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A top Catholic Bishop has taken a pop at the not-quite-faithful-enough, who are treating the confessional as little more than a cheaper, albeit darker, version of the psychologist's couch.
Archbishop Mauro Piacenza went on Vatican radio to bemoan the "deep crisis" that has overtaken the sacrament of penance, aka the sacrament of reconciliation aka confession, the Associated Press reports.
Piacenza said part of the problem was that even Catholics are having trouble distinguishing between good and evil, despite the Church's handy organisation of non-good things into Ten Commandments, and the even briefer 7 deadly sins.
With the greying of the line between good and evil, Catholics are less likely to heed the call to the confessional and cough up to taking money out of the collection plate and coveting their neighbours' ass, in return for being hit with penance of a dozen decades of the rosary and a commitment to help out at the next St Patrick's day dance.
In fact, some might be confusing it with a psychiatrists' couch, Piacenza suggested, presumably burdening the hard-pressed confessor with the whys and wherefores of where they went wrong in some half-arsed bid to show that it's really not their fault, and that if only their mother hadn't made them go to Church, they wouldn't have burned it down in the first place.
Piacenza, to be fair, accepted that the dwindling supply of priests isn't helping matters, admitting that "It's not always easy to find a priest ready to listen to the confessions of the faithful for hours."
A situation that hasn't been helped by the Vatican's sensible refusal to entertain the idea of confession over the web or by mobile phone.
Others say the Church should shoulder even more of the blame. Francis Rocca, a Vatican correspondent for the Religion News Service, told the Guardian:
"About 30 years ago the church started calling penance 'reconciliation', which to some Catholics might sound more like therapy than a sacrament".
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2019 Can-Am Maverick MAX 900 X ds Turbo R
UTV Motorcycle for sale by RideNow Gainesville in Gainsville, Florida 32609
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subset: commoncrawl


text:
Do you know your aliases?
This little PowerShell script you can check how familiar you are with all the built-in aliases in PowerShell V2 CTP2.
For each alias there are 7 cmdlet names to choose from. There are 10 questions, and at the end of the quiz you can review your results and optionally run the quiz again.
You need to have PowerShell V2 CTP2 installed for the script to run.
Good luck :)


text:
Photography doesn't usually have the problem that it's too noisy an art form, but that was exactly the challenge that faced the organizers of Photoville, a new photo festival that will open in Brooklyn, New York, on June 22. One of the major components of the show is an exhibit inside a warren of industrial shipping containers. Forty-two of them, to be exact, laid out in a maze carefully planned with both exploration and safety in mind.
"Getting a container is simple. Getting 42 of them placed in an intricate pattern is complicated. The most complicated thing is they'll show up, they'll dump it and they'll drive away. I've learned that their preferred hour of doing that is 4:30 in the morning," says Sam Barzilay, formerly of the New York Photo Festival, who is one of the three minds behind the festival. "Dumping a container as it grinds off the truck onto cobblestone is about the loudest thing I've ever heard."
But when the festival opens, the containers will be there, full of photos. And that won't be all: Photoville will also include about 1000 feet of fencing covered with community-centric photography, presentations from organizations like the Magnum Foundation and Photo District News, a number of workshops and even a beer garden and a dog run with a dog photo booth. And it's all completely free.
Photoville is the product of United Photo Industries, a year-old cooperative comprising Sam Barzilay, Laura Roumanos and Dave Shelley. Barzilay says that the idea behind the event, and United Photo Industries' other projects, is the realization that Real Estate in New York City affects the art scene. Empty storefronts have meant that small pop-up galleries have been relatively accessible during the last few years, but that won't last forever. "The writing on the wall was sooner or later the economy would pick up again and people will be back in business, opening the stores," says Barzilay. "Those spaces weren't going to last." They wanted to figure out a way to continue to present artwork without the overhead needed for a giant space. And once the shipping-container idea struck, the ideas just kept coming.
The end result is meant to appeal to photographers and civilians alike. "Even though it's the most easily relatable art medium at this point, because everybody carries a camera, I think a lot of the time people are afraid of photography exhibitions," says Barzilay. "We're trying to cater to a full spectrum of people. I want people to come and enjoy it." That's why the free and open model is so important to the organization.
Barzilay and Shelley have both worked for the New York Photo Festival in the past, but Photoville is not meant to be competition for the more established festival. New York is big enough and "art-loving enough" to support many festivals, says Barzilay—and, besides, Photoville isn't even meant to be a festival in a traditional sense of the word. "We're trying to build a destination, trying to build a place where you go and spend a day listening to lectures and participating in a workshop, probably having a beer, to bring your dog to the dog run," he says. "It's a place to spend physical time with the photography, not so much as a passive viewer."
Photoville will be held in Brooklyn from June 22 through July 1. More information about the event is available here.
See more work from Bruce Gilden, one of Photoville's featured photographers, here.


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The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP's 16S data sets to several reference 16S collections to create a 'most wanted' list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the 'most wanted', and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the 'most wanted' organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.
Citation: Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, et al. (2012) The "Most Wanted" Taxa from the Human Microbiome for Whole Genome Sequencing. PLoS ONE 7(7): e41294. https://doi.org/10.1371/journal.pone.0041294
Editor: Matthias Horn, University of Vienna, Austria
Received: March 26, 2012; Accepted: June 19, 2012; Published: July 26, 2012
Copyright: © Fodor et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was undertaken on behalf of the Human Microbiome Project Consortium (http://commonfund.nih.gov/hmp/and http://www.hmpdacc.org) and generously supported by the National Institutes of Health, National Human Genome Research Institute and National Institute of Allergy and Infectious Diseases (HHSN2722009000018C and U54HG004969 to Bruce W. Birren and U54HG004968 to George M. Weinstock). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: One author is affiliated with the company Second Genome. His employment at this company does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials. Furthermore, the other authors have declared that no competing interests exist.
The human body is home to an enormous number and diversity of microbes. These microbes, the human microbiome, are increasingly thought to be required for normal human development, physiology, immunity, and nutrition [1]–[3]. While we owe many of these insights to 16S rRNA gene (16S)-based studies aimed at classifying and quantifying the microbes present among different people and body habitats [4]–[11], 16S sequences are insufficient proxies for the contents of the entire genome. Whole-genome sequences are an essential prerequisite for analyses that reveal how the metabolic potential of the microbiome might impact human health and disease. Moreover, a more complete set of assembled genomes from the human-associated microbiome will assist in the proper taxonomic and functional assignments of short sequence reads from whole-genome shotgun metagenomic, metatranscriptomic and metaproteomic studies, which are becoming increasingly feasible with the decreasing costs of DNA and protein sequencing methods.
The mission of the Human Microbiome Project (HMP) is to understand the role of human-associated microbial communities in health and disease. As part of this mission, the HMP seeks to generate a comprehensive reference collection of microbial genomes that represent the "healthy" human microbiome [12]–[14]. Through the efforts of the HMP and other sequencing projects, nearly 5,000 bacterial strains have been isolated from the human body, grown in culture and submitted for whole genome sequencing. While these organisms represent a wide range of taxonomic groups and origins of isolation, studies suggest that many microbes, including those that inhabit humans, have not been cultured and, thus, elude conventional methods for DNA preparation and sequencing [15], [16]. Consequently, reference genome collections remain incomplete. However, recent advances in culture- and single-cell-based technologies are making it possible to isolate and sequence these hard-to-culture microbes [17]–[19].
To guide these isolation efforts and selection of microbes from the microbiome for sequencing, we sought to identify and to create a list of high priority organisms from the human microbiome that remain un-represented in reference genome collections. This 'most wanted' list of organisms is meant to serve as a resource for the community interested in the isolation and sequencing of elusive members of the microbiome. To create the 'most wanted' list, we relied upon the HMP's survey of healthy volunteers, the largest and most comprehensive survey of the human microbiome currently available [12], [14], [20], [21]. We compared the HMP's 16S-based survey data from 18 different body habitats from more than 200 'healthy' volunteers to other 16S reference collections. These comparisons helped us to define a scheme for prioritizing taxa that are both distantly related to already sequenced organisms and found frequently among the microbiome of HMP volunteers and other healthy humans.
The resulting 'most wanted' list of taxa is currently being used by the community for isolation and sequencing of previously un-sequenced organisms found in association with humans. The completion of these genomes will bring us closer to completing the reference genome collection and, hence, the gene-catalog of the human microbiome.
A Modest Number of OTUs can Account for Nearly all of the Non-chimeric Sequences in the V1–V3 and V3–V5 HMP 16S Datasets
At the time of this study, the HMP's survey of over 200 healthy volunteers and 18 body habitats was the single largest and most diverse data set from the human microbiome available [14]. As such, the HMP's data were chosen to identify organisms from the human microbiome that had not yet been sequenced. To begin, we, separately, combined all available data from each of the HMP's two major 16S-based surveys, targeting the V1–V3 and V3–V5 variable regions (Table 1). Each combined data set was clustered into operational taxonomic units (OTUs), using AbundantOTU [22] with the default setting of 97% average sequence identity (ID) for OTU inclusion. The resulting 1,440 V1–V3 and 1,258 V3–V5 OTUs contained nearly all (>95%) of the individual reads (Table 1). The majority of reads that did not cluster into OTUs were chimeric (as detected by UCHIME [23]) suggesting that many singleton reads represent PCR amplification error [24]. Rank abundance curves (Fig. 1) showed the unequal distribution of sequences within the OTUs; a small number of OTUs contained large numbers of 16S sequence reads while most OTUs contained many fewer reads. This pattern of a highly unequal distribution of sequences across OTUs is consistent with observations from other metagenomic surveys [25]–[27]. In addition, we observed a substantial number of chimeras within the HMP dataset, which were removed with the program UCHIME (Document S1 and Figures S1, S2, S3) [23], resulting in 773 V1–V3 and 695 V3–V5 non-chimeric HMP OTUs (hereafter referred to as the "HMP OTUs"). The sequence counts and average relative abundance for each chimeric and non-chimeric OTU, together with their consensus sequences, are available at http://hmpdacc.org/most_wanted.
(A) The number of sequences in each OTU. (B) Cumulative rank abundance. For both V1–V3 and V3–V5, on the order of 10–15 OTUs captured half of all individual sequences.
There were Few Novel and Many Uncultured Taxa within the HMP OTUs
To understand which organisms were represented by the 773 V1–V3 and 695 V3–V5 non-chimeric HMP OTUs, we classified the consensus sequence associated with each HMP OTU using the RDP classifier (see Methods) [28]. As expected [29], we observed distinct phylogenetic communities in different body habitats (Fig. 2, left panel) reflecting the different microbial communities that inhabit the distinct niches within the human body. The observed community compositions were consistent across both V1–V3 and V3–V5 HMP OTUs, especially when phylum level classifications were taken into consideration (Fig. 2, left panel bar plots). However, even genus-level concordance was high; only ∼10% of HMP OTUs from each V region lacked a genus-level classification match to the other data set (data not shown).
The distributions of 1,468 non-chimeric HMP OTUs (left panel) and 119 most wanted OTUs (right panel) are shown as phyla (outer circle) and genera (inner circle) at each of the 5 sampled body habitats. Distribution profiles were based on the habitat in which the HMP OTU was found most frequently. Bar graphs illustrate the relative proportion of HMP OTUs from each 16S variable region, shown as phyla. Color codes for all phyla and 'most wanted' genera with more than one representative are shown in left and right figure legends, respectively.
To determine which HMP OTUs have not yet had a representative strain sequenced, we used the program align.seqs, within the package Mothur (see Methods) [30] to report the percent identity (across a global alignment) of the best matching sequence from several reference databases (Table S1) to each HMP OTU. We performed this search against v. 1.04 of the Silva database [31] (Fig. 3A), which is a comprehensive collection of full-length sequences as well as against numerous databases representing cultured or sequenced organisms (Fig. 3B–3F). When compared to the comprehensive Silva database (Fig. 3A), nearly all of the HMP OTUs had a compelling match (>98% identity) to a previously characterized full-length 16S sequence. From this, we concluded that there are only modest numbers of novel taxa within the HMP OTUs. We noted, however, that the taxonomic annotations given to the majority (70%) of matching Silva sequences did not include species designations and contained the word 'uncultured' or 'clone' indicating that these organisms may remain uncaptured. To directly determine which HMP OTUs represent taxa that have been cultured and sequenced, we also compared the HMP OTUs to (i) the GOLD database [32] (Fig. 3B), which represents microbes for which high-quality whole-genome sequences are available, (ii) the "GOLD-Human" database (Fig. 3C), which is a subset of the "GOLD" database representing strains isolated from the human body, (iii) "HMP strains" database (Fig. 3D), which represents whole-genome sequenced strains isolated from humans that are being completed as part of the HMP, (iv) the Greengenes "named" database (Fig 3E), which represents microbes (>3,000 genera and >7,000 species) that are in a culture collection and have been assigned a binomial name and (v) the Greengenes "unnamed" database (Fig. 3F), which represents microbes (5,869 16S sequences mostly from aquatic and terrestrial environments) that are in a culture collection, but lack binomial names. In all of these cases (Fig. 3B–3F), we see a similar pattern in which there are large numbers of HMP OTUs with poor matches to these reference collections. Taken together, these data demonstrate that while there are few truly novel 16S sequences in the HMP OTUs (Fig. 3A), there are many more taxa for which whole-genome sequences have not been determined (Fig. 3B–3D) and which have not been cultured (Fig. 3E-3F).
Panels A through F present results from aligning HMP OTUs to six separate 16S sequence databases, indicated. For each HMP OTU, the y-axis of each panel shows the percent identity for the best matching sequence from the queried database, as determined by the program align.seqs in Mothur [30]. The x-axis of each panel shows the fraction of samples in which the OTU was present, at the body site of its highest prevalence. For example, a value of 0.5 means that the OTU was present in, at most, 50% of samples from a particular body site. The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. Horizontal lines indicate 98% and 90% sequence identity.
Many HMP OTUs were Well Represented in Other Human Microbiome Cohorts
While the close match of most of the HMP OTUs to the Silva database (Fig. 3A) indicated that most of the common taxa within the HMP OTUs have been seen before, the Silva database contained many sequences that are from environmental samples and may, therefore, not be relevant targets for the human microbiome. In order to determine whether the HMP OTUs are likely to be reproducibly observed in human cohorts, we compared the V1–V3 HMP OTUs to three recently completed metagenomic surveys of the human microbiome (details in Table S2) [33], [34]. Fig. 4A shows that the HMP OTUs most prevalent in stool were also largely present in the stool samples taken from the non-HMP cohort. We concluded from this that the more prevalent a taxa was within HMP stool samples, the more likely it is to be observed in other cohorts. A similar pattern was seen when comparing HMP V1–V3 saliva samples (Fig. 4B) and vaginal samples (Fig. 4C). We concluded that, at least for the most common taxa, there are sets of microbes that reproducibly appear in multiple cohorts. Since the organisms represented by these HMP OTUs were reproducibly observed across cohorts, obtaining their whole-genome sequences would represent a rich and universal resource that would inform multiple studies.
Databases were created from non-HMP enrolled healthy volunteers in which stool (4A), saliva (4B) and vaginal (4C) microbiomes were characterized (see Table S2). For each HMP OTU, the y-axis of each panel shows the percent identity for the best matching sequence from the queried database, as determined by the program align.seqs in Mothur [30]. The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. Horizontal lines indicate 98% and 90% sequence identity.
Selection of a "Most Wanted" Group of Taxa Prioritized for Genome Sequencing
Though 97% 16S sequence identity is commonly used to define two organisms as the same 'species' and can perform well to distinguish species, there are many examples of how imperfectly 16S relatedness performs as a proxy for taxonomic and genomic relatedness [35], [36] including those that show significant genomic variation among organisms sharing >99% 16S sequence identity [37]. We, therefore, might posit that any HMP OTU lacking 100% identity to a sequenced genome has not been well represented among sequenced organisms and should be targeted for isolation and sequencing. While sequencing all organisms with less than perfect identity to an already sequenced organism would be ideal, we sought to define percent identity thresholds that would better help us to prioritize organisms for whole genome sequencing (described in Document S2 and Table S3).
We considered HMP OTUs that had less than 90% identity to either the GOLD-Human or HMP strains database to be "high priority" or "most wanted" taxa since these were most distant from already-sequenced genomes and are likely to represent un-sequenced genera (or higher level taxonomic groups e.g., family) from the microbiome. We kept taxa in our "high priority" set even if they had a close match to the GOLD database because we reasoned that environmental strains, not associated with the human microbiota, might have significantly different genome contents even if the 16S rRNA genes were closely related. HMP OTUs with greater than 90% identity and less than 98% identity to GOLD-Human or HMP strains database were assigned to a "medium priority" group and are likely to represent un-sequenced species from the microbiome. Finally, HMP OTUs with greater than 98% identity to either the GOLD-Human or HMP strains database were put into a "low priority" group since these share the highest identity to already sequenced organisms isolated from humans. Also, because in this initial pass, we wanted to avoid directing resources toward isolating and sequencing microbes that are not prevalent within the human microbiome, we also assigned to the "low priority" group any microbe that did not occur in at least, 20% of samples from any body habitat. We reasoned that sets of taxa below this threshold might include many environmentally derived taxa that would not be reproducibly associated with the human microbiome. Supporting this, less frequent HMP OTUs were also less likely to share high identity to 16S data from other human derived samples (Fig. 4A–C) further suggesting that less frequent taxa are transient organisms from the microbiome, not held widely by healthy humans.
Cultivated Organisms are Well Characterized by Whole-genome Sequencing
In order to determine to what extent taxa that have been sequenced are also the taxa that have been cultivated, we compared, for each HMP OTU consensus sequence, the best match within two 16S sequence databases of cultured organisms, "named" and "unnamed", to the best match from a sequenced human database (GOLD Human or HMP strains) (Fig. 5). Almost without exception, taxa that have been whole-genome sequenced have an equal or better match in the databases of cultured organisms. Taxa within our "low priority" group were assigned that designation because they have >98% identity to a sequenced taxa; nearly every one of these taxa also had a >98% identity to a cultured taxon (Fig. 5A; grey symbols). This unsurprising result reflects current pipelines for microbial whole-genome sequencing that are dependent on culturing; while not every taxon with >98% identity to cultured organisms has been sequenced, nearly all sequenced taxa are present at high identity in the databases of cultured taxa. In contrast, only 30% of the 338 "medium priority" OTUs (blue symbols Figs. 3, 4, 5) and 17% of the 119 highest priority HMP OTUs, our "most wanted" (Figs. 3 4, 5, red symbols), had >98% identity to cultured organisms suggesting that completing the genome sequences for many of our "high" and "medium" priority organisms may require new methods for isolation. The fact that the "medium" and "most wanted" HMP OTUs were, on average, 10-fold less abundant than the low priority OTUs (average relative abundance was 0.015 versus 0.002) further suggests that it may take special culture- and, possibly, single cell-based methods to capture these less abundant, "most wanted" organisms.
For each taxa, the percent identity from the best match to a human sequenced database (GOLD-Human or HMP-strains) versus the best match to a sequence database of cultured organisms (named or unnamed). The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. (A) OTUs that are present in at least 20% of all samples in at least one body habitat; (B) all HMP OTUs.
The "Most Wanted" Distribution and Hope for Capture
The right panel of Fig. 2 illustrates the relative distribution of the "most wanted"" HMP OTUs among the five major body habitats in which they were found most frequently. Though we did not attempt to identify "high priority" organisms from every body habitat, between 1.7% and 10% of total OTU diversity from body habitats (Fig. 2, left panel) were among our "most wanted" OTUs (Fig. 2, right panel). The taxonomic assignments of these "most wanted" were also diverse; 11 of 15 total bacterial phyla and 121 of 275 total bacterial genera identified within the HMP volunteers were represented. Though we observed that the proportion of V1–V3 and V3–V5 "most wanted" OTUs (Fig. 2, right panel bar plots) was not as consistent as for the total set of HMP OTUs (Figure 2, left panel bar plots), we were able to explain this by the identity threshold applied; V3–V5 HMP OTUs appeared to have less overall sequence divergence from our databases as compared to the V1–V3 HMP OTUs. We did not attempt to correct the V1–V3 and V3–V5 regions for different rates of evolution.
Finally, to demonstrate that the "most wanted" HMP OTUs can be captured, we compared HMP OTUs to publicly available 16S sequences from 238 bacterial single cells sorted from a stool sample taken from one healthy non-HMP volunteer (Roger Lasken, personal communication and http://hmpdacc.org/HMMDA16S/#data). Table S4 summarizes the global alignment results for this comparison. We identified 6 single cell 16S sequences with high identity to 6 different "most wanted" HMP OTUs belonging to the Firmicutes phylum (93.5–100% identity), all of which were found most frequently among stool samples of HMP volunteers. In addition, we identified 33 single cell 16S sequences with high identity to 12 HMP OTUs that met all of the criteria for "most wanted" inclusion except for their low (<20%) frequency among HMP stool samples. The presence of these 12 low frequency HMP OTUs, including one with identity to otu_1054_V1V3, previously identified as a novel organism related to Barnesiella [38], suggests that our frequency threshold of 20% might ultimately prove to be too strict and that some infrequent taxa might be present in the healthy human microbiome at a higher frequency than these data predict. Alternatively, the 16S sequencing depth achieved by the HMP with 454 technology may have been too low (with an average of 6,200 reads/sample) to reliably observe common, but low abundance taxa. Despite these concerns, these data demonstrate that the "most wanted" OTUs should be relatively easy to find. Certainly, our ability to identify and initiate whole-genome sequencing on more than 10% of all the "most wanted" OTUs from stool (Fig. 2, right panel) within a single stool sample supports the feasibility of our goal of constructing a comprehensive reference genome catalog of the human microbiome.
The goal of our project is to identify and create a prioritized list of common and unsequenced members of the microbiome for whole genome sequencing. We assert that a modest sequencing effort (on the order of one hundred "most wanted" taxa described in Table 2) combined with existing databases will result in genome sequences being available for a large majority of the most common microbial taxa present in the human microbiome. Generation of such a resource will assist in the ongoing efforts to understand how pathways encoded in microbial genomes contribute to human health and disease phenotypes and make more tractable phylogenetic assignment for short read whole-genome metagenomic experiments.
We were able to achieve a simplified view of the human microbiome where a modest number of taxa (on the order of 1,000) were able to capture ∼95% of all the V1–V3 and V3–V5 HMP sequences (Fig. 1). The majority of the sequences not contained in an OTU were chimeric (Table 1) suggesting a high rate of error in unincorporated sequences. For this reason, we ignored all sequences not incorporated into an OTU. Removal of OTUs that had a chimeric consensus sequences (see Document S1) further simplified our view of the taxa present in the HMP OTUs with on the order of ∼800 non-chimeric OTUs found for both the V1–V3 and V3–V5 sequence sets (Table 1). These non-chimeric OTUs generally had a very close match in the Silva database (Fig. 3A). Because the Silva database largely reflects uncultured taxa, this is unsurprising. The most prevalent OTUs found in the HMP V1–V3 dataset were clearly also present in stool (Fig. 4A), saliva (Fig. 4B) and vaginal samples (Fig. 4C) from other cohorts. It was, therefore, clear that many of the same taxa occur across different subjects in multiple cohorts. While the 16S sequences representing these taxa were repeatedly observed across different experiment sets, many of these taxa have not yet been captured in culture collections (Fig. 3E-3F) or characterized with whole genome sequencing (Fig. 3B–3D).
The initial observations based on 454 pyrosequencing reported what appears to be near infinite diversity in environmental habitats [39], [40]. It currently remains unclear the degree to which such diversity reflects rare sequencing errors and chimerism. Because our study utilized the program AbundantOTU [22], which required construction of a consensus sequence from multiple reads in order to form an OTU, our analysis path deliberately avoided rare taxa. Our study is, therefore, neutral to the question of whether the rare biosphere represents true novel taxa or sequencing or PCR error. Moreover, our assignment of any taxa that was not seen in, at least, 20% of all samples from any body habitat to the "low priority" group further weights our priority lists against taxa that are not highly prevalent. We assert that emphasizing the sequencing of the most prevalent taxa first represents a rational deployment of sequencing resources. Of course, a limitation of this or any study that relies on the 16S rRNA view of a microbial community is that this one gene may not perfectly reflect the content of the rest of the genome or the evolutionary distance between organisms. Genome sequences will assist in this regard.
In this paper, we used percent identity from a global alignment as our metric to compare a query sequence to a reference database. Percent identity has some obvious advantages over other metrics. First, it is easy to calculate and makes intuitive sense, even to those without a background in phylogeny. Second, in a recent paper [41], it was shown that percent identity based on global alignments yielded more accurate matches to reference databases than a local alignment strategy based on best BLAST hit. There are, however, obvious disadvantages with the use of percent identity as a distance metric as well. Percent identity does not correct for different rates of evolution in different regions of the 16S sequence. This likely explains why we observed more "most wanted" V1–V3 OTUs than V3–V5 because the rate of evolution of V1–V3 is known to be more rapid [42]. An approach based on phylogenetic trees may have corrected for these sorts of differences by normalizing the background rate of evolution. We assert, however, that our collection of "most wanted" OTUs would be similar even if we had taken such an approach. When we used the phylogenetic tree-based method, pplacer [43], to place the HMP OTUs into a reference tree of sequenced taxa, we observed a highly overlapping set of HMP OTUs that were most distant from sequenced taxa on this tree and the "most wanted" taxa based on the global alignment criteria (data not shown). We are confident, therefore, that our results are not fundamentally a product of our choice of distance metric.
The HMP cohort was designed to measure the variation within healthy individuals. We would expect, therefore, that there will be some pathogenic taxa that are associated with disease that are not prevalent within the HMP cohort. We would anticipate future sequencing efforts to capture the genomes of these disease-associated microbes. As the cost of sequencing continues to decrease, and Illumina sequencing of 16S sequences becomes more common, the number of sequences per sample will increase well beyond the ∼6,000 sequences seen on average in HMP samples. In these future metagenomic sequencing experiments, some low abundance taxa that were not regularly detected with the sequencing depths of the 454-based HMP OTUs may appear as more highly prevalent. Nonetheless, given the current view of the human microbiome that is generated with the HMP OTUs through 454 sequencing technology, we assert that our list of high priority taxa is a reasonable use of resources to fill in the gaps of the phylogenetic tree representing the human microbiome.
The National Institutes of Health (NIH) is actively supporting the development of new culture- and single cell-based methods for bringing "most wanted" organisms to the sequencer. So far, the results have been very promising; the HMP is currently sequencing new isolates and single cells representing priority organisms. Though these efforts will continue, we appeal to the broader community to use the "most wanted" list, available at http://hmpdacc.org/most_wanted, to expand culture and genome collections to include these elusive members of the healthy microbiome. Finally, we believe that the simplified analysis path used to create the "most wanted" list can also be used to measure and direct progress of whole genome sequencing and culturing efforts for ongoing and future microbiome-related studies, human-related or otherwise.
Clustering 454 Data with AbundantOTU and Chimera Removal
V1–V3 and V3–V5 16S rRNA sequences were taken from the LQ HMP pipeline (from the files "hmp1.v13.lq.seq.summary" and "hmp1.v35.lq.seq.summary" provided in version 2.0 of the release to the 16S working group by Pat Schloss (ftp.hmpdacc.org;/16S/Production/Analysis/PPS-and-SRP002395-1.0/Schloss_Lab-2.0/finalData). The file "pds.metadata" within that release was used to assign subjects and body habitats. The non-HMP data sets, described in Table S2, were either downloaded from NCBI SRA (oral study, SRA024393, and vaginal study, SRP002463) or were obtained directly from the authors (stool study). The program AbundantOTU v2.0 and v4.2.40 [22], with the default parameters, was used to cluster 16S sequences from the HMP and non-HMP data, respectively (Table 1 and Table S2). Chimeric sequences were removed with the program UCHIME [23]. OTUs were considered chimeric if their consensus sequences were flagged by UCHIME in either de novo mode, in which the number of times each consensus sequence was observed was set to the number of reads which mapped to the corresponding OTU, or in the reference mode, where the reference was the GOLD database, which contains 16S sequences from fully sequenced genomes and therefore cannot contain chimeras. For non-HMP data sets, only the reference mode was used with GOLD serving as the database. The website, http://hmpdacc.org/most_wanted/, includes links to AbundantOTU output files that enable retrieval of the individual 454 reads 'assigned' to each HMP OTU.
Global Alignment of OTUs
Consensus sequences for each OTU (provided in the cons output file from AbundantOTU available at http://hmpdacc.org/most_wanted/) were used to represent each taxa. Global alignments were performed against each reference database by using the program align.seqs in version 1.15 of Mothur [30]. For non-HMP data sets, version v1.20.3 of Mothur [30] was used to align HMP OTUs to non-HMP consensus sequences. For single cell analysis, version v1.20.3 of Mothur [30] was used to align single cell forward and reverse 16S sequences to a database of HMP consensus sequences. For each single cell, the 16S sequence with the highest aligning fraction (alignment length/query read length) was assessed for "most wanted" status. RDP taxonomy was assigned with version 2.1 of the standalone version of the RDP classifier [28]. No confidence criteria were enforced since selection of priority OTUs did not rely on accurate taxonomies. All of the databases for which the HMP OTUs were searched are listed in Tables S1 and S2 and the results of these searches are available at http://hmpdacc.org/most_wanted/.
Creation of 16S Reference Data Sets
Greengenes [44], [45] holds publicly available 16S rRNA gene sequence records from NCBI >1250 bases in length and verified as 16S by NAST alignment [46]. Each reference data set was created as described in Table S1.
Stool Single Cell Preparation and 16S Sequence Generation
Flow sorting and genomic DNA amplification from single microbial cells from fecal and oral samples was carried out according to Chitsaz et. al. [47] except a bacterial fraction was enriched from stool samples by nycodenz centrifugation [48] prior to sorting and both stool and oral cells were flow sorted into 2 µl of modified TE (10 mM Tris, 0.1 mM EDTA, pH8.0). Following cell lysis, MDAs were carried out using GenomiPhi HY Kit (GE Health Sciences) as per the manufacturer's instructions except reactions were scaled to 12.5 µl volumes (personal communication from Roger S. Lasken). 16S amplification and sequencing was performed as described in Chitsaz et al. [47]. Stool single cell 16S sequences can be found at http://hmpdacc.org/HMMDA16S/#data by clicking the "Fecal Samples" link.
Supporting Information
Figure S1.
The UCHIME ref score, against GOLD database, versus the fraction of reads chimeric in each OTU for each consensus sequence. Left panel: V1–V3; right panel V3–V5. Gray indicates a consensus sequence called chimeric by UCHIME against the GOLD database.
Figure S2.
UCHIME Ref scores versus UCHIME de novo scores for V1–V3 (left panel) and V3–V5 (right panel). Colors indicate whether the consensus sequence was called chimeric by just UCHIME de novo (red), just UCHIME ref to the GOLD database (gray), both methods (blue) or neither method (black).
Figure S3.
Silva percent identity versus max UCHIME score (max of UCHIME ref and UCHIME de novo) for V1–V3 (left panel) and V3–V5 (right panel). Colors indicate whether the consensus sequence was called chimeric by just UCHIME de novo (red), just UCHIME ref to the GOLD database (gray), both methods (blue) or neither method (black).
Table S1.
Reference 16S sequence databases against which HMP OTUs were compared.
Table S2.
Non-HMP data sets against which HMP OTUs were compared.
Table S3.
Comparing species- (A) and genus-level (B) assignments to define percent identity cut-off values for prioritizing HMP OTUs. (See Document S2).
Table S4.
Comparison of single cell and HMP OTU consensus 16S sequences to identify "most wanted" single cells for whole genome sequencing.
Document S1.
Exploring high chimera rates among HMP OTUs.
Document S2.
Determining percent identity prioritization thresholds.
We thank the HMP Strains Working Group, Roger Lasken, George Weinstock and the HMP Technology Development Grantees for helpful feedback throughout the project, Leslie Gaffney (Broad Institute) for much needed help with figures and editing and Kim Lewis (Northeastern University) for inspiring the start of this work.
Author Contributions
Conceived and designed the experiments: AF TD KW ES JB BB AE. Performed the experiments: AF TD KW JB TH AE. Analyzed the data: AF AE. Contributed reagents/materials/analysis tools: AF TD PH YY KL HH-C. Wrote the paper: AF AE.
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Tagged: VW
Lovely Lavenham
Last weekend the 3rd International Vintage Volkswagen Show was held in the historic town of Lavenham in Suffolk, UK. I had helped to organise the first two shows which take place every four years but this on was organised by The UK Historic VW Club who I entrusted it to after deciding it need a bigger, dedicated team for it to continue to happen.
I set off for the 150 mile, 3 hour drive to Lavenham at 5.30am on Saturday morning. The sun was already out and the weather was looking promising for the day. When I arrived in Lavenham, I managed to park near the Market Square which was to be home to the oldest Beetles and Busses – following the same format as the previous shows. There was a great turn out with around 160 vehicles pre registered for the weekend, arriving from all over Europe. I hung around the Square taking photographs until it was full and chatted with some old friends who I've not seen for a while – probably the last show in Lavenham 4 years ago!
Moving on, I followed the 'Vintage VW Trail' which lead me to Lavenham Hall which was a new display area which hasn't been used before for the show. The house and gardens made a fantastic setting for the Karmann Ghias and Commercial Busses. The house is home to sculptor Kate Denton and her sculptures are placed around the grounds and gallery, next to the house and barns.
Continuing along the trail, I was directed to the sports field which was the location of the sixties beetles, later split busses, military VWs and the trade stands. Lots more traders present this year which was great to see. I stopped to chat with Rob and Paul for a while over coffee and bacon rolls and then headed back to the market square just in time for the first rain shower of the day. The rain quickly passed and the sun returned for a while before the next shower rolled in. I headed home having had a great day as a visitor to the show. Thanks to The Historic VW Club and everyone involved for putting on a fantastic show, well done!
Click on the first picture for full screen images…
Original '55 for sale – again!
Well, after selling my very original 1955 Stratos Silver Beetle to Laurent Gachoud from Switzerland a few months ago, It would seem that Laurent would be required to restore the car to be able to register it in Switzerland! Laurent has therefore decided that the car is far too original and would be far better staying as it is so would like to sell the car to someone who's local vehicle laws are not as strict as those in Switzerland. There are lots of photos on my previous post and you can contact Laurent directly at: email@example.com if you are interested in purchasing the beetle.
Original '55 for sale
Thanks for all the interest, Sale pending…
I've decided that after six years of ownership, it's time to sell my very original 1955 Oval-Window Beetle.
It's an unrestored 1955 VW Oval Beetle still in original Stratos Silver paint, one of the nicest colours for a vintage VW. It has driven just 139084 KM (86422 Miles) from new and only had one owner in Sweden from 1955 -2003 when it had 68,000 Miles on the clock. It has never required any welding and is in remarkable condition for a 60 year old beetle, a true survivor!
The Stratos Silver paint and all the bodywork is completely original and has a lovely patina. It appears that just a single semaphore was replaced at some point in it's early life in Sweden. It has it's original 30hp engine from April '55 which has just been serviced and drives great – as you would expect for a low-mileage VW.
The interior is original too and has the original floor mats, carpets, upholstery, door-cards and headlining. VW lap belts are fitted at the front and a single 3-point belt at the back.
I've always kept the beetle in my garage and it's only covered 700 miles since I bought it in 2009.
It has several period accessories fitted including original Swedish wheel trims which it would have had from new, a dash-clock, Bambus parcel shelf, VW Gear leaver lock (no key), Passenger sun-visor and a high-level rear LED Brake light in the back window which helps overcome the size of the small heart-shaped rear brake lights! It also has an optima red-top battery so it always starts easily even after several months.
If originality is your thing, I doubt you will find a better early oval-window beetle. I'm happy to help with world wide shipping at the buyers expense. I would consider a trade for a VW T4 or T5 Camper with a similar value in the UK.
I can be contacted through this blog or directly via: email@example.com
3 years ago today…
I just got a reminder from WordPress that it was exactly 3 years ago today that I made my first post on Bandwagen. And it's also a double celebration as today the followers counter ticked over the 6,000 mark. So a big thank you to everyone out there who is following my blog. If you look back at my earlier posts, I think that my photography has improved a bit over the 3 years – And the photos have gotten bigger too! Here are some of the photos from that first post, way back in 2011 from the REME show…
Stanford Hall 2014 Continued…
VWs at Vintage Stony
Last month I made it along to the annual summer classic car gathering in Stony Stratford, about 30 minutes drive from where I now live. It was a very hot day which was perfect for getting everyone out in their classics for the day. As usual, there were just a hand full of Volkswagens but the quality definitely made up for the quantity! I've posted some other pictures from the show on my other blog, MHPIX.
The Chiltern Hills Rally 2014
As is was a nice day, I decided to pop along to the Chiltern Hills Rally. I've not been to this car show before but, there have beed signs for the show on my route to work and I pass the show site every day. Out of the 1000 or so vintage vehicles there were only a hand full of VWs on display. The Chiltern Hills Vintage Vehicle Rally is organised by The Game Club to raise money for local good causes. The Rally is a well established annual event which enables the owners of classic and vintage vehicles to gather together in the Buckinghamshire countryside. Just for a change I took along my Sigma 10-20mm wide angle lens instead of my Canon 24-70 2.8L lens which is attached to my 60d most of the time. I think you'll agree the pictures look a little different from the ones I normally take a t shows and post on here. Let me know what you think.


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Expanded line up?
Expanded line up?
There will be revealed more variants that will have the same skateboard platform as the Tesla Model S and the Tesla Model X. Elon Musk has said that he wants to reveal one model every year. I am not sure if that really is possible, but if he really wants it, then he will really make it happen. But anyhow, there will be at least one new model in less than 2 years time (48 months). Just be patient, because he will deliver.
Tesla Motors did invest a lot of effort, time, energy, money etc. to realise the Tesla Roadster, which originally was the Lotus Elise (ICE vehicle). Therefore I do not expect Tesla Motors offering "idiot-proof conversions for popular past platforms" any time soon.
And I think that it would be better to wait for the Tesla Gen3, instead of convert old platforms to electric. I do not know what other people think of your idea?
TWC seems to think TMC's goal is like his: produce a car that impresses car buffs. To the extent it ever does that, it does so only as a means to an end, or incidentally. To persuade the public to drive electric and thus, Elon thinks, save the planet from the off chance that CO2 is harmful (IMO, it is not), he has to produce electric cars they want, and sell millions.
Catering to conversion buffs is not a way to that goal. They are an insignificantly tiny portion of the population, with little clout.
Along the way, he concluded he needed to produce "the best car in the world" (in all the dimensions that matter, he adds. And his definitions of "matter" include technology, ride, safety, etc. Unfortunately, perhaps, they do not include parking sensors.)
I doubt there is anyone (except certain probable trolls who shall remain nameless) here who doubts that he's produced the best value per auto dollar by a wide margin. The discussion with the rest of the world is just beginning on the issue!
Some Tesla followers seem to think that Tesla will never develop lower-priced cars, and that they will basically always stay in the realm of a BMW like line-up. The in-development Bluestar has probably a $30,000 price tag as its base. So it's steal not an affordable car for many people.
Personally, I don't necessarily think it would be weird for Tesla to develop a whole range of cars from cheap to luxury, be it all under the same brand, or under newly created brands. There are many other industries with companies like that (and a few other car manufactures too, like Hyundai). It's not really that strange. However, even if that does happen, I feel that's many years away, more than ten. We're still in the early adopter phase IMO.
However, even if it's not Tesla that eventually develops the cheap, yet fully capable cars, I still feel that if Tesla succeeds, someone will be doing it. It could be Tesla partnering with other auto makers and selling their powertraing technology, or it could simply be competitors who are finally catching up.
lol, not sure how I managed that, but:
steal = still
Hey TommyTwinCams, you might have to change your name. How about TommyTwinCoils?
Or TommyTwinBrushes?
@dstiavnicky - Sorry, there's no brushes either. Tesla (and others) use an AC induction motor - originally conceived by Nicola Tesla which is where they took their name from...


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Custom Continuum Notifier – Step 2: Build a dummy notifier
Now that we have Continuum building without any problems, the next step is getting a basic notifier coded up and Continuum aware of it.
The Continuum user wiki makes this process seem simple enough: create a new notifier extending AbstractContinuumNotifier and register the new notifier in application.xml. Essentially, this is true … with a few minor modifications.
- Create your new notifier project
- Under the continuum-notifiers Maven module, create a new module called continuum-notifier-web as a standard Maven project (or dupe one of the existing ones)
- Modify the new module's pom.xml to have continuum-notifiers as its parent and add the continuum-notifier-api artifact as a dependency
<project ...> <parent> <artifactId>continuum-notifiers</artifactId> <groupId>org.apache.continuum</groupId> <version>1.2.3</version> </parent> <modelVersion>4.0.0</modelVersion> <artifactId>continuum-notifier-web</artifactId> <name>Continuum :: web-Dashboard</name> <dependencies> <dependency> <groupId>org.apache.continuum</groupId> <artifactId>continuum-notifier-api</artifactId> <version>1.2.3</version> </dependency> </dependencies> </project>
- Add the new sub-module to the continuum-notifiers parent pom.xml.
<modules> <module>continuum-notifier-api</module> <module>continuum-notifier-irc</module> <module>continuum-notifier-jabber</module> <module>continuum-notifier-msn</module> <module>continuum-notifier-wagon</module> <module>continuum-notifier-web</module> </modules>
- In your new project, create a basic notifier that simply logs that it was called. This class should extend AbstractContinuumNotifier and implement getType() and sendMessage():
package org.apache.maven.continuum.notification.atkpwadashboard; import org.apache.maven.continuum.notification.AbstractContinuumNotifier; import org.slf4j.Logger; import org.slf4j.LoggerFactory; public class WebNotifier extends AbstractContinuumNotifier { private Logger log = LoggerFactory.getLogger(getClass()); public String getType() { return "web"; } public void sendMessage(String messageId, MessageContext context) throws NotificationException { log.info("Web Notifier has been called!"); } }
- Build your new module either by a full build of Continuum or by just building your sub module (mvn package).
- Deploy your new notifier
- Copy the newly created notifier .jar into your Continuum intallation at <CONTINUUM_BASE_DIR>/apps/continuum/WEB-INF/lib/continuum-notifier-web.jar
- Modify <CONTINUUM_BASE_DIR>/apps/continuum/WEB-INF/classes/META-INF/plexus/application.xml to register the new notifier by adding the following code:
<component> <role>org.apache.maven.continuum.notification.Notifier</role> <role-hint>web</role-hint> <implementation>org.apache.maven.continuum.notification.atkpwadashboard.WebNotifier</implementation> </component>
- Restart Continuum
- On one of your managed applications, modify the pom.xml to use the new notifier:
<ciManagement> <system>continuum</system> <url>http://localhost:8080/</url> <notifiers> <notifier> <type>web</type> </notifier> </notifiers> </ciManagement>
- Profit.
Things to note:
- Continuum uses Plexus for its dependency injection. Since your notifier is extending AbstractContinuumNotifier which has dependencies, you MUST register your notifier as needing these inject or you will see some lovely and confusing NullPointerExceptions when you try to use the notifier.
- Technically you don't need to get Continuum to compile to build a new notifier, but having the source handy and being able to see how the rest of the project is structured helps.
- I haven't figured out how to get Continuum builds to auto install my notifier yet …. it is on my to-do list.
- To simplify creating the new project, I just copied continuum-notifier-jar and made modifications as necessary.
- The email notifier is called "mail" and is in the continuum-core module.
Big Frustrating Gotcha: Continuum's notifier plugin architecture only extends to the internals of Continuum but does NOT include any of the web-app's GUI. This means that your new notifier will not show up in any of the admin screens as an option, or have any edit/configuration screens a web user can see. These GUI elements are managed in the continuum-core and continuum-web-app modules, separate from the notifier code themselves. For what I was doing I didn't need this, but it would have been nice. It looked to be fairly simple to add the new notifier to the approrpiate .jsp's and have full graphical interface power.
Helpful Links:
- Continuum user wiki page on building a notifier
- Email chains one and two talking about doing the same thing
- Configure your notifier in the application.xml wrong and you might get an error like this
Last step is to make the notifier actually do something related to build ….
Custom Continuum Notifier – Step 1: Get Continuum to Compile
This past week I was charged with creating a custom Continuum notifier which would push a build's Selenium TestNG test results to a second system for reporting. Changing project priorities, distractions, poor documentation and some weird issues made this simple task take much longer than it should have. Hopefully, this series of posts will help make the process just a little bit smoother for the next person.
Visibility into the quality of a software project is crucial to delivering a top notch product. One direct way to achieve this is monitoring the team's UAT results over time. I have been slowly pushing the client's development teams to fully automate their user acceptance testing along side the rest of their build process. Enter Continuum and Maven, the client's choices for continuous integration and "one button" builds. Out of the box, Continuum had pretty much everything we needed from a testing/reporting standpoint, except that the development teams were spread out across several Continuum installations and management wanted a single place to see ALL teams' test results. Luckily, I found that Continuum has a plugin architecture for its notifiers – the plugins which decide what to do with the builds' results. Out of the box, Continuum comes with the ability to email and/or IM your build results in several ways. What I needed was a notifier that would send the testng-results.xml file generated by Maven's surefire testing plugin via a multi-part HTTP POST request to our reporting app. Sounded simple enough.
Use the Source Luke
A few quick Google searches taught me a couple things: 1) a number of people have wanted to to do exactly what I needed, and 2) there didn't seem to be any good end-to-end documentation on how to do it. First step, download the source and get it to compile. Next, according to the directions on the main site and the user wiki, was a simple mvn install.
First Build – Fail
Unfortunately, the continuum-release module's tests fail. I am still looking into why the release module tries to do a SVN commit during a install of the main project and not a deploy, but for the time being, it fails. In order to get past the release module's issues (the other modules install just fine and pass their tests) I sinned and added a -Dmaven.test.skip=true to the build and continuum-release installed like a champ.
Second Build – I forgot
Boom! Not so fast. OutOfMemoryError from maven while building the web module. Setting MAVEN_OPTS to increase the max heap memory Maven has fixed the problem.
Third Build – Fell off the log
Boom! Again. java.lang.NoClassDefFoundError on Commons Logging coming from the JSPC plugin (precompiling JSPS). It turns out that plugins live in the same classloader as Maven itself and the JSPC plugin requires commons logging. It also turns out that in the latest version of Maven (2.2.0) the internal dependencies changed and the version JSPC is no longer included in Maven's "uber" .jar. Fix? Dropped 1.1.1 commons logging three .jars into Maven's lib folder. Fixed.
Fourth Build – Houston, We Have Compilation
Finally, everything compiled and installed without problems. Next up, writing a dummy notifier and getting Continuum to use it.


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Tim Harbison
The Liberty Flames men's soccer team takes to the road one last time in the 2012 regular season, when they visit the Radford Highlanders for a Big South Conference match, Tuesday evening. Game time is scheduled for 6 p.m. at Patrick D. Cupp Stadium.
The Flames enter the match with a seven-game unbeaten streak (5-0-2). Liberty has not suffered a setback in the month of October.
How to Follow the Flames Live stats will be available for Tuesday evening's contest via LibertyFlames.com by clicking the live stats link under men's soccer in the schedule bar on the main page. Live stats are provided by the Radford Athletics Communications Office.
A Look at Liberty Liberty (7-6-2, 5-1-2) ran its unbeaten streak to seven games with a 1-1 tie against Gardner-Webb, Saturday. Goalkeeper Scott Sutarik recorded his fourth shutout of the year in the contest. The sophomore goalkeeper will enter the week with a 1.18 goals-against average and .737 save percentage. Sutarik has started every game of Liberty's unbeaten streak, posting a 0.66 goals-against average and three shutouts. Forward Kyle Breitmeyer leads the Flames with 15 points on the season. He enters the week tied for fifth in the Big South in goals. With his game-winner in Liberty's 2-1 overtime win over High Point Tuesday, Duininck is now second on Liberty with three goals and six points. Fellow defender Greg White is the only other Flame with more than one goal on the season with two goals. Midfielder Johnny Torres and defenders Tim Harbison and Uriah Bentick are tied for the team lead with three assists each. Head Coach Jeff Alder has led the Flames to a 115-85-21 record during his 12 seasons, capturing his 100th victory in a 2-0 win at No. 10 Virginia on Sept. 13, 2011. Alder's Flames posted an 11-6-3 record in 2011, en route to their second Big South Conference crown and fifth consecutive season with a double-digit win total.
All-Time Against Radford Tuesday's match between the Flames and Highlanders will be the 45th meeting between the two schools on the soccer field. Liberty has met Radford more than any school in soccer, with the Flames holding a 21-15-8 mark in the all-time series. After playing to a scoreless tie, Liberty advance on penalty kick, the last time the two teams met in the first round of the 2011 Big South Championship, Nov. 10 at Boiling Springs, N.C. The Flames also took the regular season match-up, 3-0, at Osborne Stadium on Nov. 2. Last meeting between the two in Radford, the Highlanders won 1-0, Sept. 18, 2010. Liberty has not won at Radford since 2004. Look at Radford After suffering their first Big South setback in a 4-1 loss to Coastal Carolina, Saturday, Radford (8-4-4) will enter Tuesday's game looking to snap a two-game losing streak. The Highlanders were unbeaten for eight straight contests (7-0-1) until falling at Virginia Tech on Oct. 23. Midfielder Bernardo Ulmo leads Radford with 10 goals and 23 points. Ulmo is tied for second in the Big South in goals. Fellow midfielders Chel Ho Park Kim and Ramzi Dridi each have four goals. Kim also has assisted on four goals. Radford goalkeeper Ryan Taylor has played every minute this season in the Highlander net. He has posted a 0.99 goals-against average and a .767 save percentage. The senior has five shutouts. Head coach Marc Reeves is in his third year at Radford. The Highlanders have posted a 24-21-9 record during his tenure.
The Conference Run Down Liberty is in the midst of seven consecutive Big South games to complete the 2012 regular season. Tonight's contest will be the sixth game of the stretch. The Flames have posted a 3-0-2 record thus far during the span. Currently, Liberty has 17 points with a 5-1-2 record and is one point behind Campbell in the standings. However, the Flames have two conference games left, while the Fighting Camels have one remaining. Coastal Carolina tops the Big South standings with a 9-0 record and 27 points. Radford is in second place with a 6-1-1 mark and 19 points. The Big South regular season comes to an end on Saturday, after which the top four seeds for the conference's tournament will be determined. Those four seeds will host games next Tuesday.
Overtime Overload Liberty has had its last four matches need more than the regulation 90 minutes to determine the outcome. The Flames have played extra minutes in each of their games since a 3-2 overtime victory at VMI on Oct. 16, posting a 2-0-2 record.
A Look Ahead Liberty will finish its regular season against the UNC Asheville Bulldogs at Osborne Stadium on Friday. Game time is at 7 p.m. Before the game, the seniors on the Liberty roster will be recognized.
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Species In-Depth
At the Aquarium
Our ruddy ducks are fed a waterfowl pellet food supplemented with mealworms, bloodworms, krill, mussels, and romaine lettuce. They live in the Shorebird Sanctuary exhibit outdoors on the second floor.
Geographic Distribution
U.S. coastlines north to British Columbia, Canada and Massachusetts and inland to Missouri. Introduced:Great Britain and Europe.
They are found in permanent fresh water or alkaline marshes. These ducks require areas that have open water as well as vegetative cover for protection during nesting. They breed in freshwater marshes and ponds. Freshwater is needed for the hatchings whose salt glands are poorly developed. The prairie potholes located in the Great Plains are favored areas. Winter shelters are shallow protected saltwater bays and estuaries along the coasts.
Physical Characteristics
Ruddy Ducks have a small, compact, chunky body with a characteristically vertically held tail and a proportionally large head and bill.
In the winter, both male and female birds have similar appearances. They are gray/brown with a dark cap, white breasts lightly barred with brown, white bellies, feet that are large, gray, and webbed, and a gray concave bill. In the spring the male's bill changes to a blue-gray color and his plumage also changes. He develops a red-brown or cinnamon colored chest, rump, and flank and conspicuous white cheeks. Females have a horizontal brown streak through their white cheeks and a less heavy bill.
With wings folded, ruddy ducks are approximately 35 to 43 cm (14 to 17 in) in length. Their wingspan is 53.3 to 61 cm (21 to 24 in) and they weigh 0.5-0.6 Kg (1.1-1.3 lbs). Males are larger than females.
They are primarily herbivores with about 75 percent of their diet some form of plants. Their food preferences vary by age, season, and location, and are influenced by nutritional demands for breeding, molting and feather growth, and migration. They feed on roots, underground tubers, green herbaceous foliage, and seeds of aquatic plants, seagrasses, and pondweeds. They also eat zooplankton, clams, snails, mollusks, brine shrimp, and insects, especially midge larvae. Midges are the bulk of their insect diet.
They forage almost exclusively by diving but occasionally will skim the water's surface of the water, straining food items from it.
Breeding of these ducks was once confined to the prairie states, but it is now more widespread to Manitoba, Canada and the Great Plains.
Ruddy Ducks pairs are usually seasonally monogamous. Reproduction begins with an elaborate display by the male in front of the female. The male will swim by her several times with his tail that is usually at a 45° angle raised to 90°. He puffs out his chest, bows, and slaps his bill against his chest to produce a drumming sound and to also create bubbles that rise from beneath his chest.
The female builds a basket-like nest from surrounding marsh plants about 20 cm (8 in) above shallow water. Material is not carried to the nest; the female reaches out and pulls it under her. She firmly attaches the nest to growing reeds, often arching the reeds over the nest to conceal it. She lines the nest with down. Usually 6 to 10 eggs that are white or a cream color and about 62 mm (2.5 in) long are laid. The incubation period is about 23 days. During the incubation the female imprints on the embryos by making low calls.
The dense whitish down of the new hatchling both traps air to make it more buoyant and serves as an excellent insulator. The precocious chicks are able to dive skillfully when only two days old. They begin to develop feathers at about two weeks of age and fledge 42 to 49 days after hatching.
Ruddy Ducks usually do not start their migrations to warmer habitats as long as food is available in their breeding areas and there is open water that is ice-free. The northward migration of these ducks to breeding areas usually occurs from February into April and the southern from cold to warmer areas from September through October annually. Migration usually occurs at night and large flocks of several hundred birds may travel together.
They have a difficult time getting air-borne. They seem to 'run' on the water using their broad webbed feet for several yards, always positioning their takeoff against the wind. Once in the air Ruddy Ducks are swift flyers. The rapid strokes of their small wings produce a whirring sound. On land they walk very awkwardly because of the far back placement of their legs so they prefer to escape danger by diving deep and swimming away from it instead of taking to the air.
These ducks are highly adapted for their aquatic lifestyle. They are excellent underwater swimmers due to the shape of the body, small wings, feet located at the extreme rear, and the stiff tail that makes a good rudder. Their feet are among the largest feet in relation to body size of all ducks. They dive obliquely using leg stokes, not their wings, to propel themselves downward. Ruddy ducks can disappear from sight without diving. Resting on the surface of the water, they can slowly sink under without causing a ripple in the water.
Molting to change to breeding (alternate or summer) plumage or non-breeding (basic or winter) plumage occurs twice a year. Nutritional demands are high during this time and the ducks seek habitat that will provide an adequate source of food and cover to hide them from predators. They cannot fly during the five weeks of molting because of loss of their flight feathers.
Ruddy Ducks are protected in North America under the Migratory Bird Treaty Act. In contrast in England where this species was introduced from the United States, they are considered to be an invasive species. Known as the 'pushy American duck", they are now being eradicated.
Some of the introduced birds escaped from captivity in 1940, bred successfully in the wild, and naturalized. Then they migrated to Spain where the former American ducks out-competed the male White-headed Ducks, (Oxyura leucocephala), an endangered European species. Successful mating has resulted in hybrids that, unlike many hybrids, are fully fertile. Pairs of wandering Ruddy Ducks are more aggressive than and can out-compete White-headed Ducks for nesting sites and food.
Special Notes
The size of the eggs laid by female Ruddy Ducks is the largest in relation to body size of all ducks. The female lays a clutch of one a day and the weight of the total number laid often exceeds her body weight.
Ruddy Ducks are brood parasites or parasitic egg layers. They often lay their eggs in abandoned nests of other birds such as the American Coot, in feeding stations of muskrats, and in active nests of other birds.


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Holmes County Sheriff�s Office announced multiple drug arrests over the weekend.
HOLMES COUNTY � Holmes County Sheriff�s Office announced multiple drug arrests over the weekend.
According to the report, on Jan. 18 Deputies received a tip of illegal drug activity at a residence in the Poplar Springs community.
When Deputies arrived, they observed a van in the driveway. Deputies made contact with the driver of the van, Melissa Hayes, 33, of Bonifay.
Deputies received consent from Hayes to search her vehicle and located a small amount of methamphetamine in her purse. Hayes was placed under arrest for possession of methamphetamine.
Also on Jan. 18, Deputies received another call of illegal drug activity at a residence in the Hickory Hill community. When Deputies arrived at the residence, they made contact with Lorraine Renee Kilzer, 38, of Westville.
Deputies then located several used syringes with methamphetamine residue. Kilzer, who is currently under the supervision of the Florida Department of Corrections, was placed under arrest for possession of drug paraphernalia.
On Jan. 21 a Holmes County Deputy conducted a traffic stop in the Gritney community for a registration violation.
The driver of the vehicle Donnie Ray Calhoun, 38, did not have a valid driver�s license. During a subsequent search, a small amount of methamphetamine and a glass pipe with burnt residue were located on his person.
Calhoun was placed under arrest for driving while license suspended, possession of methamphetamine and possession of drug paraphernalia.
�Cases the community�s involvement in fighting the war on drugs is essential,� said Sheriff Tim Brown.
Brown also asks if you have any information on illegal drug activity in your community please contact the Holmes County Sheriff�s Office at 850-547-3681 or Holmes County Crime Stoppers at 1-866-689-8477.


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It's A Proven Solution
Landscaping Bennet NE
Landscaping Bennet NE maintains all horticultural material and outdoor litter and debris control. The staff also maintains roads, bridges, walks, ornamental pools and outdoor furniture. The department works at construction sites to install or repair the landscape around those areas. We thrive for customer satisfaction. With 99% of our work coming from repeat customers and through referrals, its safe to say we like to build long term relationships with our clients.
We are family owned and operated. We provide professional quality services every time we visit you. We respond quickly to your concerns and we stand behind any service we provide. We have many years of experience in the landscaping with extensive knowledge in different areas such as grasses, trees, plants, bushes and ground covers. Our Knowledge of plants and their habitats will allow us to give you the best, long lasting results in Bennet, NE. We take pride in our work and we guarantee that our services will meet your highest standards! We are committed to providing the best our company has to offer in Bennet, NE, and the surrounding communities.
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College Basketball Poll Rankings
Indiana still No. 1, Duke up to No. 2 in AP poll
Indiana is still No. 1 in The Associated Press' college basketball poll. The holiday weekend tournaments caused a lot of change below.
Duke moved up to take Louisville's old spot at No. 2 after beating the Cardinals in the championship game of the Battle 4 Atlantis. Michigan moved up one place to third.
There were four newcomers to the Top 25 on Monday, all ranked in the last five: Georgetown, Minnesota, Illinois and New Mexico.
Indiana received 47 first-place votes from the 65-member national media panel, 29 more than Duke, which jumped three places.
Ohio State, Louisville, Syracuse, Florida, Kentucky, Arizona and Kansas round out the Top 10.
The teams that dropped out were UCLA, which was 11th, and Memphis, both of which lost two games last week. Connecticut and Baylor fell out after losing once.


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"Rust Hazely" kimono: Novella Royale || Studded denim shorts: Zara || Route 66 top: Urban Outfitters || Gypsy Rocker boots: Spell Designs
in today's outfit post I'm wearing one of my signature looks again, you all know how much I love wearing a biker tee, denim shorts and a kimono all together. :-) I could get my hands on this beautiful printed kimono by Novella Royale a few months ago when it was finally on sale. I loved it immediately when I saw it on Instagram, then I waited for it to be on sale (it was too expensive!) and thankfully it happened pretty soon. This is my third Novella Royale kimono and they're definitely my faves besides Spell & Arnhem kimonos. I really like its warm brownish/cream colorway which goes with almost everything. Because it's still summer and pretty hot outside I didn't want the outfit too be too dark, so I combined it with my grey biker top and some washed blue denim shorts. The whole look couldn't get any more comfortable, too.
Hugs x


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Chapter Release
Yosuke Ejima and his wife Keiko are visiting Mexico to research ancient civilizations. Their bus is heading for the Teotihuacan ruins when they suddenly get involved in gang related violence. Can they survive...?!
(C)KOJI MAKI / Beaglee Inc.
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|Series Title
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|Japanese Title
|ミキストリ (Miquiztli)
|Alternative Title
|Miquiztli: Taiyou no Shinigami, Mikisutori
|Koji Maki
|Beaglee Inc.
|Manga ,Chapter Release ,Seinen ,Supernatural ,Action
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Prison Planet.com
Wednesday, May 13, 2009
Police in the UK are encouraging citizens to report people who drive nice cars or buy expensive items to the authorities in a new campaign entitled, 'Too Much Bling? Give Us a Ring'.
"The Gloucestershire force is encouraging members of the public to report people wearing too much 'bling' during the recession. They are also urging people to shop anyone who drives flash cars or buys expensive items without the apparent means to afford them during the credit crunch," reports the Daily Mail.
Posters for the campaign indicate that the targets of the stasi-like crackdown are well-dressed people who own expensive cars, boats and smoke cigars. Apparently, police in the UK think that actually being middle class and able to afford a nice lifestyle is a sign of probable criminal behavior.
Gloucestershire's Chief constable Dr Timothy Brain said, "In the current time of financial uncertainty, those who live a lavish lifestyle with no discernable, legitimate income become even more apparent."
Former Home Secretary Ann Widdecombe responded, "Is this a joke? If the police spent half as much time tackling crime and getting out on the beat as they do coming out with this ridiculous stuff, we'd all be better off….How are you meant to judge if someone buying a piece of jewellery can afford it?"
As we have previously covered in-depth, UK police authorities routinely launch expensive PR campaigns encouraging citizens to report on each other for the most mundane activities.
Examples of suspicious behavior and potential terrorist activity worthy of being reported to police includes looking at CCTV cameras, owning a mobile phone, a van, a computer or a camera, living in an apartment, getting a refund on an item bought in a store, throwing away chemical and pharmaceutical products, or taking photographs.
Around 60,000 citizens are currently being trained by the domestic security service MI5 as "terrorist spotters" who case the streets looking out for such activities.
FLASHBACK: London Police Encourage Citizens To Report Contents Of Each Others' Bins To Prevent Terrorism
FLASHBACK: Tourists Or Terrorists? Police Erase London Sightseers Photographs Citing Terrorism
FLASHBACK: Civilian Force Of 60,000 Trained As "Terrorist" Spotters
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Student or Learner
Quizzes -> Beginner English -> Articles -> Last & the last:
Question 2 is missing a space.
Not a big deal, but thought I'd mention it.
Quizzes -> Beginner English -> Vocabulary -> Remember & Remind:
The last question (10) makes no sense to me.
Cheers, y'all!
Last edited by pehpsi; 02-Jan-2010 at 07:27.
Thanks- sorry I only just saw this. #10 is like send my regards.


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Glad To Be Here
Last July 4th, I wrote a column about how America was an okay place to be. There's a lot of crap that has happened in the past year to make some people doubt that, but I still stand by my assertion.
Some people say they want to move – that Europe or Australia or anywhere but America would be better. But I like it here. So I will honor our country this July 4th by making fun of the crap that happened everywhere else this weekend.
Let's start with Finland, where 7,000 people watched two Estonian students win Finland's seventh annual wife-carrying world championship by carrying a woman 830 feet through a pool and over hurdles in just over a minute. The champions were pumped by the crowd who loudly cheered, "why the hell are we watching this?" Okay, so the crowd really enjoyed it. But a wife-carrying world championship? I guess there are rednecks everywhere.
There are also hookers everywhere, as evident in the new policy in which the Dutch government hands out "seals of quality" for better run brothels. I can just imagine the size of the line forming to inspect them. "I don't know, these hookers aren't as clean as the ones from the last brothel we had sex in."
And while strippers aren't always hookers, I felt this would be a good time for a lovely Canadian story that involved two "dancers" attacking a third at a strip club. According to the Associated Press, the two felt the dancer had a "snooty attitude." I haven't been in that many strip clubs, but isn't that kind of the point?
Speaking of strippers, a 55-year-old German sex therapist who has been repeatedly arrested for jogging nude was just fined $750. The man argued that being naked is his civil right. That's just weird - maybe he should see a sex therapist. Actually, this guy's strategy for drumming up business is brilliant. You know much erectile dysfunction he's causing just by jogging naked?
And here's a quaint erectile dysfunction story: South Korean police arrested a man and confiscated 3,000 phony Viagra pills. Which is too bad, because the guy would have been the toast of the cell block if those pills were real.
"Ah, geez – am I really getting paroled? We're busy!"
Authorities say that people should have been tipped off to the fake Viagra because of how cheap it was. I suggest that they also notice that someone is trying to sell them sex medicine out of the trunk of a Buick.
One thing that's not cheap is a scoop of mud from England's Glastonbury music festival. The mud sold for the equivalent of $890 US on eBay, birthing the new phrase, "dirt expensive." The mud was more expensive than the standard price for a scalped ticket, making the purchase a bit curious. And reinforcing the already birthed phrase, "dirt stupid." When asked what he'd do with all the money, the mud's auctioneer said he planned on inspecting some brothels.
I know, I know. There are plenty of dumb things that happen in America, too, but we've got 364 days a year to talk about that stuff. But for all my foreign readers, there is one American story from this weekend that bears mentioning.
As if the Florida election board wasn't made fun of enough already, a list of residents who couldn't vote due to their felony convictions was released this weekend. Almost 50,000 people on it never committed a crime, making authorities scramble to fix the error. However, many of the wrongly categorized citizens have not bothered to come forward and identify themselves, confessing, "we were just going to vote for Buchanan anyway." Which, if it happened, would probably make me move.
Happy July 4th, everybody. I'm going to go practice for next year's wife carrying championships.