HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies. The method  is advantageous since Hi-C libraries are extremely complex and even with current high-throughput technologies often only a small proportion of a Hi-C library is sequenced. Selecting for di-tags in this way makes it possible to gain a more complete and higher resolution contact profile for loci of interest.A recent variation of the protocol involves enriching Hi-C libraries for di-tags in which one or both reads align to pre-selected regions of a genomeReaching valid conclusions regarding genomic interactions requires Hi-C data to be mapped unconventionally (described below) as compared with most paired-end experiments. Following this, artefacts inherent to the Hi-C protocol should be removed. To meet these demands we developed HiCUP, an easy-to-use Hi-C bioinformatics pipeline which has few dependencies and is coded in Perl. HiCUP produces a detailed quality control (QC) report in an interactive HTML format, enabling the user easily to assess the quality of a library and how the experimental protocol may be improved in the future. HiCUP was designed for mapping Hi-C data and removing artefacts. It does not perform the normalisation and statistical tests needed to interpret Hi-C experiments, rather it is intended as the starting point of processing Hi-C datasets and should be used in conjunction with other Hi-C pipelines.5, which is used to generate renormalised contact maps by correcting for pre-determined systematic biases, such as the GC content around the Hi-C ligation junction. Similarly, HiC-Lib6 comprises a set of Python scripts for drawing corrected contact heatmaps, only this technique uses an iterative correction algorithm so that potential biases do not need to be identified prior to processing. Homer7 also creates iteratively corrected heatmaps and includes extra features, such as scripts to identify topologically-associated domains (TADs). In addition, Fit-Hi-C8 takes renormalized data to identify mid-range intra-chromosomal interactions; and GOTHiC9, a Bioconductor package, performs a cumulative binomial test to identify contacts between distal genomic loci that have significantly more reads than expected by chance. Finally, CHiCAGO10 is an open-source R package for interaction detection in CHi-C datasets. Many of the existing tools — including CHiCAGO, Hicpipe, Homer and GOTHiC — can take the output of HiCUP as input for the analyses they perform.There are numerous packages available to perform different steps in the analysis of Hi-C data. These include HicpipeHiCUP takes paired-end FASTQ files along with a FASTA reference genome and associated aligner indices and then reports valid di-tags in BAM/SAM format.Mapping: The first stage in the HiCUP pipeline involves truncating reads at the modified restriction site (if present) that separates two DNA fragments. The rationale for this step is similar to that responsible for adapter trimming, namely to remove bases that would otherwise prevent a read mapping to the specified reference genome. After truncation, the resulting trimmed read sent for alignment should, in theory, represent a contiguous genomic sequence derived from a single restriction fragment (i.e. not a hybrid sequence comprising more than one restriction fragment).11 or Bowtie 212 to map Hi-C di-tags, allowing only unique high-quality alignments. Since valid Hi-C reads do not represent one continuous genomic sequence, the pipeline maps forward and reverse reads independently and then re-pairs sequences in which both ends aligned unambiguously to the genome.HiCUP uses BowtieFiltering: HiCUP removes sequences representing experimental Hi-C artefacts and other uninformative di-tags, which is important since even a small number of invalid di-tags could lead to incorrect conclusions being drawn concerning genomic structure. HiCUP identifies and removes such sequences by positioning putative di-tags on anin silico digestion of the reference genome. The processes by which these artefacts are generated experimentally, and how HiCUP identifies them, are described below.Re-ligation of adjacent restriction fragments. The Hi-C protocol does not prevent entirely two adjacent restriction fragments re-ligating, but HiCUP discards such di-tags since they provide no useful three-dimensional proximity information. Similarly, multiple fragments could re-ligate forming a contig, but here paired reads will not map to adjacent genomic restriction fragments (agments . FurtherHiCUP takes the expected size range of the sample (which is predetermined by a di-tag length selection step during library construction) and identifies di-tags in which reads, when mapped to the genome, are separated by a distance falling within the size-selection range. Such di-tags are assumed to comprise a contig spanning several restriction cut sites, and so are discarded.Paired reads mapping to the same restriction fragment. Read pairs mapping to the same restriction fragment do not describe three-dimensional contacts and therefore should be discarded. A mechanism for generating such aberrant species is when fragments circularise by ligating to themselves and then, following sonication, form linear molecules possessing a valid Hi-C junction. Indeed, inadequate cross-linking can make this problem worse, increasing the frequency with which individual restriction fragments become separated and are therefore unable to ligate to other DNA molecules13. These artefacts are identifiable because the read pairs that map to the same genomic restriction fragment are orientated away from each other when aligned to the reference genome . Reads not beginning exactly at a cut site are removed. Furthermore, to be considered valid a di-tag should have been generated by blunt-ended ligation between fragment ends created by the first restriction enzyme used in the protocol.PCR duplicates. Considering the huge number of theoretical pairwise interactions, it is likely that observed duplicate di-tags are the result of PCR amplification13 (as demonstrated in the Results section). These duplicates will unduly strengthen the case for a given genomic interaction and therefore HiCUP removes all but one representative copy of the di-tag  with Perl (tested using v5.10.1) installed. The pipeline requires a functional version of Bowtie (tested using v1.1.0) or Bowtie 2 (tested using v2.2.5) for mapping reads to a specified reference genome. Compression of SAM files to BAM format requires SAMtools (v0.1.18 or later). HiCUP may also compress or decompress files using gzip (tested using v1.3.12). For full functionality HiCUP requires the statistical programming language R (tested using v3.1.2). We recommend each file processed in parallel is allocated at least 5GB RAM.The main body of the pipeline consists of four Perl scripts each performing a specific task. The first stage is the truncation step in which the putative Hi-C ligation junction is identified and reads are cut at this point. The second stage involves mapping reads independently and then pairing each read with its counterpart. The third stage filters out di-tags that are Hi-C artefacts, and the final de-duplication step involves removing identical di-tags. There is also a HiCUP master script that regulates data flow and executes each step of the pipeline .2, except that all four barcode adapters were mixed at equimolar ratios in the ligation reaction. The two technical replicates named here as Sample 1 (European Nucleotide Archive accession SAMEA2421737) and Sample 2 (European Nucleotide Archive accession SAMEA2421733) were CHi-C libraries of foetal liver cells from mouse (strain C57BL/6) embryos at day 14.5 of development.As discussed previously, the final stage of HiCUP removes — retaining one copy — duplicate di-tags from the dataset. When considering the theoretical number of di-tags that may be generated it is reasonable to assume that exact duplicates are the result of PCR amplification and do not represent independent Hi-C ligation events. We addressed whether this assumption is valid with an experiment in which one of four barcode adapters were ligated randomly to both ends of a di-tag. We followed our standard Capture Hi-C protocolAssuming equal numbers of each barcode, all 16 barcode-barcode permutations should occur with equal frequency. Crucially, the barcodes are incorporated into the di-tags before PCR amplification, providing a test for the origin of the duplicates: those representing independent Hi-C events are most likely to possess differing barcodes , whereasThe two independent libraries were sequenced and the resulting FASTQ reads were classified by barcode i.e. the first four base pairs of the polynucleotide. The reads were mapped and filtered with HiCUP, but duplicates were retained. The barcode sequences were then quantified revealing that 71.3% corresponded to a pre-defined sequence in Sample 1 and 71.5% in Sample 2. Each valid barcode was then quantified. For both samples the barcode CCTT was most prevalent , and for both samples the barcode CGCT was the least common .bone fide initial Hi-C interaction events.Despite the deviation from the ideal and expected result in which all barcode combination frequencies were equal, it was still possible to address the source of duplicate di-tags. To achieve this, the barcode combination of each duplicate was recorded. Duplicates arising from PCR amplification should have had identical barcode combinations, in contrast toTo assess the impact of retaining duplicate di-tags we detected significant interactions in HiCUP-processed CHi-C datasets using the CHiCAGO pipeline . The analysis showed that removing duplicate di-tags substantially reduced the number of called significant interactions see. This wa14, and that only a small number of observed fragment-fragment contacts are needed to qualify an interaction as statistically significant, retaining PCR duplicates will lead to an erroneous interpretation of the data. Furthermore, this over-calling of significant interactions becomes more problematic as the proportion of duplicate di-tags increases.Consequently, when considering that PCR results in certain di-tags being amplified disproportionatelyCaulobacter crescentus (SRR824843)15; human refers toHomo sapiens (SRR027963)1; fruit fly refers toDrosophila melanogaster (SRR389762)16 and yeast was a strain ofSchizosaccharomyces pombe (SRR1271321)17.HiCUP was used to process several Hi-C datasets available on public repositories.The table shows key statistics produced by HiCUP when processing Hi-C datasets. All the samples except Fruit Fly (in which the protocol did not include the fill-in/blunt-ended ligation step) show an appreciable percentage of truncated reads, meaning that the Hi-C ligation junction sequence was identified. Failure to detect the ligation junction sequence after following a standard Hi-C protocol provides a first indication that the Hi-C library is of poor quality. The samples mapped with variable efficiency to their respective reference genomes and the percentage of valid di-tags also varied considerably, but the yeast sample is particularly noticeable in returning a high proportion of internal fragments. This may be the result of additional technical difficulties in generating Hi-C libraries from yeast cells, requiring certain areas of the protocol to be further refined for reasons discussed previously.13. The summary statistics also include the proportion oftrans  interactions tocis  interactions. A hightrans/cis ratio is indicative of a poor library, since spurious ligation events will tend to be between genomic loci on different chromosomes18.HiCUP is software tailored for processing Hi-C data and has been publicly available for several years. HiCUP maps sequence data in a manner optimised for the Hi-C protocol and then removes commonly encountered experimental artefacts which could otherwise lead to incorrect inferences being made about the conformation of a genome. Furthermore, HiCUP provides statistics summarising each stage of the pipeline which may help in refining the experimental protocol. For example, a high proportion of circularised di-tags suggests inadequate cross-linking, whereas a high proportion of dangling ends implies the chewback step to remove biotin from unligated restriction fragments was inefficient4, Homer19 and Hicpipe18. One recent study used HiCUP-processed Hi-C data to shed light on how GWAS SNPs found in genome deserts may modulate gene activity20. Another publication characterised architectural changes in genome organisation in age-related cellular senescence19. HiCUP was also used in a study to compare the efficiency of two different Hi-C protocols18. Finally, four other research articles pioneered targeted Hi-C capture techniques, enriching for gene promoter-containing fragments to elucidate regulatory networks in mice21 and humans3. In addition to these studies, HiCUP is being used to process data in numerous ongoing projects and is under active development to meet the demands of the burgeoning fields of Hi-C and CHi-C in furthering our understanding of three-dimensional genomic structure, organisation and regulation.HiCUP is flexible, allowing the user to specify numerous parameters and the final output is in the commonly used BAM/SAM format: which is compatible with, or may be converted to a format compatible with a myriad of analysis tools. Indeed, HiCUP has already been used to process and analyse Hi-C and CHi-C data in conjunction with GOTHiC1. www.bioinformatics.babraham.ac.uk/projects/hicupURL link to where the software can be downloaded from or used by a non-coder:2. www.bioinformatics.babraham.ac.uk/projects/hicupURL link to the author’s version control system repository containing the source code:3. http://dx.doi.org/10.5281/zenodo.3338822Archived source code as at time of publication:4. Software license: GNU GPL v3 or later. How does the pipeline handle the case of restriction sites that are very close to the beginning of a read? Is there a minimum size for a truncated read to be included in the analysis?The “Relegation of adjacent restriction fragments” section is not completely clear to me. Fragment nr. 4 in Figure 2b could be quite large and removing fragments which include 2 restriction sizes  might remove true events corresponding to local looping of the DNA. Is there any experimental evidence that such fragments are predominantly artifacts of re-ligation or incomplete digestion and should be excluded? Or are the authors using the theoretical length of the Hi-C insert to inform this type of filtering? A more explicit description of size-selection would be beneficial here.The authors present evidence that duplicate di-tags are PCR artifacts. This is in true for the standard Hi-C protocol, which from what I can see, was used to generate the datasets described in the result section. Because the HiCUP pipeline has been developed to handle the double-digestion protocol as well, could the author comment about duplicate di-tags and PCR artifacts in this context? With a double digestion protocol, the probability of truly obtaining the same fragment multiple times is much higher because the DNA is cut at fixed locations (as opposed to randomly via sonication).The pipeline removes fragments with insert size less than expected by size selection. Structural variation (e.g. deletions) could yield di-tags with larger than expected theoretical insert size. Such di-tags would be valid and informative. Either an exploration or discussion of how structural variation affects this filtering step would be be helpful.The percentages reported in Table 3 are difficult to interpret and compare. They clearly do not sum to 100%, so the authors should provide a more detailed description of what each percentage corresponds to .The authors describe a novel pipeline for mapping and littering of Hi-C data and demonstrate evidence that duplicate di-tags are PCR artifacts. This pipeline has already been successfully used in several studies. Following is a list of questions and comments that should be addressed by the authors to improve the clarity of their manuscript.I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. This manuscript by Wingett and collaborators describes HiCUP, a pre-processing pipeline for Hi-C data. The pipeline is designed as an executable command-line tool that includes the most common pre-processing steps for Hi-C datasets, including read truncation and mapping, filtering, assignment of read to restriction fragments, detection and removal of PCR duplicates and generation of quality evaluation plots. The pipeline is solid and well implemented. We have downloaded and tested the current version of the pipeline using one of our locally produced Hi-C datasets, and the filtering results of the pipeline are equivalent to our locally implemented pre-processing pipelines. Therefore, we are happy with the implementation of the software and have no major concerns with the manuscript.Table 1It would be useful to include a further column that would display the % calculated against the total number of di-tags per sample. This would allow the user to quickly determine the overall amount of PCR-duplicates included in the library.HTML reportingGiven that the tool is aimed to provide the user with an easy way to highlight errors with Hi-C libraries, it would be useful to implement the following in the HTML report:- include a clearer description of how the cutoff for reads that are “too short to map” is chosen, and indicate if this can be changed by the user- include labelling to indicate what part of the reporting corresponds to the “read” level and what corresponds to the “pairs” level.et al., (2013)1. This is already calculated by the pipeline, but the representation of the data will help the user to determine whether the library has specific issues with under-digestions or ligation artefacts.- include a plot with the inwards/outwards bias as function of distance from restriction fragment as proposed by JinScreenshotsThe manuscript could include some screenshots of the reporting output to guide the user through it and to highlight what are the key indicators of good/bad quality datasets (some of these could even be obtained using simulated datasets with specific biases). This can also be provided as a guided example in the online documentation of the pipeline.Ratio trans/cis interactionsThe manuscript states that “A high trans/cis ratio is indicative of a poor library, since spurious ligation events will tend to be between genomic loci on different chromosomes [ref 18]”.While we agree that this is a possible interpretation of that scenario, it should be noted that the trans/cis ratio depends on the genome’s size and the number of chromosomes that each species has, and it might also be related with specific higher-order chromatin conformations, or depend on the specific Hi-C protocol used in that experiment. Therefore, the authors might not want to generalise the interpretation of the high trans/cis ratio, or, at least, give more specific guidance regarding the interpretation of this ratio. For example, the four datasets included in this manuscript would produce trans/cis ratios of 0, 0.18, 0.52 and 1.18 for bacteria, yeast, fly and human, respectively, which in this case correlate with the genome size and the number of chromosomes in each species, but that are not necessarily indicative of the quality of these datasets.Implementation and code availabilityRun on a sample of one of our locally produced Hi-C data sets (12 million paired reads), the HiCUP pipeline finishes in a reasonable amount of time .The configuration file could be very convenient, but required some copy-pasting of file paths. Regarding this, it is unclear why R can be automatically detected, but the full path of bowtie2 has to be specified. In addition, it might be convenient to also add the HiCUP_digester step of the pipeline to the main HiCUP executableThe link to the software package was identical to the version control system link, and it was not straightforward to find the link to the self-hosted bug report system. We think that having the ability to review code online, file bug reports, and contribute to the package using a more generally used online repository (such as GitHub) would make HiCUP even more useful.We only have a few minor comments that we hope will help the authors to improve the software.We have read this submission. We believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. et al. which is a single step of matrix balancing.Even though mentioned as out of scope, it would still be useful to have a simple normalization method implemented with HiCUP. Maybe as simple as "vanilla coverage normalization" mentioned in RaoAnother useful feature would be to have HiCUP generate an HTML report that basically links together all different figures created by the pipeline. I wrote such scripts to generate an HTML for my local HiCUP installation."Fit-Hi-C takes renormalized data to identify mid-range intra-chromosomal interactions" --> "Fit-Hi-C takes normalized data to identify statistically significant intra-chromosomal interactions".If possible, modify Figure 2F to reflect that one copy of the duplicates is valid and others are discarded.Sequence variation between sample and the reference can be in the form of copy number changes or other aberrations. It should be noted that HiCUP does assume these do not happen.In "Operation", put the names of scripts in parentheses where they are described.In Figure 3, indicate in which steps the restriction cut site information is used .In "Results", mention explicitly that they hold for the analyzed case where sonication is the choice instead of a second digestion with a restriction enzyme. It may be the case that a substantial part of duplicates are not PCR related for the latter case where the theoretical number of di-tags is limited compared to sonication.In Table 3, use horizontal lines to demarcate where one step ends and the other starts. Otherwise, it is difficult to understand what each percentage is out of.This article describes the HiCUP pipeline that has already been used by many for mapping and initial processing of Hi-C data. HiCUP is a useful tool for processing both traditional Hi-C data and more recent Capture Hi-C data. The article clearly describes what HiCUP does and what it does not. It also provides a nice study on the origin of duplicated di-tags showing that nearly all such duplicates are due to PCR amplification. Other than my few comments below, I am happy with the article and want to note that I have successfully downloaded and used HiCUP pipeline to process number of different Hi-C data sets.I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.


We argue that most existing bibliometric indicators are inconsistent, biased, and, worst of all, susceptible to manipulation. Here, we pursue a principled approach to the development of an indicator to quantify the scientific impact of both individual researchers and research institutions grounded on the functional form of the distribution of the asymptotic number of citations. We validate our approach using the publication records of 1,283 researchers from seven scientific and engineering disciplines and the chemistry departments at the 106 U.S. research institutions classified as “very high research activity”. Our approach has three distinct advantages. First, it accurately captures the overall scientific impact of researchers at all career stages, as measured by asymptotic citation counts. Second, unlike other measures, our indicator is resistant to manipulation and rewards publication quality over quantity. Third, our approach captures the time-evolution of the scientific impact of research institutions.How to quantify the impact of a researcher’s or an institution’s body of work is a matter of increasing importance to scientists, funding agencies, and hiring committees. The use of bibliometric indicators, such as the  The explosive growth in the number of scientific journals and publications has outstripped researchers’ ability to evaluate them . To chooScience Citation Index (SCI) in 1963 [h-index [h-index include its dependence on discipline and on career length [The introduction of the  in 1963  and the [h-index . However[h-index –15. For r length .g-index [R-index [ch-index [ad-hoc heuristics, lacking insight about why or how scientific publications accumulate citations.In recent years, researchers have proposed a veritable alphabet soup of “new” metrics—the g-index , the R-i[R-index , the ch-ch-index , among oextremely susceptible to manipulation. For example, inflating the findings of a publication in the abstract can lead to misleading press reports [The onslaught of dubious indicators based on citation counts has spurred a backlash and the introduction of so-called “altmetric” indicators of scientific performance. These new indicators completely disregard citations, considering instead such quantities as number of article downloads or article views, and number of “shares” on diverse social platforms –22. Unfo reports , and jou reports .Citations are the currency of scientific research. In theory, they are used by researchers to recognize prior work that was crucial to the study being reported. However, citations are also used to make the research message more persuasive, to refute previous work, or to align with a given field . To compIt behooves us to develop a measure that is based on a thorough understanding of the citation accumulation process and also grounded on a rigorous statistical validation. Some researchers have taken some steps in this direction. Examples include the ranking of researchers using PageRank  or the bOne crucial aspect of the process of citation accumulation is that it takes a long time to reach a steady state . This reManually disambiguated citation data pertaining to researchers at the top United States (U.S.) research institutions across seven disciplines : chemicaCitation data from the chemistry departments of 106 U.S. institutions classified as “very high research activity”.Here, we depart from previous efforts by developing a principled approach to the quantification of scientific impact. Specifically, we demonstrate that the distribution of the asymptotic number of accumulated citations to publications by a researcher or from a research institution is consistent with a discrete lognormal model , 38. We Significantly, our findings enable us to develop a measure of scientific impact with desirable properties.We perform our first set of analyses on the dataset described by Duch et al. . This daWe perform our second set of analyses on the publication records of the chemistry departments at the top U.S. research institutions according to . Using tIn our analyses we distinguish between “primary” publications, which report original research findings, and “secondary” publications, which analyze, promote or compile research published elsewhere. We identify as primary publications those classified by WoS as “Article”, “Letter”, or “Note” and identify all other publications types as secondary publications.Moreover, to ensure that we have enough statistical power to determine the significance of the model fits, we restrict our analysis to researchers with at least 50 primary research publications. These restrictions reduce the size of the researchers dataset to 1,283 researchers and 148,878 publications. All 106 departments in our dataset have a total of more than 50 primary research publications.n(t) of citations to publications published in a given journal in a given year converges to a stationary functional form after about ten years [na to the publications of an individual researcher as well as the set of all researchers in a department at a research institution.Prior research suggests that a lognormal distribution can be used to approximate the steady-state citation profile of a researcher’s aggregated publications , 41. Stren years . This reen years  which isna is a function of a latent variable ψ representing a publication’s “citability” [ψ results from the interplay of several, possibly independent, variables such as timeliness of the work, originality of approach, strength of conclusion, reputation of authors and journals, and potential for generalization to other disciplines, just to name a few [ψ will be a Gaussian variable, ψ ∈ N, where μa and σa are respectively the mean and standard deviation of the citability of the publications by researcher a. Therefore, the impact of a researcher’s body of work is described by a distribution characterized by just two parameters, μ and σ. Similarly, because in the U.S. departments hire faculty based on their estimated quality, the researchers associated with a department will presumably be similar in stature or potential.We hypothesize that ability” . The citme a few , 45. In ψ are neither easily observable nor easy to quantify. Moreover, mapping ψ into citations is not a trivial matter. Citation counts span many orders of magnitude, with the most highly cited publications having tens of thousands of citations [h-index has a power-law dependence on the number of publications Np of a researcher [na. In effect, we take na to be the result of a multiplicative process of the same variables determining ψ. Thus, we can calculate the probability pdln(na) that a researcher or department will have a primary research publication with na citations, as an integral over ψ:Unlike citations, which are observable and quantifiable, the variables contributing to itations . Large-sitations . Citatiosearcher . Here, wfs is the fraction of secondary publications in a body of work and ps(na|θ) represents the probability distribution, characterized by parameters θ and not necessarily lognormal, of na for secondary research publications. We found that in practice δ is the Kronecker delta. Surprisingly, we found that μ′ ≈ μ and σ′ ≈ σ, suggesting that secondary publications have citation characteristics that are significantly different from those of primary publications.Most researchers also communicate their ideas to their peers via secondary publications such as conference proceedings which, in many disciplines, are mainly intended to promote related work published elsewhere. Some secondary publications will have significant timeliness, in particular review papers and editorial materials, and therefore will likely be cited too. Most of them, however, will not be cited at all. If accounting for secondary publications, χ2 goodness-of-fit test with re-sampling [μ and σ provides an accurate description of the distribution of the asymptotic number of citations for a researcher’s body of work and for the publications from an academic department.sampling , we findτKendall = 0.62, p = 0.069) between the median value of orted in  we find scipline . This con factor , 31, 49.fs, for all the researchers. We find that nearly a fourth of the publications of half of all researchers are secondary, but intra-discipline variation is high. Inter-discipline variability is also high: 17% of the publications of a typical researcher in chemistry are secondary, whereas 60% of the publications of a typical researcher in industrial engineering are secondary.We also plot the fraction of secondary publications, Np, both at the individual level—testing the effect of sample size—and at the discipline level—testing overall dependence on Np. To test for sample size dependence, we fit the model to subsets of a researcher’s publication list. We find that estimates of σ are more sensitive to sample size than estimates of μ (Np ≥ 50).We next investigate the dependence of the parameter estimates on number of publications, tes of μ  Figs. HoNp. We find no statistically significant correlation, except for a very weak dependence  of Np for chemical engineering . In order to make sense of this comparison, we must note a few aspects about the data. The researchers in the database were affiliated with the top 30 chemistry departments in the U.S., whereas the set of chemistry departments covers all the chemistry departments from very high research activity universities. Thus, it is natural that the typical Finally we estimate the parameters in The ever-growing size of the scientific literature precludes researchers from following all developments from even a single sub-field. Therefore researchers need proxies of quality in order to identify which publications to browse, read, and cite. Three main heuristics are familiar to most researchers: institutional reputation, journal reputation, and author reputation.Author reputation has the greatest limitations. Researchers are not likely to be known outside their (sub-)field and young researchers will not even be known outside their labs. Similarly, if we exclude a few journals with multidisciplinary reputations , the reputation of a scientific journal is unlikely to extend outside its field. Institutional reputations are the most likely to be known broadly. Cambridge, Harvard, Oxford, and Stanford are widely recognized. However, one could argue that institutional reputation is not a particularly useful heuristic for finding quality publications within a specific research field.μ. Thus, for a researcher whose publications are characterized by a very high μ, authorship of a publication may give a stronger quality signal about the publication than the journal in which the study is being published. Conversely, for an unknown researcher the strongest quality signal is likely to be the journal where the research is being published or the institution the researcher is affiliated with. Our results thus provide strong evidence for the validity of the heuristics used by most researchers and clarify the conditions under which they are appropriate.Our results show that the expected citability of scientific publications published by (i) the researchers in a department, (ii) a given scientific journal, or (iii) a single researcher can be set on the single scale defined by χ2 statistical test. We bin the empirical data in such a way that there are at least 5 expected observation per bin. To assess significance we calculate the i = 1, ⋯, 1,000). We then extract a p-value by comparing the observed statistic χ2 distribution. Finally we use a multiple hypothesis correction [false discovery rate of 0.05, when comparing the model fits with the null hypothesis.We estimate the discrete lognormal model parameters of rrection , with a μ between 0.5 and 2.0. We then generate 1,000 datasets of 50 and 200 publications by random sampling from h-index, average number of citations, total number of citations and median number of citations to publications with at least one citation. Finally, for each value of μ, we calculate the average and the 95% confidence interval of all the indicators.For each discipline we take the average value of h-index of a researcher by self-citations alone, i.e., we assume the researcher does not receive citations from other sources during this procedure. The procedure works by adding only the minimum required citations to those publications that would cause the h-index to increase. Consider researcher John Doe who has 3 publications with {na} = . Doe’s h is 2. Assuming those publications don’t get cited by other researchers during this time period, to increase h by 1, Doe needs to publish only one additional publication with two self-citations; to increase h by 2 he must instead produce five publications with a total of eight self-citations, four of which to one of the additional five publications. We execute this procedure for all researchers in the database until they reached a h-index of 100.We try to increase the μ is based on μ by increasing the median number of citations to publications which have at least one citation already. We consider only self-citations originating from secondary publications, i.e., publications that will not get cited. For a given corpus of publications we first define a target increase in median, x and then calculate the number of self-citations needed to increase the current median by x citations and the corresponding number of secondary publications. We then take the initial corpus of publications and attempt to increase the median citation by x + 1. We repeat this procedure until we reach an increase in median citation of 2000.The manipulation of S1 FileFor a detailed description of the plots see the caption in (PDF)Click here for additional data file.S1 FigNp≥ 50, the dependence on sample size is negligible for most researchers. Researchers with Np < 100 are omitted from the calculation on the subset of size 100.We fit the model to 1,000 randomized subsets of each researcher’s publication list and compare the (TIFF)Click here for additional data file.S2 FigNp< 100 are omitted from the calculation on the subset of size 100.We use the same procedure as in (TIFF)Click here for additional data file.S3 FigWe used the same procedure as in (TIFF)Click here for additional data file.S4 Figtop) and the fraction of secondary publications (bottom) for chemistry departments and chemistry journals in select years, and for all chemistry researchers in our database. The black horizontal dashed lines mark the value of the corresponding parameter for the Journal of the American Chemical Society in 1995. For clarity, we do not show We show the maximum likelihood fitted (TIFF)Click here for additional data file.S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.


A 28-year-old healthy female presented to her primary care physician with lymphadenopathy, fatigue, malaise, and night sweats. Symptoms persisted despite conservative treatment and eventually the patient underwent multiple lymph node resections and a bone marrow biopsy before a diagnosis of IgG4-related disease (IgG4-RD) was made. IgG4-RD is a relatively new disorder first histopathologically recognized within the last decade. As the disease can affect a single organ or multiple organs, symptoms can vary greatly among patients. With symptoms ranging from mild, such as lower extremity edema, to severe, such as spinal cord compression, IgG4-RD must be considered in appropriate patients. Diagnostic criteria have been proposed based on organ involvement, serum IgG4 levels, and histopathological criteria. Diagnosis can be difficult to make with many studies suggesting different values for diagnostic criteria, such as the level of tissue IgG4+/IgG+ cell ratio to delineate IgG4-RD. Treatment consists of high dose glucocorticoids as a first line therapy with some patients choosing instead to simply undergo observation. This case illustrates the difficulty in diagnosis and the need for increased awareness among medical professionals. IgG4-RD is a relatively newly classified condition with unifying histopathologic features recognized only since the early 2000s . The disA 28-year-old female with no significant past medical history presented to her primary care physician with lymphadenopathy, night sweats, fatigue, and malaise. She was treated empirically and partially responded to a short course of glucocorticoids and an antibiotic. When initial laboratory workup was unrevealing for an obvious etiology and symptoms persisted, computed tomography (CT) of the neck and chest with contrast was performed that showed diffuse adenopathy  and hepaHowever, when her symptoms again worsened, she was referred to Infectious Disease who entertained a broad differential including Kikuchi's syndrome, Epstein-Barr virus (EBV), cytomegalovirus (CMV), toxoplasmosis, or human immunodeficiency virus (HIV) infection. Extensive serological testing was unrevealing and a second lymph node was removed, again without an obvious etiology. Rheumatology was then consulted and expanded the differential to include systemic lupus erythematosus, Sjögren's syndrome, Castleman's disease, autoimmune lymphoproliferative syndrome, and IgG4-related disease (IgG4-RD). The diagnosis of IgG4-RD can be difficult to make and misdiagnosis is common. One set of proposed diagnostic criteria as outlined in While the diagnostic criteria discussed earlier suggest an IgG4+/IgG+ cell ratio of >40%, other proposed diagnostic criteria recommend more stringent requirements such as a ratio of >50%. Others suggest that some cases of IgG4-RD may present with an even lower ratio such as >30% , 4. A reAnother aspect of the proposed diagnostic criteria state the serum IgG4 concentration should be >135 mg/dL. However, the serum IgG4 level can be misleading, with approximately 30% of patients with otherwise classic findings for this disease having normal serum IgG4 concentrations [Tissue biopsy and evaluation play a central role in diagnosis. Although IgG4-RD can manifest in nearly any organ system, it shares unique histologic findings regardless of location including dense lymphoplasmacytic infiltrate rich in IgG4-positive plasma cells, storiform fibrosis which is that of an irregularly whorled pattern, obliterative phlebitis, and an eosinophilic infiltrate , 6. WhilDiagnosis can be difficult but the most important first step is a high clinical suspicion. This disease requires specific testing to be recognized and therefore must be sought out, not revealing itself on routine labs or biopsy. Furthermore, because of some shortcomings in the current diagnostic criteria, one must thoroughly consider other disorders in the differential diagnosis. In our case of unexplained generalized lymphadenopathy, fatigue, and night sweats, the differential diagnosis included various infections , lymphoma/leukemia, metastatic neoplasia, systemic lupus erythematous, Castleman's disease, autoimmune lymphoproliferative syndrome, and Sjögren's syndrome . HoweverTreatment strategies have not yet been validated by large randomized controlled trials. Recommendations are currently limited to case reports and consensus statements, with glucocorticoids considered first. Several glucocorticoid sparing regimens have also been suggested, with rituximab showing efficacy even in refractory disease , 6. TreaIgG4-RD is a new disease that has been present for many years but only better appreciated within the last decade. The currently proposed diagnostic criteria incorporate organ involvement, the serum IgG4 level, and tissue evaluation with IgG4+/IgG+ ratio and IgG4 cells/HPF. These criteria must be interpreted in the right clinical setting and diagnosis made only after a thorough consideration and exclusion of alternative diagnoses. Clinical features of the disease can be difficult to piece together given the wide variety of potential systems that can be involved and, therefore, the physician must have a high clinical suspicion. Treatment based on case reports and consensus consists mainly of glucocorticoids or similar agents that suppress lymphocytes. As the disease definition and our understanding of it continues to evolve, greater physician awareness is needed so that this diagnosis is not overlooked in future patients. Ongoing study of patient's with IgG4-RD will provide a better understanding of this disorder, how to best approach treatment, and potentially a more refined diagnostic scheme.


IgG4-related disease (IgG4-RD) is a new clinical entity of unknown etiology characterized by elevated serum IgG4 and tissue infiltration by IgG4-positive plasma cells. Although aberrancies in acquired immune system functions, including increases in Th2 and Treg cytokines observed in patients with IgG4-RD, its true etiology remains unclear. To investigate the pathogenesis of IgG4-RD, this study compared the expression of genes related to innate immunity in patients with IgG4-RD and healthy controls.Peripheral blood mononuclear cells (PBMCs) were obtained from patients with IgG4-RD before and after steroid therapy and from healthy controls. Total RNA was extracted and DNA microarray analysis was performed in two IgG4-RD patients to screen for genes showing changes in expression. Candidate genes were validated by real-time RT-PCR in 27 patients with IgG4-RD and 13 healthy controls.DNA microarray analysis identified 21 genes that showed a greater than 3-fold difference in expression between IgG4-RD patients and healthy controls and 30 genes that showed a greater than 3-fold change in IgG4-RD patients following steroid therapy. Candidate genes related to innate immunity, including those encoding Charcot–Leyden crystal protein (CLC), membrane-spanning 4-domain subfamily A member 3 (MS4A3), defensin alpha (DEFA) 3 and 4, and interleukin-8 receptors (IL8R), were validated by real-time RT-PCR. Expression of all genes was significantly lower in IgG4-RD patients than in healthy controls. Steroid therapy significantly increased the expression of DEFA3, DEFA4 and MS4A3, but had no effect on the expression of CLC, IL8RA and IL8RB.The expression of genes related to allergy or innate immunity, including CLC, MS4A3, DEFA3, DEFA4, IL8RA and IL8RB, was lower in PBMCs from patients with IgG4-RD than from healthy controls. Although there is the limitation in the number of patients applied in DNA microarray, impaired expression of genes related to innate immunity may be involved in the pathogenesis of IgG4-RD as well as in abnormalities of acquired immunity. IgG4-related disease (IgG4-RD) is a new emerging disease entity characterized by elevated serum IgG4 concentrations and tissue tumefaction or infiltration by IgG4-positive plasma cells , 2. Clin+CD25+Foxp3+ regulatory T cells (Tregs) in affected tissues and peripheral blood are significantly higher in patients with IgG4-RD than in healthy controls [IgG4-RD is also characterized by several aberrant findings in the acquired immune system. For example, the numbers of CD4controls –8. In adcontrols , 10. Furcontrols , 11, 12.Although its true etiology remains unclear, infections with various pathogens, including Helicobacter pylori , 14, graInitially, we utilized DNA microarray analysis to select candidate genes with levels of expression three times higher or lower in patients with IgG4-RD than in healthy controls. Subsequently we compared expression of genes in patients with IgG4-RD before and after steroid treatment to identify genes up- and down regulated by steroids. Finally, we performed transcriptome analysis of PBMCs from 27 patients with IgG4-RD and 13 healthy controls to validate the significance of these genes.IgG4-RD was diagnosed according to the comprehensive diagnostic criteria for IgG4-RD . These pFor DNA microarray, heparinized peripheral blood was obtained from these two IgG4-RD patients before and 3 months after starting steroid therapy and from four healthy normal controls . For validation assays, heparinized peripheral blood was obtained from 27 patients with IgG4-RD  before steroid therapy and from 13 healthy controls . Peripheral blood was also obtained from 20 patients with IgG4-RD three to six months after commencement of steroid treatment. Subject characteristics are shown in This study was approved by the institutional ethics board of each institution; Kanazawa Medical University, Kanazawa University, Gunma University Graduate School of Medicine, University of Toyama, Nagaoka Red Cross Hospital, Kansai Medical University, Tokyo Metropolitan Komagome Hospital, National Hospital Organization Nagasaki Medical center, Ehime Graduate School of Medicine, Isahaya Health Insurance General Hospital, Sapporo Medical University School of Medicine, Shinshu University School Hospital, Nagasaki Graduate School of Health Sciences, University of Occupational and Environmental Health, University of Tsukuba, Mitoyo General Hospital, and Kyoto University. Informed consent for publication of all data and samples was obtained from each patient. The research was conducted in compliance with the Declaration of Helsinki.260/280 ratio) and by images of 18S and 28S ribosomal bands in agarose gel electrophoresis.Immediately after blood collection, PBMCs were separated using Lymphoprep , according to the manufacturer’s instructions. Total RNA was extracted using RNeasy Plus Mini kits , according to the manufacturer’s protocol. The concentration and quality of these RNA samples were assessed by measuring UV absorbance at 260 and 280 nm . The microarray expression data discussed in this paper (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66465).To exclude any gender-related differences in gene expression, DNA microarray analysis was performed only on samples obtained from male patients and controls. Total RNA was reverse transcribed to cDNA using Ambion WT Expression kits , labeled with GeneChip WT Terminal Labeling and Controls kits , and hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix), which include 28869 probes. Digitalized image data were processed using GeneChip Operating Software (Affymetrix). Following background correction and 50is paper  have beeGenes showing ≥ 3-fold differences in expression between patients and healthy controls, and before and after steroid therapy in IgG4-RD patients, were selected, and statistically processed by K-means clustering. In addition to clustering, average fold changes were determined to screen for genes with altered levels of expression. Gene pathway databases were assessed by Ingenuity Pathways Analysis  , 20.Total RNA from PBMCs was reverse transcribed to cDNA using Sensiscript RT kits  and oligo (dT) primers according to the manufacturer’s instructions. Primers and TaqMan probes were purchased from Applied Biosystems. Real-time PCR was performed with an ABI Prism 7700 Sequence Detector (Applied Biosystems), using a TaqMan gene expression assay (Applied Biosystems) and Thunderbird Probe qPCR mix . The relative quantity of each target mRNA was normalized relative to that of the internal control, β-actin.t test. All statistical analyses were performed using Stat View version 5.0. In all analyses, P < 0.05 was defined as statistically significant.In real-time PCR analysis, between-group comparisons were performed using the Mann—Whitney U-test or Student’s DNA microarray analysis was performed to identify candidate genes that may be involved in IgG4-RD pathogenesis . Total RTo identify genes affected by steroid treatment, transcriptomes in IgG4-RD patients were compared before and after steroid therapy. Average values from two typical IgG4-RD patients with extreme elevation of serum IgG4 and multiple organ involvement  and fromHelicobacter pylori [Mycobacterium tuberculosis [Infections with various pathogens, including r pylori , 14, grar pylori  and Mycorculosis , have beWe also assessed the effects of steroid therapy on the levels of expression of these genes. Steroid therapy had no effects on the expression levels of the genes encoding CLC, IL8RA and IL8RB Fig –2C, but Elevated serum IgG4 concentration and tissue infiltration by IgG4-positive cells are key events in IgG4-RD. IgG4 itself may play anti-inflammatory rather than proinflammatory roles due to its unique structure and functions. For example, the interactions of IgG4 with the Fcγ receptor and C1q are weaker than those of the other immunoglobulin subclasses . MoreoveIt is not clear, however, whether IgG4 itself is the major factor involved in the pathogenesis of IgG4-RD. Efforts have therefore been made to identify more important upstream pathogenetic changes. Abnormalities in the acquired immune system have been observed in patients with IgG4-RD, such as increased numbers of Tregs in peripheral blood and focal lesions, including the organs involved in IgG4-RD, increases associated with the etiopathogenesis of IgG4-RD , 8. Incr+CD25+ Tregs, with little expression in CD4+CD25-T cells [Among the genes showing ≥3-fold differences in expression between IgG4-RD patients and controls, we selected CLC because of its clinical association with type I hypersensitivity such as bronchial asthma , 24. Fur-T cells . We foun+ T cells when co-cultured with Tregs, as well as augmenting the proliferation of the Tregs themselves. Furthermore, transfection of CLC siRNA into Tregs increased IFN-γ and TNF-α production, while having no effect on surface markers and transcription factors, such as CD25, CTLA-4, CD45RO, CD62L, and Foxp3 [In addition, inhibition of CLC expression in Tregs in vitro has been reported to lead to the proliferation of CD4nd Foxp3 . A mutatnd Foxp3 , 28. Thend Foxp3 , 30, decAs IgG4 itself may play anti-inflammatory roles due to its unique properties, we selected three genes showing increased expression in IgG4-RD patients after steroid therapy, i.e. MS4A3, DEFA3 and DEFA 4. MS4A3, also called HTm4, belongs to the MS4A family, which includes CD20 (MS4A1) and Fcε RI antigen receptor β-chain (MS4A2). These proteins have four transmembrane domains in their N-terminal regions and act as cell surface signaling molecules and intercellular proteins, as well as having C-terminal cytoplasmic regions . Among cWe also found that the expression of the DEFA3 and DEFA4 genes was lower in patients with IgG4-RD than in controls . DefensiOur analysis of gene expression in response to steroid treatment showed that the levels of expression of genes encoding bactericidal substances, such as myeloperoxidase, cathepsin G, bactericidal/permeability-increasing protein and lactotransferrin, were lower in IgG4-RD patients prior to steroid treatment than in healthy controls . Our finAssessment of tissue lesions from patients with IgG4-RD showed that the levels of expression of the Th1 cytokine, IFN-γ, and the Th2 and inhibitory cytokines, IL-10 and transforming growth factor-β (TGF-β), were all elevated compared with healthy controls . Our genTo our knowledge, however, no previous reports have measured serum IL-10 and TGF-β concentrations in IgG4-RD patients. Thus, our results suggest that the levels of inhibitory cytokines are not increased in the peripheral blood of IgG4-RD patients.We found that the levels of expression of genes involved in allergy development and innate immunity, including those encoding CLC, MS4A3, DEFA3, DEFA4, IL8RA, and IL8RB, were lower in PBMCs from IgG4-RD patients than from healthy controls. These findings suggest that impairments in the innate immune system may be responsible, at least in part, for the pathogenesis of IgG4-RD. Stimulation of nucleotide-binding oligomerization domain (NOD)-like receptors (NLR) on monocytes was found to increase IgG4 production by B cells . MoreoveS1 TableTotal RNA was prepared from PBMCs of two patients with IgG4-RD  and from(XLS)Click here for additional data file.


Inguinal hernia repair is a clean surgical procedure and surgical site infection (SSI) rate is generally below 2%. Antibiotic prophylaxis is not routinely recommended, but it may be a good choice for institutions with high rates of wound infection (>5%). Typical prophylaxis is the intravenous application of first or second-generation cephalosporins before the skin incision. However, SSI rate remains more than 2% in many centers in spite of intravenous antibiotic prophylaxis. Even a 1% SSI rate may be unacceptable for the surgeons who specifically deal with hernia surgery. A hernia center targets to be a center of excellence not only in respect of recurrence rate but also for other postoperative outcomes, therefore a further measure is required for an excellent result regarding infection control. Topical gentamycin application in combination with preoperative single-dose intravenous antibiotic may be a useful to obtain this perfect outcome. Data about this subject are not complete and high-grade evidence has not been cumulated yet. Prospective randomized controlled trials can make our knowledge more solid about this subject and help the surgeons who seek perfect outcome regarding infection control in inguinal hernia surgery. Surgical site infection (SSI) is an annoying complication for both surgeons and patients. SSI consumes extra time and money, accounting for 20% of all healthcare-associated infections . SSI devInguinal hernia repair is a clean surgical procedure and the SSI rate is generally below 2%; however, every institution has its own infection figure and many of them cannot produce that low rate. General hospitals, especially centers who receive every kind of surgical case, including trauma and contaminated cases, may have SSI rates >5% –5. AntibTypical antibiotic prophylaxis for an inguinal hernia repair is the intravenous application of first- or second-generation cephalosporins before skin incision , 8. It iTopical antibiotics have been employed for the treatment of infected wounds. Some antimicrobial agents have also been used topically to reduce SSI rates. Topical antibiotic application has many potential advantages over systematic use, though some specific disadvantages also exist . The cliCommonly used antibiotics for topical prophylaxis are cephalosporins, aminoglycosides, glycopeptides, chloramphenicol, and bacitracin ; the dosThe benefits of topical antibiotic prophylaxis with various agents have been documented for multiple surgical disciplines, including ophthalmic, orthopedic, neurological, urological, and general surgeries –16; howeThe first clinical study to examine the merit of topical antibiotic prophylaxis in inguinal hernia repairs was published in 1967 , carriedJohn Nicholls also used an antibiotic solution, made using penicillin powder, into the deep and superficial tissues during the wound closure of inguinal hernia repairs after he read Ryan’s article . He did Andersen and colleagues published their experience with topical ampicillin application in patients that underwent McVay repair for inguinal hernias in 1980 . They deLazorthes et al., in 1992, published their controlled clinical studies on local antibiotic prophylaxis in inguinal hernia repair . PatientAs mesh repairs became the procedure of choice in most centers, intravenous antibiotic prophylaxis gained popularity in inguinal hernia repair but topical antibiotic use for SSI prophylaxis did not. In 2004, the journal Hernia published a letter from Professor Maximo Deysine, MD, FACS (1931–2009) entitled, “Post mesh herniorrhaphy infection control: Are we doing all we can?” . He wrotDeysine was the author of the article entitled, “Pathophysiology, prevention, and management of prosthetic infections in hernia surgery” published in the “Groin Hernia Surgery” issue of the classical series of the Surgical Clinics of North America in 1998 . Upon stS. aureus and S. epidermidis. The empirical choice of a highly concentrated gentamycin solution may explain our results because, at the concentration used, gentamycin would be bactericidal and not bacteriostatic. Most important, gentamycin shows antimicrobial synergy when used in combination with B-Lactams; thus our preoperative intravenous injection of Cefazolin may have contributed to successful bacterial killing whereupon both activity curves are combined. In other words, B-Lactams seem to increase the antimicrobial effect potential of gentamycin.As a surgeon who has a specific interest in hernia surgery, this was my first real notice regarding topical gentamycin use in hernia repairs with mesh. I kept reading Deysine’s paper and refreshed my knowledge about gentamycin: it is an amino-sugar linked by a glycosidic bond to a central aminocyclitol ring. It causes a concentration-dependent bacterial killing that is independent of the inoculum’s size, by first diffusing passively across the bacterial pores’ outer membrane and then transversing the membrane by an energy-dependent system. Once in the cytoplasm, gentamycin binds the 30S ribosomal subunit, which leads to faulty reading of mRNA codons, i.e., the wrong amino acids are incorporated into bacterial proteins. The gentamycin killing effect is concentration-dependent and is followed by a bacteriostatic effect. Other killing mechanisms, like electrostatic interaction, have been postulated to explain the rapidity of its lethal effect. Although it is most effective against Gram-negative bacteria, gentamycin also has killing activity against staphylococci, including both In fact, the first paper about topical gentamycin prophylaxis in the prosthetic repair of hernias was published by Musella and colleagues in 2001 . In thisIn vitro analysis showed efficient antibiotic effects of the gentamycin supplementation compared to the pure PVDF mesh  mesh samples is feasible with gentamycin with no cytotoxicity . AfterwaVDF mesh .Obviously, all five studies from the Aachen group are experimental rat studies, which do not examine the effects of gentamycin application on clinical SSI rates; however, they provide important data about the potential clinical benefits of topical gentamycin use in inguinal hernia repair with prosthetic materials. These findings may be relevant to the best outcome after mesh repair of abdominal wall hernias.Like other aminoglycosides, gentamycin is not accepted or suitable for a single-agent prophylaxis in surgical procedures ; howeverA recent randomized study from Nigeria, carried out in a pediatric population, showed that single-dose intravenous gentamycin prophylaxis can obtain a virtually zero percent SSI rate, whereas the control group developed a 4.8% wound infection rate (Level of Evidence 2B) . FinallyIn fact, preventing hematoma formation reduces wound infection rate in many kinds of surgical procedures –39. SurgElective inguinal repair is a clean surgical procedure that has a <2% SSI rate. Proper intravenous antibiotic prophylaxis provides that low infection rate in many institutions; however, it is possible to almost eliminate wound infection following elective inguinal repair by using topical gentamycin application in combination with preoperative single-dose intravenous antibiotic. Data about this subject are not complete and high-grade evidence has not been collected yet. Prospective randomized controlled trials can solidify our knowledge about this subject and help surgeons who seek perfect SSI outcomes in inguinal hernia surgery.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The convergence of the iterative sequences generated by algorithm is also proved.In this paper, we studied the existence theorems and techniques for finding the solutions of a system of nonlinear set valued variational inclusions in Hilbert spaces. To overcome the difficulties, due to the presence of a proper convex lower semicontinuous function 49J40; 47H06 It is well known that variational inequality theory and complementarity problems are very powerful tools of current mathematical technology. In recent years, the classical variational inequality and complementarity problems have been extended and generalized to study a large variety of problems arising in economics, control problems, contact problems, mechanics, transportation, equilibrium problems, optimization theory, nonlinear programming, transportation equilibrium and engineering sciences, see Aubin . HassounInspired and motivated by the research work going on this field, in this works, the methods for finding the common solutions of a system of nonlinear set valued variational inclusions involving different nonlinear operators and fixed point problem are considered and studied, via proximal method in the framework of Hilbert spaces.Since the problems of a system of a nonlinear set valued variational inequalities and fixed point are both important, the results present in this paper are useful and can be viewed as an improvement and extension of the previously known results appearing in literature, which are improves the results of Chang et al. H be a real Hilbert space whose inner product and norm are denoted by 〈·,·〉 and ∥·∥ respectively and K be a nonempty closed convex subset of H. Let CB(H) be the family of all nonempty closed convex and bounded sets in H and ϕ:H→ be a proper convex lower semicontinuous function on H. Let Ni:H×H→H be a nonlinear function, gi:K→H be a nonlinear operator, Ai,Bi:K→CB(H) be the nonlinear set valued mappings and let ri be a fixed positive real number for each i=1,2,3. Set The system of nonlinear setvalued variational inclusions involving three different nonlinear operators is defined as follows:Let Find We denote the set of all solutions We first recall some basic concepts and well known results.g:H→H is said to be(i)monotone, if (ii)strictly monotone, if g is monotone and(iii)υ-strongly monotone, if there exists a constant υ>0 such that(iv)Lipschitz continuous, if there exists a constant υ>0 such thatA mapping A:H→2H is said to be υ-strongly monotone, if there exists a constant υ>0 such thatA set valued mapping A:H→CB(H) is said to be τ-Lipschitz continuous if there exists a constant τ>0 such thatA set valued mapping where Brezis M is maximal monotone operator on H then for any λ>0the resolvent operator associated with M is defined byIf ∂ϕ of a proper convex lower semicontinuous function ϕ:H→ is a maximal monotone operator.It is well know that a monotone operator is maximal iff its resolvent operator is defined every where. Furthermore the resolvent operator is single valued and nonexpansive. In particular the subdifferential u,z∈H satisfies the inequalityBrezis  The poinif and only ifλ>0 is a constant.where For any g:H→H is a surjective mapping and from Lemma 1 and (1) we have the following proximal point problem:Assume that K⊂gi(H) for each i=1,2,3.provided Weng an},{bn} and {cn} be three sequences of nonnegative real numbers such thatLet {n0 is a nonnegative integer, {tn} is a sequence in  with an→0 as n→+∞.where A,B:H→2H be set valued mappings and N:H×H→H be a nonlinear mapping. (i)N is said to be A-strongly monotone with respect to the first argument, if there exists a constant υ>0 such that for all x,y∈H(ii)N is said to be B-relaxed monotone with respect to the second argument, if there exists a constantξ>0 such that for all x,y∈H,v1∈B(x),v2∈B(y)Let We begin with some observations which are related to the problem (1).x∗,y∗,z∗)∈ SNSVVIDIf (K⊂g1(H).provided S is a Lipschitz mapping such that x∗∈F(S), then it follows from (3) thatConsequently if By virtue of (4) and Nadler’s Theorem Nadler , we suggAlgorithm 1 Let εn be a sequence of nonnegative real number with εn→0 as n→∞. Let r1,r2,r3 be three given positive real numbers in . For arbitrary chosen initial x0∈H, compute the sequences {xn},{yn} and {zn} in H, such thatwhereαn} is a sequence in  and S:H→H is a mapping.and {K be a nonempty closed and convex subset of a real Hilbert space H and ϕ:H→ be a proper convex lower semicontinuous function. Let Ai:H→2H be a μi-Lipschitz continuous mapping with μi<1 and Bi:H→2H be a σi-Lipschitz continuous mapping with σi<1, i=1,2,3. Let Ni:H×H→H be a ρi-Lipschitz continuous with respect to the first variable and ηi-Lipschitz continuous with respect to the second variable and Ni be Ai-strongly monotone with constant υi>0 and Bi-relaxed monotone with constant ξi>0, i=1,2,3. Let gi:H→H be a λi-strongly monotone and γi-Lipschitz continuous mapping, i=1,2,3. Let S:H→H be a τ-Lipschitz continuous mapping with 0<τ≤1. If (i)Let (ii)(iii)i=1,2,3for each where whereM= supn≥1εn.where αn}⊂ such that (iv) {xn},{yn},{zn},{un,i},{vn,i} suggested by Algorithm 1 converge strongly to x∗∈F(S).Then the sequences {Proof. Let x∗∈F(S). By (2) and (4) we haveConsequently, by (5) and (6), we haveN1 is ρ1-Lipschitz continuous with respect to the first variable and η1-Lipschitz continuous with respect to the second variable, and A1 is μ1-Lipschitz continuous, and B1 is σ1-Lipschitz continuous, we haveSince N1 is A1-strongly monotone with constant υ1>0 and B1-relaxed monotone with constant ξi>0, it follows from (10) thatSince i.e.,whereNote thatg2 is λ2-strongly monotone and γ2-Lipschitz continuous mapping, we haveSince where On the other hand, by (2) and (5), we haveN2,A2,B2, g2 and by using the same method as given in the proofs in (11) and (13), we can obtain thatIn view of the assumptions of whereandFrom (15), (16) and (14), we haveCombining (12), (13) and (17) we obtainedObserve thatand in view of (2) and (5), we haveN3,A3,B3 and g3, we haveBy using the assumptions on whereSubstituting (21) and (22) into (20), we haveCombining (19), (23) and (24), it yields thatThis imply thatSubstituting (26) into (18) we havethat isFrom (11) and (28), we getg1 is λ1-strongly monotone and γ1-Lipschitz continuous mapping, we haveOn the other hand, since i.e.,Similarly, we haveSubstituting (28) into (31), we haveSetSubstituting (30), (31), (32) and (33) into (9), we getSinceℓn≤ℓ. Therefore from (34) we have thatletting By condition (iii)this imply thatthat isPutτ≤1, it follows thatBy the assumption that 0<tn∈. From assumption (iv) we haveThis imply that xn→x∗ as n→∞. Consequently from (26) and (28), we have zn→z∗ and yn→y∗ as n→∞, respectively. Moreover since Ai is μi-Lipschitz continuous and Bi is σi-Lipschitz continuous with μi<1, σi<1, we can also prove that {un,i} and {vn,i}, i=1,2,3 are Cauchy sequences. Thus there exists n→∞. Moreover by using the continuity of mappings i=1,2,3, it follows from (5) thatThese show that all conditions in Lemma 2 are satisfied. Hence Hence from Lemma 2 it follows that A1(y∗)∈CB(H), we must have That is


Full-text searches of articles increase the recall, defined by the proportion of relevant publications that are retrieved. However, this method is rarely used in medical research due to resource constraints. For the purpose of a systematic review of publications addressing shared decision making, a full-text search method was required to retrieve publications where shared decision making does not appear in the title or abstract.The objective of our study was to assess the efficiency and reliability of full-text searches in major medical journals for identifying shared decision making publications.A full-text search was performed on the websites of 15 high-impact journals in general internal medicine to look up publications of any type from 1996-2011 containing the phrase “shared decision making”. The search method was compared with a PubMed search of titles and abstracts only. The full-text search was further validated by requesting all publications from the same time period from the individual journal publishers and searching through the collected dataset.The full-text search for “shared decision making” on journal websites identified 1286 publications in 15 journals compared to 119 through the PubMed search. The search within the publisher-provided publications of 6 journals identified 613 publications compared to 646 with the full-text search on the respective journal websites. The concordance rate was 94.3% between both full-text searches.Full-text searching on medical journal websites is an efficient and reliable way to identify relevant articles in the field of shared decision making for review or other purposes. It may be more widely used in biomedical research in other fields in the future, with the collaboration of publishers and journals toward open-access data. Full-text searches of articles are known to increase the recall, also called sensitivity, and defined by the proportion of relevant publications that are retrieved -3. Full-In contrast to a PubMed search, a full-text search permits the identification of articles whose keywords appear not only in the title or abstract, but also in the main content . Furthermore, a full-text search can help to retrieve publications without abstracts. Those articles, such as editorials and debates, have an impact on readers ,8, and mIn a recent study , we perfThe aim of the present study was to assess the reliability and efficiency of full-text searches in major medical journals for identifying publications containing the phrase “shared decision making” and to compare the results with a traditional PubMed search. If reliable and efficient, this methodology may be used for retrieving publications for systematic reviews on topics other than SDM.We selected the 15 journals with the highest 5-year impact factors in 2010 in the “general and internal medicine” category from the ISI Web of Knowledge Journal Citation Reports . MoreoveTo identify publications containing the phrase shared decision making, referred to as SDM publications, we built a search strategy combining the following 6 phrases (1) shared decision making, (2) informed decision making, (3) shared medical decision making, (4) informed medical decision making (5) informed and shared decision making, and (6) informed shared decision making. None of the terms exist as a Medical Subject Heading (MeSH) term.All publications released between January 1996 and December 2011 were eligible, because the concept of SDM began to appear significantly in medical literature in the mid 1990s ,16. MorePublications were retrieved through the full-text search function on the journals' websites, usually located on the “advanced search” web page or on the publisher website if not available. The search engine of each journal website is handled similarly to that of PubMed, with Boolean operators and filters. It demands no particular informatics competency, but some manpower is required as the operation has to be repeated on each journal website. We refer to this search method as website full-text search. We included publications of any type, with the exception of cover pages, tables of content, and indexes .To assess the performance of the website full-text search, we compared it with a PubMed search using a similar strategy . PubMed searches were limited to titles and abstracts since full texts are usually not directly available on the PubMed platform, but rather through links to the journal websites.We next compared the type of publications retrieved through website full-text vs. PubMed searches. We categorized the publication type through a bibliometric analysis and then dichotomized the results between research and non-research publications. Research publications included interventional and observational studies, systematic reviews, guidelines, and consensus publications, whereas non-research publications included non-systematic reviews, editorials, comments, letters, book reviews, conference publications, and others.In contrast to PubMed searches, the website full-text search method relied on journal or publisher websites whose search syntaxes were not explicit. To compare our results with a validation dataset, we contacted the editorial board of each selected journal to request authorization to obtain all published materials since 1996. After receiving their authorization, we collected published material in an electronic version to build a custom-designed database of full-text publications. We designed and launched an automated search script . We used the same 6 SDM-related phrases for publication retrieval. This text retrieval method on a locally stored full-text corpus is referred to as downloaded full-text search . We asseThrough the website full-text searches, we included 1286 SDM publications out of a total of 229,179 publications in the 15 journals from 1996-2011 .Through the PubMed searches, 119 SDM publications were included. Of these publications, only 2 were missed by the website full-text searches; one due to unavailable data on the journal website for years 1996-1997, and while the other was available on the journal website, the browser failed to retrieve it . The BMJOf the 15 journals, 6 complied with our request to download all materials published during the study period. When limited to these 6 collaborating journals, 646 SDM publications were found through the website full-text searches, while the downloaded full-text searches retrieved 613 publications . When maThe website full-text searches identified 1286 SDM publications in 15 major medical journals, which was about 10 times more than through the corresponding PubMed searches. The search method was reliable with a good concordance rate when compared with a validation dataset of downloaded publications.To our knowledge, full-text searches have never been assessed on medical journal websites. Our results are concordant with those of previous studies in other fields , where the sensitivity of detecting keywords in full-text publications is much higher than when limited to a title and abstract PubMed search ,20. ThisIn a Cochrane review, handsearching identified more reports of randomized controlled trials than electronic searching through MEDLINE, particularly trials reported as letters, editorials, or journal supplements . In the The website full-text searches were fast and simple to perform compared to the downloaded full-text searches. While it took a few days to search the journal websites, it took 10-12 months of long negotiations to sign contracts with copyright holders to gain access to their material. However, we finally reached the goal for less than half of the contacted journals. Unfortunately, similar copyright issues have previously been reported in the text mining field .Our study has some limitations. First, we did not develop a comprehensive search strategy, but selected only 6 phrases related to SDM. As a result, we did not assess the performance of an elaborate PubMed search strategy for SDM, compared with a full-text search method. We thought it was reasonable to explore this novel method with a simplified search strategy, as it is closer to the approach used by researchers and clinicians on a daily basis. Further studies should use a more comprehensive search strategy to compare extensively the new search method with PubMed or other search engines. Second, a gold standard search method could not be established, because it was not possible to verify that all publications with inclusion criteria were retrieved. For that matter, all three methods failed to identify all SDM publications, probably due to the lack of consistent indexing mechanisms and technical defects, like in the OCR. Third, for multiple resource constraints, we have not been able to perform the full-content analysis of the 1286 included publications. We are therefore unable to report on the meaning and the potential relevance of each publication. It is possible that some publications mentioned SDM just as a fashionable concept in a sentence or as a replacement term for other terms . From this perspective and without a gold standard, we were unable to measure the proper recall and precision of the search method.Full-text searching of terms in medical journal websites is a reliable and efficient way to identify relevant articles in the field of SDM for review or other purposes. It may be more widely used in medical research in the future, with the collaboration of publishers and journals toward open-access data.


Overutilisation of antibiotics may contribute to the emergence of antimicrobial drug resistance, a growing international concern. This study aimed to analyse the performance of UK general practices with respect to antibiotic prescribing for respiratory tract infections (RTIs) among young and middle-aged adults.Data are reported for 568 UK general practices contributing to the Clinical Practice Research Datalink.Participants were adults aged 18–59 years. Consultations were identified for acute upper RTIs including colds, cough, otitis-media, rhino-sinusitis and sore throat.For each consultation, we identified whether an antibiotic was prescribed. The proportion of RTI consultations with antibiotics prescribed was estimated.There were 568 general practices analysed. The median general practice prescribed antibiotics at 54% of RTI consultations. At the highest prescribing 10% of practices, antibiotics were prescribed at 69% of RTI consultations. At the lowest prescribing 10% of practices, antibiotics were prescribed at 39% RTI consultations. The median practice prescribed antibiotics at 38% of consultations for ‘colds and upper RTIs’, 48% for ‘cough and bronchitis’, 60% for ‘sore throat’, 60% for ‘otitis-media’ and 91% for ‘rhino-sinusitis’. The highest prescribing 10% of practices issued antibiotic prescriptions at 72% of consultations for ‘colds’, 67% for ‘cough’, 78% for ‘sore throat’, 90% for ‘otitis-media’ and 100% for ‘rhino-sinusitis’.Most UK general practices prescribe antibiotics to young and middle-aged adults with respiratory infections at rates that are considerably in excess of what is clinically justified. This will fuel antibiotic resistance. The findings are derived from a large, representative sample of UK general practices.Findings did not include information concerning severity of illness or the presence of comorbidity, which might have accounted for the prescription of antibiotics in some cases.Only prescriptions issued by the practice were analysed, as it was not possible to estimate from electronic health records whether prescriptions were dispensed, or whether a delayed prescribing strategy was intended.Overuse of antibiotic drugs is leading to increasing antimicrobial drug resistance. As there are now fewer new antibiotic drugs being developed, it is important to preserve the effectiveness of presently available antibiotics for future generations.6In 2008, the National Institute for Health and Care Excellence (NICE) recommended that most acute RTIs, including colds, coughs, sore throats, otitis-media and rhino-sinusitis, could be managed without antibiotics and recommended that either a ‘no antibiotic’ or ‘delayed antibiotic prescribing’ strategy should be agreed for most patients.4We recently completed a large cluster randomised trial to reduce antibiotic prescribing among general practices that contribute to the Clinical Practice Research Datalink (CPRD).The UK CPRD provided the data source for the study. The CPRD is a database of prospectively collected electronic medical records from approximately 7% of UK general practices. It includes records for all prescriptions issued and medical diagnoses recorded.Individual participants were adults aged 18–59 years. This was consistent with the eligibility criteria for the trial,6The selection of general practices and patients into the analysis is outlined in Consultations for ‘cough and bronchitis’ accounted for 39% of RTI consultations; ‘sore throat’ 27%; ‘colds and URTI’ 19%; ‘rhino-sinusitis’ 9%; and ‘otitis media’ 6%. National guidance in the UK recommends that most patients presenting with acute RTIs can be managed with either no antibiotic prescribing or delayed antibiotic prescribing, with a prescription only being used if symptoms do not improve.4Our study had the strengths of a large, representative sample of UK general practices. We acknowledge that we did not include information concerning severity of illness or the presence of comorbidity, which might have accounted for the prescription of antibiotics in some cases. We only analysed prescriptions issued by the practice and it was not possible to estimate from electronic health records whether the prescription was dispensed, or whether a delayed prescribing strategy was intended. There is a Read code for deferred antibiotic therapy (8BP0.00) but this was recorded for fewer than 0.5% of medical events. It is unlikely that delayed prescribing can fully account for the high prescribing rates. In an observational study in 13 000 adults with sore throat, immediate antibiotics were issued in 42% and 12% given delayed antibiotics.The present results have implications for communications with the public as well as for practice prescribing policies. Respiratory infections in this age group are both self-limiting and carry a low risk of complications, moreover the impact of antibiotics on symptom severity and duration is at best marginal. Respiratory infections may be better managed through patient self-care rather than primary care consultation. The high rates of antibiotic prescribing reported by this study indicate a need to shift the entire distribution for antibiotic prescribing to lower levels, since there are very few practices that are not prescribing antibiotics to excess, fuelling the development of antibiotic resistance. In addition, there are immediate direct costs from prescribing antibiotics, as well as risks of drug side effects and the perpetuation of unnecessary consultation patterns. There needs to be an active professional debate concerning an overall level of antibiotic utilisation for RTI that might be acceptable, and the size of reduction that individual practices should aim to achieve as a matter of urgency.


Methadone maintenance treatment (MMT) is recognized as one of the most effective treatments for heroin addiction but its effect is dimmed by the high incidence of heroin relapse. However, underlying neurobiology mechanism of heroin relapse under MMT is still largely unknown. Here, we took advantage of a resting-state fMRI technique by analysis of regional homogeneity (ReHo), and tried to explore the difference of brain function between heroin relapsers and non-relapsers in MMT.Forty MMT patients were included and received a 12-month follow-up. All patients were given baseline resting-state fMRI scans by using a 3.0 T GE Signa Excite HD whole-body MRI system. Monthly self-report and urine test were used to assess heroin relapse or non-relapse. Subjective craving was measured with visual analog scale. The correlation between ReHo and the degree of heroin relapse was analyzed.Compared with the non-relapsers, ReHo values were increased in the bilateral medial orbitofrontal cortex, right caudate, and right cerebellum of the heroin relapsers while those in the left parahippocampal gyrus, left middle temporal gyrus, right lingual gyrus, and precuneus were decreased in heroin relapsers. Importantly, altered ReHo in the right caudate were positively correlated with heroin relapse rates or subjective craving response.Using the resting-state fMRI technique by analysis of ReHo, we provided the first resting-state fMRI evidence that right caudate may serve as a potential biomarker for heroin relapse prediction and also as a promising target for reducing relapse risk. Drug addiction is a kind of chronic cerebral dysfunction . Unlike In recent years, a body of studies have been making the attempt on neural circuits and brain functions in heroin addiction by using resting-state fMRI method. By comparing heroin addicts with healthy controls, researchers revealed a heroin-related organization pattern. For instance, Ma et al.  observedRecently, the regional homogeneity (ReHo) method  has beenIn the present study, we included forty heroin addicts, and by using the resting-state fMRI technique to investigate the difference of resting-state brain function between heroin relapser and non-relapser in MMT patients by analysis of ReHo changes, trying to provide a further insight into the neurobiological mechanism underlying heroin relapse in MMT patients.Sixty male former heroin addicts were recruited from the outpatient of the Baqiao Methadone Maintenance Treatment Center in Xi’an, Shaanxi Province, China. Patients were eligible for enrollment if they (a) met the diagnostic criteria of DSM-IV  for heroin addiction; (b) willingly received long-term and stable MMT; (c) received at least three-month MMT; (d) were right-handed as judged by the Edinburgh Handedness Inventory . PatientAdditionally, co-morbidity of addiction and psychiatric disorders is very common in heroin addicts, and to avoid the potential influence of psychiatric symptoms, we excluded the patients who reported having a current or past psychiatric illness other than heroin addiction, as described in exclusion criteria. We also evaluated the baseline psychological problems which usually accompanied with heroin addiction, such as depression and anxiety. The Beck Depression Inventory II and Hamilton Anxiety Scale were used to evaluate the severity of depression and anxiety symptoms respectively. There were no significant differences in depression severity and anxiety level between groups (data not shown).This study was approved by Institutional Board of the Fourth Military Medical University, Xi’an, China and conducted in accordance with Declaration of Helsinki. All participants were fully informed about the details of experiment and signed the written consents for their involvement and The proposed protocol conforms to the Good Clinical Practice and has been approved by the Ethics Committee of the Institute of Tangdu Hospital, Fourth Military Medical University, Shaanxi, China.There were 60 participants recruited in the study. According to the inclusion criteria exclusion criteria, 20 participants were excluded for having other active neurological and psychiatric disorders, head trauma, or contraindications to MRI examination, and 40 were included and then received a baseline resting-state fMRI scanning following with a succeeding 12-month clinical follow-up. During the follow-up, they were supervised under monthly structured interview and urine tests. The participants with once self-reported heroin use or/and positive urine tests were defined as heroin relapser, and those with negative results in tests were defined as non-relapser. Relapse rate of each heroin relapser was calculated as following: total numbers of positive results in tests during MMT/12. The subjective heroin craving was assessed by a 0–10 score visual analogue scale (VAS).2WI structural scan  was performed to exclude gross cerebral pathology and then a BOLD functional imaging data was acquired using T2*-weighted gradient-echo planar imaging pulse sequence . The parameters were set as follows: TR = 2000 ms, TE = 30 ms, flip angle = 90°, matrix = 64 × 64, FOV = 256 × 256 mm2, slice thickness = 4 mm, gap = 0 mm; spatial resolution = 4 × 4 × 4 mm3. The corresponding high-resolution fast spoiled gradient-echo 3D T1-weighted images were also collected for anatomical overlays of the functional data and for spatial normalization of the datasets to a standard atlas and settings were as following: TR = 7.8 ms, TE = 3.0 ms, matrix = 256 × 256, FOV = 256 × 256 mm2, spatial resolution =1 × 1 × 1 mm3.All MRI scans were conducted on a Signa EXCITEHD 3.0 T scanner  with an eight-channel head coil. A routine Thttp://www.fil.ion.ucl.ac.uk/spm) as described previously [3). The T1-weighted high-resolution image volume was also spatially normalized to the MNI template. All images spatially normalized to MNI template were transformed to Talairach and Tournoux coordinates and then filtered by using a band-passed filter (0.01–0.08 Hz) to reduce the effect of low-frequency drifts and high-frequency noise. All the data was collected and analyzed by an author  who was blinded to the present study.Data preprocessing was performed with software . The ReHo calculation procedure was performed as previously reported [For regional homogeneity (ReHo) analysis, the data were processed with a software  was considered statistically significant.To analyse the differences of ReHo values between heroin relapse and non-relapse patients under MMT, a two-sample p value was set as 0.05, and the number of tests was 8).To evaluate the association of altered ReHo in different brain regions with heroin relapse in these relapsers, we performed Spearman's correlation analysis between mean ReHo values and relapse rates (as defined above) or subjective heroin craving indicated by VAS scores of each heroin relapser. The correlation analysis was based on non-parametric Spearman correlations and included only the relapsers. Threshold levels of significance for correlation coefficients were adjusted for multiple comparisons by a Bonferroni’s correction  with relapse rates or with subjective heroin craving in relapse patients. Our results showed a positive correlation was observed between mean ReHo values in the right caudate and relapse rates or heroin craving whereas no correlation relationships were found between ReHo values and other brain regions Tables  and 4. AIn this study we carried out a 12-month follow-up study using resting-state fMRI by analysis of brain regions with abnormal ReHo in heroin relapsers under MMT, and found that compared with the non-relapsers, an increased ReHo values were evident in the bilateral medial OFC, right caudate nucleus, and right cerebellum of the heroin relapsers while a decreased ReHo in the left parahippocampal gyrus, left middle temporal gyrus, right lingual gyrus, and precuneus. Moreover, ReHo values in right caudate nucleus were correlated with relapse rates or subjective heroin-craving response.The medial OFC is a part of the limbic system, and is a functionally heterogeneous region that involved in complex adaptive behaviors. It was reported that in active cocaine abusers, OFC was hypermetabolic in proportion to the intensity of the craving experienced by the subjects  but was Caudate nucleus  is a principal brain region of mesostriatum dopamine (DA) pathway and is recognized to contribute to drug addiction . A groupAnother area of the brain with increased ReHo in the present study was the cerebellum, which is reportedly involved in addictive behavior. Previous PET and fMRI studies revealed that drug-conditioned cue could activate the cerebellum and increased its metabolism , 30. WheIn contrast, ReHo in several brain areas, especially in precuneus, were significantly decreased in heroin relapsers relative to non-relapsers. Apart from extension of the visuo-spatial processes subserved by the lateral parietal cortices, precuneus also plays an important role in a diverse array of highly integrated functions, e.g., involving in voluntary attention shifts between targets and playing a central role in the modulation of conscious process . PrecuneMoreover, we observed a positive correlation between altered ReHo values in the right caudate and relapse rates or heroin craving. These findings support the idea that heroin relapse and craving were related to the caudate nucleus, which plays an important role in the habitual nature of subjective experience of caving and compulsive drug-seeking behaviors in drug addicts , 28. ImpAdmittedly, some limitations in the present are worth noting. First, in this study, female subjects were not included. Thus, a possible gender difference in relapse susceptibility was unexplored. Second, the interval of monthly self-report and urine test to assess MMT relapse was relatively long, probably not reflecting the true relapse rates. Finally, it had certain limitations by using urine test to assess the severity of MMT relapse. In addition, in spite of the results obtained above, we still lacked the knowledge about which neural circuit played the crucial role in the relapse behavior in heroin addicts receiving MMT. Therefore, other analysis methods such as fractional amplitude of low frequency fluctuations, degree of centrality maps, and the other metrics provided by resting-state fMRI should be employed to analyze the relationship of resting functional characteristics and relapse need further exploration.In summary, compared with non-relapsers, heroin relapsers had an abnormal resting-state function. Specially, relapsers displayed increased ReHo in the bilateral medial OFC, right caudate, and right cerebellum but decreased ReHo in the left parahippocampal gyrus, left middle temporal gyrus, right lingual gyrus, and precuneus. The alterations of ReHo in these areas may involve abnormal motivation, reward, memory and visual spatial attention. Overall, our results may add to neurobiological factors associated with relapse to heroin use and also be conducive to developing a promising strategy for heroin addiction therapies.MMT, methadone maintenance treatment; OFC, orbitofrontal cortex; ReHo, regional homogeneity; VAS, visual analogue scale