sequencing experiments. Secondly, it manifests as heteroskedasticity among experimental replicates to bring about statistical woes. Surprisingly, a straightforward power-law correction that restores the distribution distortion to a single exponent value can dramatically reduce data heteroskedasticity to invoke an instant increase in signal-to-noise ratio by 50% and the statistical/detection sensitivity by as high as 30% regardless of the downstream mapping and normalization methods. Most importantly, the power-law correction improves concordance in significant calls among different normalization methods of a data series averagely by 22%. When presented with a higher sequence depth (4 times difference), the improvement in concordance is asymmetrical (32% for the higher sequencing depth instance versus 13% for the lower instance) and demonstrates that the simple power-law correction can increase significant detection with higher sequencing depths. Finally, the correction dramatically enhances the statistical conclusions and eludes the metastasis potential of the NUGC3 cell line against AGS of our dilution analysis.

CONCLUSIONS

The finite-size effects due to undersampling generally plagues transcript count data with reproducibility issues but can be minimized through a simple power-law correction of the count distribution. This distribution correction has direct implication on the biological interpretation of the study and the rigor of the scientific findings.

REVIEWERS

This article was reviewed by Oliviero Carugo, Thomas Dandekar and Sandor Pongor.

Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"

Background

Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane’s hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein’s biological functions.

Results

With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is sensitive with regard to details of TMH alignment and residue frequency normalisation and also to dataset size; therefore, this trend was obscured in previous work. We observe variations amongst taxa as well as for organelles along the secretory pathway. The effect is most pronounced for TMHs from single-pass transmembrane (bitopic) proteins compared to those with multiple TMHs (polytopic proteins) and especially for the class of simple TMHs that evolved for the sole role as membrane anchors.

Conclusions

The charged-residue flank bias is only one of the TMH sequence features with a role in the anchorage mechanisms, others apparently being the leucine intra-helix propensity skew towards the cytoplasmic side, tryptophan flanking as well as the cysteine and tyrosine inside preference. These observations will stimulate new prediction methods for TMHs and protein topology from a sequence as well as new engineering designs for artificial membrane proteins.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0404-4) contains supplementary material, which is available to authorized users.

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

BACKGROUND

While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.

RESULTS

In this work, both the speed of HMMER3 and glocal-mode alignment of HMMER2 are combined within the xHMMER3x2 framework for tackling the large-scale domain annotation task. Briefly, HMMER3 is utilized for initial domain detection so that HMMER2 can subsequently perform the glocal-mode, sequence-to-full-domain alignments for the detected HMMER3 hits. An E-value calibration procedure is required to ensure that the search space by HMMER2 is sufficiently replicated by HMMER3. We find that the latter is straightforwardly possible for ~80% of the models in the Pfam domain library (release 29). However in the case of the remaining ~20% of HMMER3 domain models, the respective HMMER2 counterparts are more sensitive. Thus, HMMER3 searches alone are insufficient to ensure sensitivity and a HMMER2-based search needs to be initiated. When tested on the set of UniProt human sequences, xHMMER3x2 can be configured to be between 7× and 201× faster than HMMER2, but with descending domain detection sensitivity from 99.8 to 95.7% with respect to HMMER2 alone; HMMER3's sensitivity was 95.7%. At extremes, xHMMER3x2 is either the slow glocal-mode HMMER2 or the fast HMMER3 with glocal-mode. Finally, the E-values to false-positive rates (FPR) mapping by xHMMER3x2 allows E-values of different model builds to be compared, so that any annotation discrepancies in a large-scale annotation exercise can be flagged for further examination by dissectHMMER.

CONCLUSION

The xHMMER3x2 workflow allows large-scale domain annotation speed to be drastically improved over HMMER2 without compromising for domain-detection with regard to sensitivity and sequence-to-domain alignment incompleteness. The xHMMER3x2 code and its webserver (for Pfam release 27, 28 and 29) are freely available at http://xhmmer3x2.bii.a-star.edu.sg/ .

REVIEWERS

Reviewed by Thomas Dandekar, L. Aravind, Oliviero Carugo and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.

Stage-Specific Relationship between Frailty and Cognitive Impairment in a Specialist Memory Clinic Setting

BACKGROUND

It is unclear if the complex relationship between physical frailty and cognition varies across the severity of cognitive impairment.

OBJECTIVES

We therefore aimed to explore if there are stage-specific differences in the relationship between frailty and cognitive impairment.

DESIGN

Cross-sectional study.

SETTING

A specialist Memory Clinic setting.

PARTICIPANTS

Mild cognitive impairment (MCI) and mild-moderate Alzheimer's disease (AD) community-dwelling subjects.

MEASUREMENTS

We obtained data on demographics, multimorbidity, cognition-related measures, nutrition, neuroimaging measures, muscle mass, Vitamin D level, apolipoprotein - e (APOE) status and physical performance measures. Frailty measures of gait speed, hand grip strength, question on exhausation and weight loss, classified subjects according to the Buchmann criteria into non-frail and frail categories.

RESULTS

Forty-five MCI, 64 mild AD and 13 moderate AD subjects (total n=122) were studied. The prevalence of frailty for MCI, mild AD and moderate AD was 35.6%, 21.9% and 46.2% respectively, indicating a u-shaped trend. Significant differences were noted in fatigue, grip strength and gait speed frailty sub-items. Significant correlation of frailty with cognition were noted in mild-moderate AD (Spearman's coefficient 0.26, p<0.05) but not in MCI (0.01, p=0.6). No other differences in multimorbidity, Vitamin D, APOE, nutritional measures, white matter lesions were observed. Sarcopenia interestingly had an inverse stage-specific relationship unlike frailty.

CONCLUSIONS

Our results suggest a U-shaped relationship between frailty and cognition, characterized by initial dissociation with cognitive impairment and subsequent convergence at later stages. Future studies incorporating immune markers and endocrine pathways with longitudinal follow-up could potentially elucidate intermediary mechanisms in the frailty cascade.

MicroRNA expression profiling of human blood monocyte subsets highlights functional differences

Within human blood there are two subsets of monocytes that can be identified by differential expression of CD16. Although numerous phenotypic and functional differences between the subsets have been described, little is known of the mechanisms underlying the distinctive properties of the two subsets. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate gene expression through promoting mRNA degradation or repressing translation, leading to alterations in cellular processes. Their potential influence on the functions of monocyte subsets has not been investigated. In this study, we employed microarray analysis to define the miRNA expression profile of human monocyte subsets. We identified 66 miRNAs that were differentially expressed (DE) between CD16(+) and CD16(-) monocytes. Gene ontology analysis revealed that the predicted targets of the DE miRNAs were predominantly associated with cell death and cellular movement. We validated the functional impacts of selected DE miRNAs in CD16(-) monocytes, over-expression of miR-432 significantly increases apoptosis, and inhibiting miR-19a significantly reduces cell motility. Furthermore, we found that miR-345, another DE miRNA directly targets the transcription factor RelA in monocytes, which resulted in the differential expression of RelA in monocyte subsets. This implicates miR-345 indirect regulation of many genes downstream of RelA, including important inflammatory mediators. Together, our data show that DE miRNAs could contribute substantially to regulating the functions of human blood monocytes.

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Background

Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies. The latter is either due to positional sequence conservation as a result of a very simple, physically induced pattern or integral sequence properties that are critical for function. Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations.

Results

Based on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. Subsequent statistical stratification of the fold-related hits into cohorts of functionally-related domains allows for the function postulation of the query sequence. Briefly, the technical problems as to how to recognize non-globular parts in the domain model, resolve contradictory HMMER2/HMMER3 results and evaluate fold-related domain hits for homology, are addressed in this work. The framework is benchmarked against a set of SCOP-to-Pfam domain models. Despite being a sequence-to-profile method, dissectHMMER performs favorably against a profile-to-profile based method-HHsuite/HHsearch. Examples of function annotation using dissectHMMER, including the function discovery of an uncharacterized membrane protein Q9K8K1_BACHD (WP_010899149.1) as a lactose/H+ symporter, are presented. Finally, dissectHMMER webserver is made publicly available at http://dissecthmmer.bii.a-star.edu.sg.

Conclusions

The proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. Overall, this translates into an opportunity for any novel protein sequence to be functionally characterized.

Reviewers

This article was reviewed by Masanori Arita, Shamil Sunyaev and L. Aravind.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0068-3) contains supplementary material, which is available to authorized users.

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Background

Protein sequence similarities to any types of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc. where either positional sequence conservation is the result of a very simple, physically induced pattern or rather integral sequence properties are critical) are pertinent sources for mistaken homologies. Regretfully, these considerations regularly escape attention in large-scale annotation studies since, often, there is no substitute to manual handling of these cases. Quantitative criteria are required to suppress events of function annotation transfer as a result of false homology assignments.

Results

The sequence homology concept is based on the similarity comparison between the structural elements, the basic building blocks for conferring the overall fold of a protein. We propose to dissect the total similarity score into fold-critical and other, remaining contributions and suggest that, for a valid homology statement, the fold-relevant score contribution should at least be significant on its own. As part of the article, we provide the DissectHMMER software program for dissecting HMMER2/3 scores into segment-specific contributions. We show that DissectHMMER reproduces HMMER2/3 scores with sufficient accuracy and that it is useful in automated decisions about homology for instructive sequence examples. To generalize the dissection concept for cases without 3D structural information, we find that a dissection based on alignment quality is an appropriate surrogate. The approach was applied to a large-scale study of SMART and PFAM domains in the space of seed sequences and in the space of UniProt/SwissProt.

Conclusions

Sequence similarity core dissection with regard to fold-critical and other contributions systematically suppresses false hits and, additionally, recovers previously obscured homology relationships such as the one between aquaporins and formate/nitrite transporters that, so far, was only supported by structure comparison.

Search for dark matter in events with a hadronically decaying W or Z boson and missing transverse momentum in pp collisions at √s=8 TeV with the ATLAS detector

A search is presented for dark matter pair production in association with a W or Z boson in pp collisions representing 20.3  fb(-1) of integrated luminosity at √s=8  TeV using data recorded with the ATLAS detector at the Large Hadron Collider. Events with a hadronic jet with the jet mass consistent with a W or Z boson, and with large missing transverse momentum are analyzed. The data are consistent with the standard model expectations. Limits are set on the mass scale in effective field theories that describe the interaction of dark matter and standard model particles, and on the cross section of Higgs production and decay to invisible particles. In addition, cross section limits on the anomalous production of W or Z bosons with large missing transverse momentum are set in two fiducial regions.

Measurement of top quark polarization in top-antitop events from proton-proton collisions at √s=7 TeV using the ATLAS detector

This Letter presents measurements of the polarization of the top quark in top-antitop quark pair events, using 4.7  fb(-1) of proton-proton collision data recorded with the ATLAS detector at the Large Hadron Collider at √s=7  TeV. Final states containing one or two isolated leptons (electrons or muons) and jets are considered. Two measurements of α(ℓ)P, the product of the leptonic spin-analyzing power and the top quark polarization, are performed assuming that the polarization is introduced by either a CP conserving or a maximally CP violating production process. The measurements obtained, α(ℓ)P(CPC)=-0.035±0.014(stat)±0.037(syst) and α(ℓ)P(CPV)=0.020±0.016(stat)(-0.017)(+0.013)(syst), are in good agreement with the standard model prediction of negligible top quark polarization.

A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequencing reads

We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with specific tag motifs. This approach was applied to the test case of fitting the enterohemorrhagic O104:H4 E.coli strain from the 2011 outbreak in Germany into the phylogenetic network of previously known E.coli-related strains and extend the method to allow assigning any new strain to the correct phylogenetic group even directly from unassembled short sequence reads from next generation sequencing data. Hence, this approach is also useful to quickly identify the most suitable reference genome for subsequent assembly steps.

Measurement of the azimuthal angle dependence of inclusive jet yields in Pb+Pb collisions at √(sNN)=2.76 TeV with the ATLAS detector

Measurements of the variation of inclusive jet suppression as a function of relative azimuthal angle, Δφ, with respect to the elliptic event plane provide insight into the path-length dependence of jet quenching. ATLAS has measured the Δφ dependence of jet yields in 0.14 nb(-1) of √(s(NN))=2.76 TeV Pb+Pb collisions at the LHC for jet transverse momenta p(T)>45 GeV in different collision centrality bins using an underlying event subtraction procedure that accounts for elliptic flow. The variation of the jet yield with Δφ was characterized by the parameter, v(2)(jet), and the ratio of out-of-plane (Δφ~π/2) to in-plane (Δφ~0) yields. Nonzero v(2)(jet) values were measured in all centrality bins for p(T)<160 GeV. The jet yields are observed to vary by as much as 20% between in-plane and out-of-plane directions.

Observation of associated near-side and away-side long-range correlations in sqrt[s(NN)]=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δø) and pseudorapidity (Δη) are measured in sqrt[s(NN)] = 5.02 TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 μb(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (ΣE(T)(Pb)) summed over 3.1 < η < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < |Δ η | < 5) "near-side" (Δø ~ 0) correlation that grows rapidly with increasing ΣE(T)(Pb). A long-range "away-side" (Δø ~ π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣE(T)(Pb), is found to match the near-side correlation in magnitude, shape (in Δη and Δø) and ΣE(T)(Pb) dependence. The resultant Δø correlation is approximately symmetric about π/2, and is consistent with a dominant cos2Δø modulation for all ΣE(T)(Pb) ranges and particle p(T).

Measurement of Z boson production in Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV with the ATLAS detector

The ATLAS experiment has observed 1995 Z boson candidates in data corresponding to 0.15  nb(-1) of integrated luminosity obtained in the 2011 LHC Pb+Pb run at sqrt[s(NN)]=2.76  TeV. The Z bosons are reconstructed via dielectron and dimuon decay channels, with a background contamination of less than 3%. Results from the two channels are consistent and are combined. Within the statistical and systematic uncertainties, the per-event Z boson yield is proportional to the number of binary collisions estimated by the Glauber model. The elliptic anisotropy of the azimuthal distribution of the Z boson with respect to the event plane is found to be consistent with zero.

Search for dark matter candidates and large extra dimensions in events with a photon and missing transverse momentum in pp collision data at sqrt[s]=7 TeV with the ATLAS detector

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV are reported. Data collected by the ATLAS experiment at the LHC corresponding to an integrated luminosity of 4.6 fb(-1) are used. Good agreement is observed between the data and the standard model predictions. The results are translated into exclusion limits on models with large extra spatial dimensions and on pair production of weakly interacting dark matter candidates.

Search for magnetic monopoles in sqrt[s]=7 TeV pp collisions with the ATLAS detector

This Letter presents a search for magnetic monopoles with the ATLAS detector at the CERN Large Hadron Collider using an integrated luminosity of 2.0  fb(-1) of pp collisions recorded at a center-of-mass energy of sqrt[s]=7  TeV. No event is found in the signal region, leading to an upper limit on the production cross section at 95% confidence level of 1.6/ϵ  fb for Dirac magnetic monopoles with the minimum unit magnetic charge and with mass between 200 GeV and 1500 GeV, where ϵ is the monopole reconstruction efficiency. The efficiency ϵ is high and uniform in the fiducial region given by pseudorapidity |η|<1.37 and transverse kinetic energy 600-700<E(kin)sinθ<1400  GeV. The minimum value of 700 GeV is for monopoles of mass 200 GeV, whereas the minimum value of 600 GeV is applicable for higher mass monopoles. Therefore, the upper limit on the production cross section at 95% confidence level is 2 fb in this fiducial region. Assuming the kinematic distributions from Drell-Yan pair production of spin-1/2 Dirac magnetic monopoles, the efficiency is in the range 1%-10%, leading to an upper limit on the cross section at 95% confidence level that varies from 145 fb to 16 fb for monopoles with mass between 200 GeV and 1200 GeV. This limit is weaker than the fiducial limit because most of these monopoles lie outside the fiducial region.

Search for direct top squark pair production in final states with one isolated lepton, jets, and missing transverse momentum in sqrt[s] = 7 TeV pp collisions using 4.7 fb(-10 of ATLAS data

A search is presented for direct top squark pair production in final states with one isolated electron or muon, jets, and missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV. The measurement is based on 4.7 fb(-1) of data collected with the ATLAS detector at the LHC. Each top squark is assumed to decay to a top quark and the lightest supersymmetric particle (LSP). The data are found to be consistent with standard model expectations. Top squark masses between 230 GeV and 440 GeV are excluded with 95% confidence for massless LSPs, and top squark masses around 400 GeV are excluded for LSP masses up to 125 GeV.

Search for a supersymmetric partner to the top quark in final states with jets and missing transverse momentum at sqrt[s] = 7 TeV with the ATLAS detector

A search for direct pair production of supersymmetric top squarks (t(1)) is presented, assuming the t(1) decays into a top quark and the lightest supersymmetric particle, χ(1)(0), and that both top quarks decay to purely hadronic final states. A total of 16 (4) events are observed compared to a predicted standard model background of 13.5(-3.6)(+3.7)(4.4(-1.3)(+1.7)) events in two signal regions based on ∫Ldt = 4.7 fb(-1) of pp collision data taken at sqrt[s] = 7 TeV with the ATLAS detector at the LHC. An exclusion region in the t(1) versus χ(1)(0) mass plane is evaluated: 370<m(t)(1)}<465 GeV is excluded for m(χ)(1)(0) ~ 0 GeV while m(t)(1) = 445 GeV is excluded for m(χ)(1)(0) ≤ 50 GeV.

Hyaluronic acid instillation following arthroscopic anterior cruciate ligament reconstruction: a double-blinded, randomised controlled study

PURPOSE

To assess the effect of hyaluronic acid instillation after arthroscopic anterior cruciate ligament (ACL) reconstruction for improving pain, range of movement, and function of the knee.

METHODS

28 men and 4 women underwent arthroscopic ACL reconstruction for isolated ACL rupture (partial or complete) and instability after recreational sports injury 2 to 120 months earlier. They were randomised to undergo arthroscopic ACL reconstruction followed by intra-articular viscoseal instillation (13 men and 3 women) or arthroscopic ACL reconstruction alone (15 men and 1 woman). The knee injury osteoarthritis outcome score (for pain, symptoms, activities of daily living, sport and recreation function, and quality of life), range of movement, knee circumference, and analgesic use were assessed on days -1, 1, and 2, and weeks 2, 6 and 12.

RESULTS

Patient demographics were similar at baseline. At postoperative days 1 and 2, all subscales of the knee injury osteoarthritis outcome score (except for quality of life) were significantly higher in the viscoseal group. At weeks 2, 6, and 12, improvement in both groups equalised. Knee swelling (change in knee circumference) was significantly less in the viscoseal group at days 1 and 2 (p=0.009 and p=0.038, respectively, Mann-Whitney U test). Only one patient in the viscoseal group had a limited range of movement. No patient developed any adverse reaction.

CONCLUSION

Intra-articular viscoseal instillation improved pain control and swelling 2 days after arthroscopic ACL reconstruction.

Search for supersymmetry in events with three leptons and missing transverse momentum in √[s]=7 TeV pp collisions with the ATLAS detector

A search for the weak production of charginos and neutralinos decaying to a final state with three leptons (electrons or muons) and missing transverse momentum is presented. The analysis uses 2.06 fb(-1) of √[s]=7 TeV proton-proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with standard model expectations in two signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric and simplified models. For the simplified models, degenerate lightest chargino and next-to-lightest neutralino masses up to 300 GeV are excluded for mass differences from the lightest neutralino up to 300 GeV.

Transmembrane helix: simple or complex

Transmembrane helical segments (TMs) can be classified into two groups of so-called ‘simple’ and ‘complex’ TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs. In practice, these simple TMs can attract statistically significant but evolutionarily unrelated hits during similarity searches (whether through BLAST- or HMM-based approaches). This is especially problematic for membrane proteins that contain both globular segments and TMs. As such, we have developed the transmembrane helix: simple or complex (TMSOC) webserver for the identification of simple and complex TMs. By masking simple TM segments in seed sequences prior to sequence similarity searches, the false-discovery rate decreases without sacrificing sensitivity. Therefore, TMSOC is a novel and necessary sequence analytic tool for both the experimentalists and the computational biology community working on membrane proteins. It is freely accessible at http://tmsoc.bii.a-star.edu.sg or available for download.

Measurement of the ZZ production cross section and limits on anomalous neutral triple gauge couplings in proton-proton collisions at sqrt[s] = 7 TeV with the ATLAS detector

A measurement of the ZZ production cross section in proton-proton collisions at sqrt[s] = 7 TeV using data corresponding to an integrated luminosity of 1.02 fb(-1) recorded by the ATLAS experiment at the LHC is presented. Twelve events containing two Z boson candidates decaying to electrons and/or muons are observed, with an expected background of 0.3 ± 0.3(stat)(-0.3)(+0.4)(syst) events. The cross section measured in a phase-space region with good detector acceptance and for dilepton masses within the range 66 to 116 GeV is σ(ZZ → ℓ+ ℓ- ℓ+ ℓ-)(fid) = 19.4(-5.2)(+6.3)(stat)(-0.7)(+0.9)(syst) ± 0.7(lumi) fb. The resulting total cross section for on-shell ZZ production, σ(ZZ)(tot) = 8.5(-2.3)(+2.7)(stat)(-0.3)(+0.4)(syst) ± 0.3(lumi) pb, is consistent with the standard model expectation of 6.5(-0.2)(+0.3) pb calculated at the next-to-leading order in QCD. Limits on anomalous neutral triple gauge boson couplings are derived.

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

BACKGROUND

Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches composed of non-polar residues. Simple, quantitative criteria are desirable for identifying transmembrane helices (TMs) that must be included into or should be excluded from start sequence segments in similarity searches aimed at finding distant homologues.

RESULTS

We found that there are two types of TMs in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intra-membrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information.

CONCLUSION

For extending the homology concept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs (and a sufficient criterion for complex TMs) in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments.

Mesenchymal transition and dissemination of cancer cells is driven by myeloid-derived suppressor cells infiltrating the primary tumor

In order to metastasize, cancer cells need to acquire a motile phenotype. Previously, development of this phenotype was thought to rely on the acquisition of selected, random mutations and thus would occur late in cancer progression. However, recent studies show that cancer cells disseminate early, implying the existence of a different, faster route to the metastatic motile phenotype. Using a spontaneous murine model of melanoma, we show that a subset of bone marrow-derived immune cells (myeloid-derived suppressor cells or MDSC) preferentially infiltrates the primary tumor and actively promotes cancer cell dissemination by inducing epithelial-mesenchymal transition (EMT). CXCL5 is the main chemokine attracting MDSC to the primary tumor. In vitro assay using purified MDSC showed that TGF-β, EGF, and HGF signaling pathways are all used by MDSC to induce EMT in cancer cells. These findings explain how cancer cells acquire a motile phenotype so early and provide a mechanistic explanation for the long recognized link between inflammation and cancer progression.

Cancer progression has been depicted as a linear process, during which the incipient cancer cell sequentially accumulates mutations that confer the ability to metastasize. However, recent studies show that cancer cells disseminate early, before such mutations can accumulate, implying the existence of a different, faster route to the metastatic phenotype. Using a mouse model of melanoma, we show that the primary tumor attracts a subset of immune cells that actively promote cancer cell motility, dissemination, and metastasis. These tumor-infiltrating immune cells do so by reactivating a cellular program (mesenchymal transition) used by melanocytes during their development to colonize the skin, and also believed to be an essential step in cancer cell dissemination and metastasis. Once the melanoma cells migrate out of the primary tumor, they can lapse back to their original phenotype and lose their migratory potential. This transient phenotypic switch may accelerate carcinogenesis and participate in the plasticity of cancer. It explains how cancer cells might spread to other organs even before the original tumor is detected. In addition to the evidence gleaned from our mouse melanoma model, we show that these immune cells induce typical features of epithelial-mesechymal transition in both melanoma and bladder human cell lines when examined in culture dishes. These findings provide an underlying mechanism for the long-recognized link between inflammation and cancer progression.

Dacarbazine promotes stromal remodeling and lymphocyte infiltration in cutaneous melanoma lesions

Dacarbazine (DTIC) is the standard first-line drug for advanced stage melanoma, but it induces objective clinical responses in only 15% of patients. This study was designed to identify molecular changes specifically induced by treatment in chemo-sensitive lesions. Using global transcriptome analysis and immunohistochemistry, we analyzed cutaneous metastases resected from patients with melanoma before and after DTIC treatment. The treatment induced similar functional changes in different lesions from the same patient. Stromal and immune response-related genes were the most frequently upregulated, particularly in lesions that responded to treatment by stabilizing or regressing. T-cell infiltration and enhanced major histocompatibility complex class II expression were observed in a subset of patients. Stable, chemo-sensitive lesions exhibited activation of genetic programs related to extracellular matrix remodeling, including increased expression of secreted protein acidic and rich in cysteine (SPARC) by tumor cells. These events were associated with local response to treatment and with superior survival in our group of patients. In contrast, SPARC expression was downregulated in lesions resistant to DTIC. Thus, chemotherapy drugs originally selected for their direct cytotoxicity to tumor cells may also influence disease progression by inducing changes in the tumor microenvironment.

Persistent hypocalcaemia in a Chinese girl due to a novel de-novo activating mutation of the calcium-sensing receptor gene

A significant proportion of patients formerly diagnosed with idiopathic hypoparathyroidism actually have activating mutation of the calcium-sensing receptor (CaSR) gene. Awareness of the possibility of activating mutation of CaSR gene in patients with sporadic idiopathic hypoparathyroidism is important because of its relevance to clinical management. This report is of a novel activating mutation of the CaSR gene identified in a 10-year-old Chinese girl who was initially diagnosed as having idiopathic hypoparathyroidism at 6 years of age after presenting with seizures. Her serum calcium level was difficult to maintain near the lower limit of normal despite treatment with high-dose calcitriol. Treatment with calcitriol produced significantly elevated urinary calcium-to-creatinine ratio. Direct sequencing of the CaSR gene showed a novel heterozygous mutation (p.Q735P (c.2204A>C)). Molecular genetic analysis of her parents demonstrated that both parents did not harbour the child's mutation, indicating that her mutation had arisen de novo.

Photoprotective potential of Cordyceps polysaccharides against ultraviolet B radiation-induced DNA damage to human skin cells

BACKGROUND

Ultraviolet (UV) radiation causes DNA damage resulting in photoageing and skin cancer. UVB (290-320 nm) interacts directly with DNA, inducing two major photoproducts: cyclobutane-pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts. Cordyceps sinensis (Berk.) Sacc. is a medicinal fungus with reported anticancer and cytoprotective effects.

OBJECTIVES

To investigate genoprotective effects of polysaccharide-rich Cordyceps mycelial components against UVB-induced damage in normal human fibroblast cells.

METHODS

Cultured human fibroblasts (BJ cells) were treated for 30 min and, separately, for 24 h with hot water extract of Cordyceps fungal mycelia or exopolysaccharides. Cells were washed, irradiated with UVB (302 nm), and immediately lysed, after which DNA damage, as strand breaks, was measured using an enzyme-assisted comet assay that detects CPDs.

RESULTS

DNA damage in UVB-irradiated cells was significantly lowered (P < 0·01) with Cordyceps pretreatment. Similar results were seen with 30 min and 24 h pretreatment. Specifically, and in comparison with irradiated cells with no Cordyceps pretreatment, there was a 27% reduction in CPDs in irradiated cells with 24 h pretreatment with 200 μg mL(-1) of the hot water Cordyceps extract, and a 34% reduction with 24 h pretreatment with 200 μg mL(-1) of the exopolysaccharide extract.

CONCLUSIONS

Clear evidence of protection against UVB-induced CPDs was seen with Cordyceps mycelial extracts. Results indicate that Cordyceps may offer photoprotection and lower the risk of basal cell carcinoma, the main skin cancer caused by CPDs. Further study is needed to identify protective mechanisms.

The Janus-faced E-values of HMMER2: extreme value distribution or logistic function?

E-value guided extrapolation of protein domain annotation from libraries such as Pfam with the HMMER suite is indispensable for hypothesizing about the function of experimentally uncharacterized protein sequences. Since the recent release of HMMER3 does not supersede all functions of HMMER2, the latter will remain relevant for ongoing research as well as for the evaluation of annotations that reside in databases and in the literature. In HMMER2, the E-value is computed from the score via a logistic function or via a domain model-specific extreme value distribution (EVD); the lower of the two is returned as E-value for the domain hit in the query sequence. We find that, for thousands of domain models, this treatment results in switching from the EVD to the statistical model with the logistic function when scores grow (for Pfam release 23, 99% in the global mode and 75% in the fragment mode). If the score corresponding to the breakpoint results in an E-value above a user-defined threshold (e.g. 0.1), a critical score region with conflicting E-values from the logistic function (below the threshold) and from EVD (above the threshold) does exist. Thus, this switch will affect E-value guided annotation decisions in an automated mode. To emphasize, switching in the fragment mode is of no practical relevance since it occurs only at E-values far below 0.1. Unfortunately, a critical score region does exist for 185 domain models in the hmmpfam and 1,748 domain models in the hmmsearch global-search mode. For 145 out the respective 185 models, the critical score region is indeed populated by actual sequences. In total, 24.4% of their hits have a logistic function-derived E-value < 0.1 when the EVD provides an E-value > 0.1. We provide examples of false annotations and critically discuss the appropriateness of a logistic function as alternative to the EVD.

RYR1-related central core myopathy in a Chinese adolescent boy

Central core myopathy is a rare, inherited neuromuscular disorder with a wide spectrum of phenotypic presentations. It is also considered an allelic disease of malignant hyperthermia. We report a case of central core myopathy in a Chinese adolescent boy presenting with atypical clinical features and a moderately elevated serum creatine kinase level. The diagnosis was made from the histopathological findings of central cores on muscle biopsy, and confirmed by the molecular genetic testing for the RYR1 gene mutation. This is the first case of central core myopathy confirmed by molecular study in our locality.

Arxes: retrotransposed genes required for adipogenesis

Retrotransposed sequences arise from messenger RNAs (mRNAs) that have been reinserted into genomic DNA by reverse transcription. Usually, these sequences are embedded in dormant regions, collect missense mutations over time and constitute processed, nonfunctional pseudogenes. There are thousands of processed pseudogenes in the mouse and human genome. Here, we report evidence for two paralog genes (termed Arxes1 and Arxes2), which arose by retrotransposition of the signal peptidase Spcs3 followed by a segmental duplication event. They gained a functional promoter that we show to be transactivated by adipogenic transcription factors. We further show that the Arxes mRNAs are highly expressed in adipose tissue and strongly upregulated during adipogenesis in different cell models. Additionally, their expression is elevated by an anti-diabetic agent in vitro and in vivo. Importantly, we provide evidence that the Arxes genes are translated and that the proteins are located in the endoplasmic reticulum. Although the sequence similarity and subcellular location are reminiscent of their parental gene, our data suggest that the Arxes have developed a different function, since their expression is required for adipogenesis, whereas Spcs3 is dispensable. In summary, we report retrotransposed-duplicated genes that evolved from a parental gene to function in a tissue and adipogenesis-specific context.

Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ

We have developed a method for reconstructing gene association networks and have applied this method to gene profiles from 3T3-L1 cells. Priorization of the candidate genes pinpointed a transcript annotated as APMAP (adipocyte plasma membrane-associated protein). Functional studies showed that APMAP is upregulated in murine and human adipogenic cell models as well as in a genetic mouse model of obesity. Silencing APMAP in 3T3-L1 cells strongly impaired the differentiation into adipocytes. Moreover, APMAP expression was strongly induced by the PPARγ ligand rosiglitazone in adipocytes in vitro and in vivo in adipose tissue. Using ChIP-qPCR and luciferase reporter assays, we show a functional PPARγ binding site. In addition, we provide evidence that the extracellular C-terminal domain of APMAP is required for the function of APMAP in adipocyte differentiation. Finally, we demonstrate that APMAP translocates from the endoplasmatic reticulum to the plasma membrane during adipocyte differentiation.

More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology

Large-scale genome sequencing gained general importance for life science because functional annotation of otherwise experimentally uncharacterized sequences is made possible by the theory of biomolecular sequence homology. Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. Having the same fold imposes strict conditions over the packing in the hydrophobic core requiring similarity of hydrophobic patterns. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal peptides (SPs) where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Thus, matching of SPs/TMs creates the illusion of matching hydrophobic cores. Therefore, inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809) contain SP/TM regions. As expected, fragment-mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, we show explicit examples that the scores of clearly false-positive hits, even in global-mode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, we find that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false-positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. We suggest a workflow of flagging problematic hits arising from SP/TM-containing models for critical reconsideration by annotation users.

Sequence homology is a fundamental principle of biology. It implies common phylogenetic ancestry of genes and, subsequently, similarity of their protein products with regard to amino acid sequence, three-dimensional structure and molecular and cellular function. Originally an esoteric concept, homology with the proxy of sequence similarity is used to justify the transfer of functional annotation from well-studied protein examples to new sequences. Yet, functional annotation via sequence similarity seems to have hit a plateau in recent years since relentless annotation transfer led to error propagation across sequence databases; thus, leading experimental follow-up work astray. It must be emphasized that the trinity of sequence, 3D structural and functional similarity has only been proven for globular segments of proteins. For non-globular regions, similarity of sequence is not necessarily a result of divergent evolution from a common ancestor but the consequence of amino acid sequence bias. In our investigation, we found that protein domain databases contain many domain models with transmembrane regions and signal peptides, non-globular segments of proteins having hydrophobic bias. Many proteins have inherited completely wrong function assignments from these domain models. We fear that future function predictions will turn out futile if this issue is not immediately addressed.

Identification of novel functional differences in monocyte subsets using proteomic and transcriptomic methods

Human blood monocytes can be broadly divided into two distinct subsets: CD14+CD16- and CD14+/lowCD16+ subsets. Perturbation in their proportions in the blood has been observed in several disease conditions. Although numerous phenotypic and functional differences between the two subsets have already been described, the roles contributed by each subset during homeostasis or disease conditions are still largely unclear. To uncover novel differences to aid in elucidating their functions, we perform a global analysis of the two subsets utilizing both proteomics and transcriptomics approaches. From the proteomics and transcriptomics data, the expression of 613 genes by the two subsets is detected at both the protein and mRNA levels. These 613 genes are assessed for up-regulation in each subset at the protein and mRNA levels using a cutoff fold change of > or =|1.5| between subsets. Proteins and mRNAs up-regulated in each subset are then mapped in silico into biological functions. This mapping reveals copious functional differences between the subsets, many of which are seen at both protein and mRNA levels. For instance, expression of genes involved in F(CY) receptor-mediated phagocytosis are up-regulated in the CD14+/lowCD16+ subset, while those involved in antimicrobial function are up-regulated in the CD14+CD16- subset. We uncover novel functional differences between the monocyte subsets from differences in gene expression at the protein and mRNA levels. These functional differences would provide new insights into the different roles of the two monocyte subsets in regulating innate and adaptive immune responses.

R-POPTVR: a novel reinforcement-based POPTVR fuzzy neural network for pattern classification

In general, a fuzzy neural network (FNN) is characterized by its learning algorithm and its linguistic knowledge representation. However, it does not necessarily interact with its environment when the training data is assumed to be an accurate description of the environment under consideration. In interactive problems, it would be more appropriate for an agent to learn from its own experience through interactions with the environment, i.e., reinforcement learning. In this paper, three clustering algorithms are developed based on the reinforcement learning paradigm. This allows a more accurate description of the clusters as the clustering process is influenced by the reinforcement signal. They are the REINFORCE clustering technique I (RCT-I), the REINFORCE clustering technique II (RCT-II), and the episodic REINFORCE clustering technique (ERCT). The integrations of the RCT-I, the RCT-II, and the ERCT within the pseudo-outer product truth value restriction (POPTVR), which is a fuzzy neural network integrated with the truth restriction value (TVR) inference scheme in its five layered feedforward neural network, form the RPOPTVR-I, the RPOPTVR-II, and the ERPOPTVR, respectively. The Iris, Phoneme, and Spiral data sets are used for benchmarking. For both Iris and Phoneme data, the RPOPTVR is able to yield better classification results which are higher than the original POPTVR and the modified POPTVR over the three test trials. For the Spiral data set, the RPOPTVR-II is able to outperform the others by at least a margin of 5.8% over multiple test trials. The three reinforcement-based clustering techniques applied to the POPTVR network are able to exhibit the trial-and-error search characteristic that yields higher qualitative performance.

Charcot foot in a Hong Kong Chinese diabetic population

OBJECTIVES

To delineate the epidemiology of Charcot foot in Hong Kong Chinese diabetic patients, and to provide baseline data for benchmarking the clinic service for this special group of patients.

DESIGN

Retrospective cohort study.

SETTING

Regional hospital, Hong Kong.

PATIENTS

Diabetic patients with Charcot foot and age- and sex-matched diabetic foot clinic attendees between 1995 and 2007.

MAIN OUTCOME MEASURES

Clinical presentations were compared in patients with Charcot foot and the controls.

RESULTS

Twenty-five patients were diagnosed with Charcot foot over 12 years; 60% were male. At the time of diagnosis, the mean age was 59 (standard deviation, 14; range, 38-85) years, with diabetes being diagnosed for a mean of 11 (standard deviation, 8; range, 0-30) years. Retinopathy was noted in 36% (n=9) and nephropathy in 20% (n=5) of the Charcot foot patients. No patient had peripheral vascular disease. This finding was statistically significant. Delayed presentation occurred in 11 patients. Presentation was usually unilateral. In the minority (n=3, 12%) with bilateral involvement, presentation was sequential. Charcot arthropathy affected the mid-foot in 64% of the patients. Superimposed infection was common (61%). Recurrent ulceration occurred in 11%, all of whom presented late. Only one patient underwent major amputation, but the 5-year mortality of Charcot foot patients could be up to 33%.

CONCLUSION

Charcot foot was uncommon in this population. Late presentation was common and might be related to superimposed infection; such patients were prone to recurrent ulcers.

Magnetic resonance imaging for ureteral fibroepithelial polyp

Ureteric tumours are rare and most of them are malignant. Of benign tumours, ureteral fibroepithelial polyps are the most common but are still considered clinical rarities. In the past, most benign ureteric tumours were only diagnosed after surgical removal. With technological advance, magnetic resonance imaging has become an effective means of assessing ureteric lesions. Non-contrast enhanced magnetic resonance urography can produce an image comparable to an intravenous urogram without use of intravenous water-soluble contrast. A polyp can be diagnosed on imaging if there is an elongated filling defect inside the ureter. Nevertheless, a definitive diagnosis relies on ureteroscopic examination with biopsy. When a non-obstructive polyp is being managed conservatively, imaging is helpful for monitoring. Equally, the information obtained from imaging can be used to plan operative treatment.

On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation

Background

The original spotted array technology with competitive hybridization of two experimental samples and measuring relative expression levels is increasingly displaced by more accurate platforms that allow determining absolute expression values for a single sample (for example, Affymetrix GeneChip and Illumina BeadChip). Unfortunately, cross-platform comparisons show a disappointingly low concordance between lists of regulated genes between the latter two platforms.

Results

Whereas expression values determined with a single Affymetrix GeneChip represent single measurements, the expression results obtained with Illumina BeadChip are essentially statistical means from several dozens of identical probes. In the case of multiple technical replicates, the data require, therefore, different stistical treatment depending on the platform. The key is the computation of the squared standard deviation within replicates in the case of the Illumina data as weighted mean of the square of the standard deviations of the individual experiments. With an Illumina spike experiment, we demonstrate dramatically improved significance of spiked genes over all relevant concentration ranges. The re-evaluation of two published Illumina datasets (membrane type-1 matrix metalloproteinase expression in mammary epithelial cells by Golubkov et al. Cancer Research (2006) 66, 10460; spermatogenesis in normal and teratozoospermic men, Platts et al. Human Molecular Genetics (2007) 16, 763) significantly identified more biologically relevant genes as transcriptionally regulated targets and, thus, additional biological pathways involved.

Conclusion

The results in this work show that it is important to process Illumina BeadChip data in a modified statistical procedure and to compute the standard deviation in experiments with technical replicates from the standard errors of individual BeadChips. This change leads also to an improved concordance with Affymetrix GeneChip results as the spermatogenesis dataset re-evaluation demonstrates.

Reviewers

This article was reviewed by I. King Jordan, Mark J. Dunning and Shamil Sunyaev.

Limb salvage in extensive diabetic foot ulceration: an extended study using a herbal supplement

OBJECTIVE

To further study the clinical value of a herbal supplement in the treatment of chronic foot ulcers in diabetic patients.

DESIGN

Double-blind randomised, placebo-control trial.

SETTING

Two general hospitals in Hong Kong.

PATIENTS

Eighty patients were recruited according to strict selection criteria.

INTERVENTIONS

Clinical measures included standard antidiabetic treatment, daily wound care including antiseptic bath, debridement, toe removal for gangrene when necessary, and the daily consumption of a herbal drink or placebo.

MAIN OUTCOME MEASURES

The primary outcome was limb salvage. Secondary outcomes included: granulation maturation, local temperature and circulatory changes, tumour necrosis factor-alpha levels, and adverse events.

RESULTS

Limb salvage was achieved in 85% of the patients. Among the early failures, three each came from the treatment and placebo groups. After shifting to herbal treatment (without unblinding of the original treatment), all were rescued in those initially assigned to herbal concoction (6 out of 6) while only 50% (6 out of 12) were rescued from among those initially assigned to placebo. The speed of granulation maturation, and decline in tumour necrosis factor-alpha levels indicating control of inflammation, were also more favourable with the herbal group. No serious adverse events were observed.

CONCLUSION

The herbal adjuvant therapy was effective in helping the healing of chronic diabetic ulcers.

Seasonal variations in non-traumatic major lower limb amputation in Hong Kong Chinese diabetic patients

OBJECTIVES

To study the relationship between hospitalisation for diabetic foot complications, non-traumatic major lower limb amputations, and seasonal variation in humidity and temperature.

DESIGN

Retrospective study.

SETTING

Regional hospital, Hong Kong.

PATIENTS

Diabetic patients hospitalised for lower limbs infection during the inclusive period 1995 to 2004.

MAIN OUTCOME MEASURES

Monthly incidence of admissions for diabetic foot sepsis and non-traumatic non-neoplastic major lower limb amputations correlated with the monthly average humidity and temperature.

RESULTS

During the study period, a total of 770 patients contributed to 1285 episodes of hospitalisation and ensued 208 corresponding major lower limb amputations. Poisson regression study showed that the monthly incidences of hospitalisation as well as amputations were related to the monthly average temperature (P<0.001 and =0.0012, respectively) but not the monthly average humidity (P=0.1560 and 0.6332, respectively).

CONCLUSION

The warm and humid weather of Hong Kong exerts a seasonal variation on the diabetic foot infection presentations. Warm temperature aggravates the severity of infection and precipitates amputation. More intensive patient education and clustering of medical services in late winter and spring might reduce the incidence of diabetic foot amputation, which is a preventable complication.