Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

Musculoskeletal injuries in Us air Force Security Forces, January 2009 to December 2018

OBJECTIVE: to determine the incidence, types, and risk factors of musculoskeletal injuries in a military security forces population. METHODS: Demographic and diagnostic data were retrieved on enlisted US Air Force security forces personnel who served on active duty between January 2009 and December 2018. Incidence rates and ratios were calculated using Poisson regression. RESULTS: During 251,787 person-years of exposure, 62,489 personnel served on active duty. Of these, 40,771 (65.2%) were diagnosed with at least one musculoskeletal injury. The majority (60.1%) of the 164,078 unique musculoskeletal injuries were inflammation and pain secondary to overuse. After adjusting for other factors, women had a 31% higher injury rate than men, and those who were overweight and obese had 15% and 30% higher rates, respectively, than normal-weight peers. CONCLUSIONS: Modifiable and non-modifiable factors contribute to musculoskeletal injuries in the security forces career field

Wind environment evaluation on major town of Malaysia

This study focus on wind flow or wind environment of residential areas in Peninsular Malaysia, Sabah and Sarawak. Natural wind flow is one of the most effective methods to help achieve the energy saving in large cities especially under the tropical climate like Malaysia. The weather in Malaysia is characterized by four monsoon regimes, namely, the southwest monsoon, northeast monsoon and two shorter periods of inter-monsoon seasons. For this study, the data of wind velocity in twentytwo (22) weather station in Malaysia obtained from Meteorological Department and considered in wind environment evaluations. Then that data of wind velocities will convert to 1.5 in height at all measuring points were calculated by using the law. The result compared by Table 2.2 in previous researches (Kubota and Miura et al., 2002). From the study, it was found out, in Malaysia there are only two type of wind. First type is weak wind means that area are discomfort thermal and the second type is comfort range to strong wind means that area are comfort thermal. The minimum value of mean wind speed from 2005 to 2009 is O.mis in mean temperature is over 2C at Sitiawan. For the maximum value of mean wind speed is I .7m/s in average value of mean temperature is 276C at Mersing. Base on results, it can be concluded that when considering wind flow at a residential area, terrace housing is not a suitable option for towns located on the south of the Peninsular. It was prefer for high-rise building because it was considered this location of towns was weak wind condition. On the other hand, the major towns exclude the south of the Peninsular including Sabah and Sarawak, they was under the comfort thermal. So, terrace housing or high-rise building is suitable option

Particle size effect on strength, failure and shock behavior in Polytetrafluoroethylene-Al-W granular composites

The variation of metallic particle size and sample porosity significantly alters the dynamic mechanical properties of high density granular composites processed using a cold isostatically pressed mixture of polytetrafluoroethylene (PTFE), aluminum (Al) and tungsten (W) powders. Quasi-static and dynamic experiments are performed with identical constituent mass fractions with variations in the size of the W particles and pressing conditions. The relatively weak polymer matrix allows the strength and fracture modes of this material to be governed by the granular type behavior of agglomerated metal particles. A higher ultimate compressive strength was observed in relatively high porosity samples with small W particles compared to those with coarse W particles in all experiments. Mesoscale granular force chains comprised of the metallic particles explain this unusual phenomenon as observed in a hydrocode simulation of a drop-weight test. Macrocracks forming below the critical failure strain for the matrix and unusual behavior due to a competition between densification and fracture in dynamic tests of porous samples were also observed. Shock loading of this granular composite resulted in higher fraction of total internal energy deposition in the soft PTFE matrix, specifically thermal energy, which can be tailored by the W particle size distribution.Comment: 35 pages, 13 figure

Delegated job design

We develop a theory of delegation within organizations where agents are privately informed about whether they should be engaged in exploitation or in exploration activities. Excessive delegation lead agents to inefficiently herd into exploration in an attempt to boost their market value. The theory is consistent with both high-delegation practices and practices where agents are assigned to activities. Our main result is that an agent should be delegated more the weaker career concerns, a variable that is made endogenous through the firm's technology and its degree of transparency. The theory sheds light on empirical regularities that are previously unexplained, such as a positive relation between wages and delegation, and delegation being more prevalent in closed environments or environments with long-term employment contracts

A cardinal role for cathepsin D in co-ordinating the host-mediated apoptosis of macrophages and killing of pneumococci

The bactericidal function of macrophages against pneumococci is enhanced by their apoptotic demise, which is controlled by the anti-apoptotic protein Mcl-1. Here, we show that lysosomal membrane permeabilization (LMP) and cytosolic translocation of activated cathepsin D occur prior to activation of a mitochondrial pathway of macrophage apoptosis. Pharmacological inhibition or knockout of cathepsin D during pneumococcal infection blocked macrophage apoptosis. As a result of cathepsin D activation, Mcl-1 interacted with its ubiquitin ligase Mule and expression declined. Inhibition of cathepsin D had no effect on early bacterial killing but inhibited the late phase of apoptosis-associated killing of pneumococci in vitro. Mice bearing a cathepsin D-/- hematopoietic system demonstrated reduced macrophage apoptosis in vivo, with decreased clearance of pneumococci and enhanced recruitment of neutrophils to control pulmonary infection. These findings establish an unexpected role for a cathepsin D-mediated lysosomal pathway of apoptosis in pulmonary host defense and underscore the importance of apoptosis-associated microbial killing to macrophage function

Historical Analysis: Tracking, Problematizing, and Reterritorializing Achievement and the Achievement Gap

For more than a century, state and federal governments and organizations have used different measures to determine if students and groups of students have achieved in a particular subject or grade level. While the construct of achievement is applied irrespective of student differences, this equal application turns out to be anything but equitable. In this chapter, we work to understand the way achievement plays out for Black students by deconstructing how the word achievement works. In doing so, we track the history of education, testing, and curriculum as it has been applied to Black youth and youth of color

The Challenges of Creativity in Software Organizations

Part 1: Creating ValueInternational audienceManaging creativity has proven to be one of the most important drivers in software development and use. The continuous changing market environment drives companies like Google, SAS Institute and LEGO to focus on creativity as an increasing necessity when competing through sustained innovations. However, creativity in the information systems (IS) environment is a challenge for most organizations that is primarily caused by not knowing how to strategize creative processes in relation to IS strategies, thus, causing companies to act ad hoc in their creative endeavors. In this paper, we address the organizational challenges of creativity in software organizations. Grounded in a previous literature review and a rigorous selection process, we identify and present a model of seven important factors for creativity in software organizations. From these factors, we identify 21 challenges that software organizations experience when embarking on creative endeavors and transfer them into a comprehensive framework. Using an interpretive research study, we further study the framework by analyzing how the challenges are integrated in 27 software organizations. Practitioners can use this study to gain a deeper understanding of creativity in their own business while researchers can use the framework to gain insight while conducting interpretive field studies of managing creativity

Dietary Supplements and Sports Performance: Herbals

This is the fourth in a series of six articles to discuss the major classes of dietary supplements (vitamins; minerals; amino acids; herbs or botanicals; metabolites, constituents/extracts, or combinations). The major focus is on efficacy of such dietary supplements to enhance exercise or sport performance

Factors Associated with herb and dietary supplement use by young adults in the United States

<p>Abstract</p> <p>Background</p> <p>Little is known about the association between use of herbs and dietary supplements (HDS) and lifestyle/behavior factors in young adults in the US.</p> <p>Methods</p> <p>Analyzing the 2002 National Health Interview Survey (NHIS), we examined the patterns of HDS (excluding vitamins/minerals) use among young adults in the United States using descriptive statistics and logistic regression.</p> <p>Results</p> <p>In our sample of 18 to 30 year olds (n = 6666), 26% were current smokers, 24% were moderate/heavy drinkers, 43% had high physical activity, and 54% and 76% use prescription and over the counter (OTC) medications respectively. Non-vitamin, non-mineral HDS was used by 17% of the overall sample in the last 12 months. In the multivariable analysis, the lifestyle and behavioral factors associated with HDS use include: current smoking (odds ratio 1.41 95% CI [1.16–1.72]); being a former smoker (1.50 [1.15–1.95]); moderate/heavy alcohol use (2.02 [1.53–2.65]); high physical activity levels (2.45 [1.98–3.03]); and prescription medication use (1.51 [1.26–1.81]). Among HDS users, only 24% discussed their use with a health care professional.</p> <p>Conclusion</p> <p>Nearly one in five young adults report using non-vitamin/non-mineral HDS.</p