Developing Data Literacy Programs: Working with Faculty, Graduate Students and Undergraduates

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113148/1/bult1720410608.pd

Developing Professional Skills in STEM Students: Data Information Literacy

Undergraduate STEM students are increasingly expected to have some data use skills upon graduation, whether they pursue post-graduate education or move into industry. This project was an initial foray into the application of data information literacy competencies to training undergraduate students to identify markers of data and information quality. The data consumer training appeared within two courses to help students evaluate data objects, including databases and datasets available on the Internet. The application of the Data Credibility Checklist provides a foundation for developing data reuse competencies. Based upon the initial presentation of the content, it became obvious that students need very basic introductions to data concepts, including definitions for database and dataset, and the process of data object discovery

Temporal and spatial patterns in the Ross Sea: Phytoplankton biomass, elemental composition, productivity and growth rates

The temporal and spatial patterns of phytoplankton biomass, productivity, and particulate matter composition in the Ross Sea were assessed during cruises in January 1990 and February 1992. Biomass and primary productivity in the southern Ross Sea were greatest during mid-January, with surface chlorophyll concentrations, particulate organic carbon levels, and integrated primary productivity averaging 4.9 Ixg L \u27l, 0.54 mg L-•, and 2.63 g C m • d \u27•, respectively. Comparable mean concentrations and rates for February were 1.1 Ixg L \u27l, 0.29 mg L \u27l, and 0.78 g C m \u27•- d \u27• (decreases of 76, 46, and 70%, respectively), indicative of the scale of temporal changes. A distinct south-north transition also was observed both in productivity and phytoplankton biomass, with the lowest values occurring in the northern Ross Sea. East-west gradients in phytoplankton biomass and composition occurred within the southern Ross Sea. The areal productivity of the Ross Sea ranged from 0.15 to 2.85 g C m • d -• and is among the highest found in the entire Antarctic. Carbon:chlorophyll ratios were uniformly high but were highest (150) in 1990 in the diatom-dominated western Ross Sea. Surface growth rates were modest, averaging less than 0.2 day \u27• during both seasons. We hypothesize that the marked seasonality in the region provides an environment in which net growth rates, although slow, are maximized through low loss rates and which allows biomass to accumulate in the surface layer. Furthermore, the temporal variations are quantitatively similar to the observed spatial variations. Therefore the dominant determinant of phytoplankton biomass and productivity at any one point on the Ross Sea continental shelf is the stage of the seasonal growth cycle

Cluster Galaxy Evolution from a New Sample of Galaxy Clusters at 0.3 < z < 0.9

(Abridged) We analyze photometry and spectroscopy of a sample of 63 clusters at 0.3<z<0.9 drawn from the Las Campanas Distant Cluster Survey to empirically constrain models of cluster galaxy evolution. Specifically, by combining data on our clusters with those from the literature we parametrize the redshift dependence of 1) M*_I in the observed frame; 2) the V-I color of the E/S0 red sequence in the observed frames; and 3) the I-K' color of the E/S0 red sequence in the observed frame. Using the peak surface brightness of the cluster detection, S, as a proxy for cluster mass, we find no correlation between S and M* or the location of the red envelope in V-I. We suggest that these observations can be explained with a model in which luminous early type galaxies (or more precisely, the progenitors of current day luminous early type galaxies) form the bulk of their stellar populations at high redshift (>~ 5) and in which many of these galaxies, if not all, accrete mass either in the form of evolved stellar populations or gas that causes only a short term episode of star formation at lower redshifts (1.5 < z < 2). Our data are too crude to reach conclusions regarding the evolutionary state of any particular cluster or to investigate whether the morphological evolution of galaxies matches the simple scenario we discuss, but the statistical nature of this study suggests that the observed evolutionary trends are universal in massive clusters.Comment: 35 pages, accepted for publication in Ap

Serological Responses of Raccoons and Striped Skunks to Ontario Rabies Vaccine Bait in West Virginia during 2012–2016

Since the 1990s, oral rabies vaccination (ORV) has been used successfully to halt the westward spread of the raccoon rabies virus (RV) variant from the eastern continental USA. Elimination of raccoon RV from the eastern USA has proven challenging across targeted raccoon (Procyon lotor) and striped skunk (Mephitis mephitis) populations impacted by raccoon RV. Field trial evaluations of the Ontario Rabies Vaccine Bait (ONRAB) were initiated to expand ORV products available to meet the rabies management goal of raccoon RV elimination. This study describes the continuation of a 2011 trial inWest Virginia. Our objective was to evaluate raccoon and skunk response to ORV occurring in West Virginia for an additional two years (2012–2013) at 75 baits/km2 followed by three years (2014–2016) of evaluation at 300 baits/km2. We measured the change in rabies virus-neutralizing antibody (RVNA) seroprevalence in targeted wildlife populations by comparing levels pre- and post-ORV during each year of study. The increase in bait density from 75/km2 to 300/km2 corresponded to an increase in average post-ORV seroprevalence for raccoon and skunk populations. Raccoon population RVNA levels increased from 53% (300/565, 95% CI: 50–57%) to 82.0% (596/727, 95% CI: 79–85%) during this study, and skunk population RVNA levels increased from 11% (8/72, 95% CI: 6–20%) to 39% (51/130, 95% CI: 31–48%). The RVNA seroprevalence pre-ORV demonstrated an increasing trend across study years for both bait densities and species, indicating that multiple years of ORV may be necessary to achieve and maintain RVNA seroprevalence in target wildlife populations for the control and elimination of raccoon RV in the eastern USA

A new method for detection of pfmdr1 mutations in Plasmodium falciparum DNA using real-time PCR

BACKGROUND: Surveillance for drug-resistant Plasmodium falciparum should be a component of malaria control programmes. Real-time PCR methods for the detection of parasite single-nucleotide polymorphisms (SNPs) and gene amplification could be useful survellance tools. METHODS: A real-time PCR assay has been developed that identifies single nucleotide polymorphisms (SNPs) at amino acids 86, 184, 1034 and 1042 in the P. falciparum multi-drug resistant (pfmdr 1) gene that may be associated with anti-malarial drug resistance. RESULTS: This assay has a sensitivity and specificity of 94% and 100% when compared to traditional PCR methods for genotyping. Only 54 of 68 (79%) paired pre- and post-culture DNA samples were concordant at all four loci. CONCLUSION: Real-time PCR is a sensitive and specific method to detect SNP's in pfmdr 1. Genotypes of parasites after in vitro culture may not reflect that seen in vivo

Placebo Oral Rabies Vaccine Bait Uptake by Small Indian Mongooses (\u3ci\u3eHerpestes auropunctatus\u3c/i\u3e) in Southwestern Puerto Rico

The small Indian mongoose (Herpestes auropunctatus) is a rabies reservoir in areas of the Caribbean including Puerto Rico, but no rabies vaccination program targeting this host exists. We used two derivatives of iophenoxic acid (IPA) to evaluate placebo oral rabies vaccine bait uptake by mongooses in southwestern Puerto Rico. We hand-distributed baits at an application rate of 200 baits/km2 at three, 400 ha, sites during autumn 2016 and spring 2017. Each site contained 90–100 cage traps in a 100 ha central trapping area. We used ethyl-IPA as a biological marker during the autumn and methyl-IPA during the spring. We live captured mongooses for 10 consecutive days, beginning 1 wk following bait application. We obtained a serum sample from captured mongooses and analyzed the sera for ethyl- and methyl-IPA by liquid chromatography mass spectrometry. During autumn 2016, 63% (55/87) mongooses sampled were positive for ethyl-IPA. In spring 2017, 69% (85/123) of mongooses were positive for methyl-IPA. Pooling seasons, accounting for recaptures between years, and disregarding marker type, 74% (133/179) unique mongooses were positive for IPA biomarker, indicating bait consumption during either the autumn, spring, or both trials. We conclude that distributing baits at an application rate of 200 baits/km2 is sufficient to reach over 60% of the target mongoose population in dry forest habitats of Puerto Rico

pfmdr1 GENOTYPING AND IN VIVO MEFLOQUINE RESISTANCE ON THE THAI-MYANMAR BORDER

Molecular markers have been proposed as a method of monitoring malaria drug resistance and could potentially be used to prolong the life span of antimalarial drugs. Single nucleotide polymorphisms (SNPs) in the Plasmodium falciparum gene pfmdr1 and increased gene copy number have been associated with in vitro drug resistance but have not been well studied in vivo. In a prospective cohort study of malaria patients receiving mefloquine treatment on the Thai-Myanmar border, there was no significant association between either pfmdr1 SNPs or in vitro drug sensitivity and mefloquine resistance in vivo. Increased pfmdr1 gene copy number was significantly associated with recrudescence (relative risk 2.30, 95% CI 1.27–4.15). pfmdr1 gene copy number may be a useful surveillance tool for mefloquine-resistant falciparum malaria in Thailand

Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women.

We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI &lt; 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value &lt; 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01). Bacteroides uniformis was significantly more abundant in lean women, irrespective of country (FDR corrected p &lt; 0.001), while lean Ghanaians had a significantly greater proportion of Ruminococcus callidus, Prevotella copri, and Escherichia coli, and smaller proportions of Lachnospiraceae, Bacteroides and Parabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genus Bacteroides and Parabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value &lt; 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptor Ffa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity

Incidence and Outcomes Associated With Clostridium difficile Infections: A Systematic Review and Meta-analysis

Importance: An understanding of the incidence and outcomes of Clostridium difficile infection (CDI) in the United States can inform investments in prevention and treatment interventions. Objective: To quantify the incidence of CDI and its associated hospital length of stay (LOS) in the United States using a systematic literature review and meta-analysis. Data Sources: MEDLINE via Ovid, Cochrane Library Databases via Wiley, Cumulative Index of Nursing and Allied Health Complete via EBSCO Information Services, Scopus, and Web of Science were searched for studies published in the United States between 2000 and 2019 that evaluated CDI and its associated LOS. Study Selection: Incidence data were collected only from multicenter studies that had at least 5 sites. The LOS studies were included only if they assessed postinfection LOS or used methods accounting for time to infection using a multistate model or compared propensity score-matched patients with CDI with control patients without CDI. Long-term-care facility studies were excluded. Of the 119 full-text articles, 86 studies (72.3%) met the selection criteria. Data Extraction and Synthesis: Two independent reviewers performed the data abstraction and quality assessment. Incidence data were pooled only when the denominators used the same units (eg, patient-days). These data were pooled by summing the number of hospital-onset CDI incident cases and the denominators across studies. Random-effects models were used to obtain pooled mean differences. Heterogeneity was assessed using the I2 value. Data analysis was performed in February 2019. Main Outcomes and Measures: Incidence of CDI and CDI-associated hospital LOS in the United States. Results: When the 13 studies that evaluated incidence data in patient-days due to hospital-onset CDI were pooled, the CDI incidence rate was 8.3 cases per 10 000 patient-days. Among propensity score-matched studies (16 of 20 studies), the CDI-associated mean difference in LOS (in days) between patients with and without CDI varied from 3.0 days (95% CI, 1.44-4.63 days) to 21.6 days (95% CI, 19.29-23.90 days). Conclusions and Relevance: Pooled estimates from currently available literature suggest that CDI is associated with a large burden on the health care system. However, these estimates should be interpreted with caution because higher-quality studies should be completed to guide future evaluations of CDI prevention and treatment interventions