Capturing and Processing Born-Digital Files in the STOP AIDS Project Records: A Case Study

In September 2012, the Manuscripts Division of the Stanford University Libraries Department of Special Collections and University Archives completed a one-year National Historical Publications and Records Commission (NHPRC)-funded project to process the records of the STOP AIDS Project, an HIV prevention non-profit organization in San Francisco, California. This project marked the department’s first large-scale processing project to capture and process born-digital records. Building upon the nascent framework outlined by the AIMS white paper and the infrastructure developed by Stanford University Libraries, the project team captured born-digital records and implemented new processing strategies using digital forensics tools. This case study will document the strategies and workflows employed by the project team to capture and process the born-digital component of the STOP AIDS Project records. We will describe the successes, challenges and roadblocks encountered while forensically imaging 3.5 inch floppy disks, Zip disks, and CDs using Forensic Toolkit (FTK) Imager software. We will then outline our approach to processing nearly 30,000 unique digital files captured from the computer media using AccessData Forensic Toolkit (FTK) software, discuss our current delivery strategy, and offer some concluding thoughts

Effects of plant diversity on productivity strengthen over time due to trait-dependent shifts in species overyielding.

Plant diversity effects on community productivity often increase over time. Whether the strengthening of diversity effects is caused by temporal shifts in species-level overyielding (i.e., higher species-level productivity in diverse communities compared with monocultures) remains unclear. Here, using data from 65 grassland and forest biodiversity experiments, we show that the temporal strength of diversity effects at the community scale is underpinned by temporal changes in the species that yield. These temporal trends of species-level overyielding are shaped by plant ecological strategies, which can be quantitatively delimited by functional traits. In grasslands, the temporal strengthening of biodiversity effects on community productivity was associated with increasing biomass overyielding of resource-conservative species increasing over time, and with overyielding of species characterized by fast resource acquisition either decreasing or increasing. In forests, temporal trends in species overyielding differ when considering above- versus belowground resource acquisition strategies. Overyielding in stem growth decreased for species with high light capture capacity but increased for those with high soil resource acquisition capacity. Our results imply that a diversity of species with different, and potentially complementary, ecological strategies is beneficial for maintaining community productivity over time in both grassland and forest ecosystems

Ecosystem function enhanced by combining four functional types of plant species in intensively managed grassland mixtures: a 3-year continental-scale field experiment

A coordinated continental-scale field experiment across 31 sites was used to compare the biomass yield of monocultures and four species mixtures associated with intensively managed agricultural grassland systems. To increase complementarity in resource use, each of the four species in the experimental design represented a distinct functional type derived from two levels of each of two functional traits, nitrogen acquisition (N2-fixing legume or nonfixing grass) crossed with temporal development (fast-establishing or temporally persistent). Relative abundances of the four functional types in mixtures were systematically varied at sowing to vary the evenness of the same four species in mixture communities at each site and sown at two levels of seed density. Across multiple years, the total yield (including weed biomass) of the mixtures exceeded that of the average monoculture in >97% of comparisons. It also exceeded that of the best monoculture (transgressive overyielding) in about 60% of sites, with a mean yield ratio of mixture to best-performing monoculture of 1·07 across all sites. Analyses based on yield of sown species only (excluding weed biomass) demonstrated considerably greater transgressive overyielding (significant at about 70% of sites, ratio of mixture to best-performing monoculture = 1·18). Mixtures maintained a resistance to weed invasion over at least 3 years. In mixtures, median values indicate <4% of weed biomass in total yield, whereas the median percentage of weeds in monocultures increased from 15% in year 1 to 32% in year 3. Within each year, there was a highly significant relationship (P < 0·0001) between sward evenness and the diversity effect (excess of mixture performance over that predicted from the monoculture performances of component species). At lower evenness values, increases in community evenness resulted in an increased diversity effect, but the diversity effect was not significantly different from the maximum diversity effect across a wide range of higher evenness values. The latter indicates the robustness of the diversity effect to changes in species' relative abundances. Across sites with three complete years of data (24 of the 31 sites), the effect of interactions between the fast-establishing and temporal persistent trait levels of temporal development was highly significant and comparable in magnitude to effects of interactions between N2-fixing and nonfixing trait levels of nitrogen acquisition. Synthesis and applications. The design of grassland mixtures is relevant to farm-level strategies to achieve sustainable intensification. Experimental evidence indicated significant yield benefits of four species agronomic mixtures which yielded more than the highest-yielding monoculture at most sites. The results are relevant for agricultural practice and show how grassland mixtures can be designed to improve resource complementarity, increase yields and reduce weed invasion. The yield benefits were robust to considerable changes in the relative proportions of the four species, which is extremely useful for practical management of grassland swards

Results of mixed effect logistic regression models to assess the association between weather variables and the log odds of <i>E</i>. <i>coli</i> O157:H7 presence in fecal pats, after adjusting for pen and date as random effects.

<p>Results of mixed effect logistic regression models to assess the association between weather variables and the log odds of <i>E</i>. <i>coli</i> O157:H7 presence in fecal pats, after adjusting for pen and date as random effects.</p

The change in the proportion of cattle fecal pats positive for <i>E</i>. <i>coli</i> O157:H7 over time.

<p>(A) The proportion of fecal pats positive for <i>E</i>. <i>coli</i> O157:H7 by control and intervention groups, pre- and post-intervention. Bars indicate 95% confidence interval after adjusting the standard errors for clustering within pens. (Number of fecal samples = 2719) (B) Box-plots of the (unadjusted) change in within-pen prevalence of positive fecal pats within each pen (post- minus pre-intervention prevalence). (Number of fecal samples = 2719).</p

Proportion of fecal pats positive for <i>E</i>. <i>coli</i> O157:H7 by pen, and pen-level variables.

<p>Data shown from pre-intervention time-point only (number of fecal samples = 1400). Light gray indicates year 1 (2014). Dark gray indicates year 2 (2015). Bars indicate 95% confidence intervals. Note: clustering of pens by sampling date is not shown.</p

Mean temperature, dew-point, relative humidity and mean precipitation during the seven days preceding each sampling date.

<p>Points show 7-day mean of average daily values. Upper and lower horizontal lines show 7-day means of maximum and minimum daily values. Bars represent mean precipitation over the 7 days preceding the sampling date.</p