Fractal Characterization of Fracture Networks: An Improved Box-counting Technique

Box counting is widely used for characterizing fracture networks as fractals and estimating their fractal dimensions (D). If this analysis yields a power law distribution given by N $\propto$ r−D, where N is the number of boxes containing one or more fractures and r is the box size, then the network is considered to be fractal. However, researchers are divided in their opinion about which is the best box‐counting algorithm to use, or whether fracture networks are indeed fractals. A synthetic fractal fracture network with a known D value was used to develop a new algorithm for the box‐counting method that returns improved estimates of D. The method is based on identifying the lower limit of fractal behavior (rcutoff) using the condition ds/dr → 0, where s is the standard deviation from a linear regression equation fitted to log(N) versus log(r) with data for r \u3c rcutoff sequentially excluded. A set of 7 nested fracture maps from the Hornelen Basin, Norway was used to test the improved method and demonstrate its accuracy for natural patterns. We also reanalyzed a suite of 17 fracture trace maps that had previously been evaluated for their fractal nature. The improved estimates of D for these maps ranged from 1.56 ± 0.02 to 1.79 ± 0.02, and were much greater than the original estimates. These higher D values imply a greater degree of fracture connectivity and thus increased propensity for fracture flow and the transport of miscible or immiscible chemicals

Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics.

Whole-genome bacterial sequences are required to better understand microbial functions, niche-specific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g., feces), as few as 13% of bacterium-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from underrepresented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full-length 16S rRNA gene sequences, clustered the sequences to ensure that no individual taxonomic group was overselected for sequencing, prioritized bacteria from underrepresented body sites (such as skin and respiratory and urinary tracts), and sequenced and assembled genomes for 665 new bacterial strains. Here, we show that addition of these genomes improved read mapping rates of Human Microbiome Project (HMP) metagenomic samples by nearly 30% for the previously underrepresented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and a clinical perspective.IMPORTANCE The human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily feces), while other sites such as the skin, respiratory tract, and urinary tract are underrepresented, resulting in as little as 13% of bacterium-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select underrepresented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies

Knowledge Translation Consensus Conference: Research Methods

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72708/1/j.1553-2712.2007.tb02378.x.pd

ALMA observations of massive molecular gas reservoirs in dusty early-type galaxies

Unresolved gas and dust observations show a surprising diversity in the amount of interstellar matter in early-type galaxies. Using ALMA observations we resolve the ISM in z∼0.05 early-type galaxies. From a large sample of early-type galaxies detected in the Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS) we selected five of the dustiest cases, with dust masses Md ∼several× 107M⊙, with the aim of mapping their submillimetre continuum and 12CO(2-1) line emission distributions. These observations reveal molecular gas disks. There is a lack of associated, extended continuum emission in these ALMA observations, most likely because it is resolved out or surface brightness limited, if the dust distribution is as extended as the CO gas. However, two galaxies have central continuum ALMA detections. An additional, slightly offset, continuum source is revealed in one case, which may have contributed to confusion in the Herschel fluxes. Serendipitous continuum detections further away in the ALMA field are found in another case. Large and massive rotating molecular gas disks are mapped in three of our targets, reaching a few× 109M⊙. One of these shows evidence of kinematic deviations from a pure rotating disc. The fields of our two remaining targets contain only smaller, weak CO sources, slightly offset from the optical galaxy centres. These may be companion galaxies seen in ALMA observations, or background objects. These heterogeneous findings in a small sample of dusty early-type galaxies reveal the need for more such high spatial resolution studies, to understand statistically how dust and gas are related in early-type galaxies

Supernova Remnants and Star Formation in the Large Magellanic Cloud

It has often been suggested that supernova remnants (SNRs) can trigger star formation. To investigate the relationship between SNRs and star formation, we have examined the known sample of 45 SNRs in the Large Magellanic Cloud to search for associated young stellar objects (YSOs) and molecular clouds. We find seven SNRs associated with both YSOs and molecular clouds, three SNRs associated with YSOs but not molecular clouds, and eight SNRs near molecular clouds but not associated with YSOs. Among the 10 SNRs associated with YSOs, the association between the YSOs and SNRs can be either rejected or cannot be convincingly established for eight cases. Only two SNRs have YSOs closely aligned along their rims; however, the time elapsed since the SNR began to interact with the YSOs' natal clouds is much shorter than the contraction timescales of the YSOs, and thus we do not see any evidence of SNR-triggered star formation in the LMC. The 15 SNRs that are near molecular clouds may trigger star formation in the future when the SNR shocks have slowed down to <45 km/s. We discuss how SNRs can alter the physical properties and abundances of YSOs.Comment: 24 pages, 5 figures, 1 table, Accepted for publication in the August 2010 edition of the Astronomical Journa

The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment

Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316T is a Gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment

Views of institutional leaders on maintaining humanism in today’s practice

Objective To explore leadership perspectives on how to maintain high quality efficient care that is also person-centered and humanistic. Methods The authors interviewed and collected narrative transcripts from a convenience sample of 32 institutional healthcare leaders at seven U.S. medical schools. The institutional leaders were asked to identify factors that either promoted or inhibited humanistic practice. A subset of authors used the constant comparative method to perform qualitative analysis of the interview transcripts. They reached thematic saturation by consensus on the major themes and illustrative examples after six conference calls. Results Institutional healthcare leaders supported vision statements, policies, organized educational and faculty development programs, role modeling including their own, and recognition of informal acts of kindness to promote and maintain humanistic patient-care. These measures were described individually rather than as components of a coordinated plan. Few healthcare leaders mentioned plans for organizational or systems changes to promote humanistic clinician-patient relationships. Conclusions Institutional leaders assisted clinicians in dealing with stressful practices in beneficial ways but fell short of envisaging systems approaches that improve practice organization to encourage humanistic care

How Physicians Draw Satisfaction and Overcome Barriers in their Practices: “It Sustains Me”

Objective Major reorganizations of medical practice today challenge physicians’ ability to deliver compassionate care. We sought to understand how physicians who completed an intensive faculty development program in medical humanism sustain their humanistic practices. Methods Program completers from 8 U.S. medical schools wrote reflections in answer to two open-ended questions addressing their personal motivations and the barriers that impeded their humanistic practice and teaching. Reflections were qualitatively analyzed using the constant comparative method. Results Sixty-eight physicians (74% response rate) submitted reflections. Motivating factors included: 1) identification with humanistic values; 2) providing care that they or their family would want; 3) connecting to patients; 4) passing on values through role modelling; 5) being in the moment. Inhibiting factors included: 1) time, 2) stress, 3) culture, and 4) episodic burnout. Conclusions Determination to live by one’s values, embedded within a strong professional identity, allowed study participants to alleviate, but not resolve, the barriers. Collaborative action to address organizational impediments was endorsed but found to be lacking. Practice implications Fostering fully mature professional development among physicians will require new skills and opportunities that reinforce time-honored values while simultaneously partnering with others to nurture, sustain and improve patient care by addressing system issues

Using pneumococcal carriage studies to monitor vaccine impact in low- and middle-income countries.

Pneumococcal disease is a leading cause of childhood mortality, globally. The pneumococcal conjugate vaccine (PCV) has been introduced to many countries worldwide. However there are few studies evaluating PCV impacts in low- and middle-income countries (LMIC) because measuring the impact of PCV on pneumococcal disease in LMICs is challenging. We review the role of pneumococcal carriage studies for the evaluation of PCVs in LMICs and discuss optimal methods for conducting these studies. Fifteen carriage studies from 13 LMICs quantified the effects of PCV on carriage, and identified replacement carriage serotypes in the post-PCV era. Ten studies reported on the indirect effects of PCV on carriage. Results can be used to inform cost-effectiveness evaluations, guide policy decisions on dosing and product, and monitor equity in program implementation. Critically, we highlight gaps in our understanding of serotype replacement disease in LMICs and identify priorities for research to address this gap