Developing a modern data workflow for regularly updated data.

Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.

The Repository of Antemortem Injury Response (REPAIR): an online database for skeletal injuries of known ages.

An accurate assessment of time since fracture is an essential component of abuse and death investigations; however, little evidence-based research exists on dating fractures, especially those of the cranial vault. This is primarily due to difficulties in procuring human fracture specimens of known posttraumatic survival times. The aim of this article is to introduce a new database through which limitations imposed by sample procurement may be mitigated. The Repository of Antemortem Injury Response (REPAIR) is a digitally accessible database of cranial vault fractures of known ages with extensive contextual information and visual documentation in the form of photography, radiography, and histological photomicrographs. This repository is a multifunctional tool that serves as a case submission portal for cranial fractures of known posttraumatic survival time, a sample database for research on fracture healing and rates of repair, a resource for comparative assessments of cranial fractures in forensic casework, and an educational tool for healing fracture histomorphology.

Declines in rodent abundance and diversity track regional climate variability in North American drylands.

Regional long-term monitoring can enhance the detection of biodiversity declines associated with climate change, improving future projections by reducing reliance on space-for-time substitution and increasing scalability. Rodents are diverse and important consumers in drylands, regions defined by the scarcity of water that cover 45% of Earth's land surface and face increasingly drier and more variable climates. We analyzed abundance data for 22 rodent species across grassland, shrubland, ecotone, and woodland ecosystems in the southwestern USA. Two time series (1995-2006 and 2004-2013) coincided with phases of the Pacific Decadal Oscillation (PDO), which influences drought in southwestern North America. Regionally, rodent species diversity declined 20%-35%, with greater losses during the later time period. Abundance also declined regionally, but only during 2004-2013, with losses of 5% of animals captured. During the first time series (wetter climate), plant productivity outranked climate variables as the best regional predictor of rodent abundance for 70% of taxa, whereas during the second period (drier climate), climate best explained variation in abundance for 60% of taxa. Temporal dynamics in diversity and abundance differed spatially among ecosystems, with the largest declines in woodlands and shrublands of central New Mexico and Colorado. Which species were winners or losers under increasing drought and amplified interannual variability in drought depended on ecosystem type and the phase of the PDO. Fewer taxa were significant winners (18%) than losers (30%) under drought, but the identities of winners and losers differed among ecosystems for 70% of taxa. Our results suggest that the sensitivities of rodent species to climate contributed to regional declines in diversity and abundance during 1995-2013. Whether these changes portend future declines in drought-sensitive consumers in the southwestern USA will depend on the climate during the next major PDO cycle.

Provoking a Cultural Shift in Data Quality.

Ecological studies require quality data to describe the nature of ecological processes and to advance understanding of ecosystem change. Increasing access to big data has magnified both the burden and the complexity of ensuring quality data. The costs of errors in ecology include low use of data, increased time spent cleaning data, and poor reproducibility that can result in a misunderstanding of ecosystem processes and dynamics, all of which can erode the efficacy of and trust in ecological research. Although conceptual and technological advances have improved ecological data access and management, a cultural shift is needed to embed data quality as a cultural practice. We present a comprehensive data quality framework to evoke this cultural shift. The data quality framework flexibly supports different collaboration models, supports all types of ecological data, and can be used to describe data quality within both short- and long-term ecological studies.

Established rodent community delays recovery of dominant competitor following experimental disturbance.

Human activities alter processes that control local biodiversity, causing changes in the abundance and identity of species in ecosystems. However, restoring biodiversity to a previous state is rarely as simple as reintroducing lost species or restoring processes to their pre-disturbance state. Theory suggests that established species can impede shifts in species composition via a variety of mechanisms, including direct interference, pre-empting resources or habitat alteration. These mechanisms can create transitory dynamics that delay convergence to an expected end state. We use an experimental manipulation of a desert rodent community to examine differences in recolonization dynamics of a dominant competitor (kangaroo rats of the genus Dipodomys) when patches were already occupied by an existing rodent community relative to when patches were empty. Recovery of kangaroo rat populations was slow on plots with an established community, taking approximately 2 years, in contrast with rapid recovery on empty plots with no established residents (approx. three months). These results demonstrate that the presence of an established alternate community inhibits recolonization by new species, even those that should be dominant in the community. This has important implications for understanding how biodiversity may change in the future, and what processes may slow or prevent this change.

Long-term community change through multiple rapid transitions in a desert rodent community.

While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-yr span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods, possibly related to climate events, where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.

Long-term monitoring and experimental manipulation of a Chihuahuan desert ecosystem near Portal, Arizona (1977-2013).

Desert ecosystems have long served as model systems in the study of ecological concepts (e.g., competition, resource pulses, top-down/bottom-up dynamics). However, the inherent variability of resource availability in deserts, and hence consumer dynamics, can also make them challenging ecosystems to understand. Study of a Chihuahuan desert ecosystem near Portal, Arizona began in 1977. At this site, 24 experimental plots were established and divided among controls and experimental manipulations. Experimental manipulations over the years include removal of all or some rodent species, all or some ants, seed additions, and various alterations of the annual plant community. This dataset includes data previously available through an older data publication and adds 11 years of data. It also includes additional ant and weather data not previously available. These data have been used in a variety of publications documenting the effects of the experimental manipulations as well as the response of populations and communities to long-term changes in climate and habitat. Sampling is ongoing and additional data will be published in the future.

Effect of remote ischaemic conditioning on clinical outcomes in patients presenting with an ST-segment elevation myocardial infarction undergoing primary percutaneous coronary intervention.

The rationale and study design for the multicentre, randomized, controlled CONDI2/ERIC-PPCI study are discussed.

Abrupt transitions in a southwest USA desert grassland related to the Pacific Decadal Oscillation.

Prediction of abrupt ecosystem transitions resulting from climatic change will be an essential element of adaptation strategies in the coming decades. In the arid southwest USA, the collapse and recovery of long-lived perennial grasses have important effects on ecosystem services, but the causes of these variations have been poorly understood. Here we use a quality-controlled vegetation monitoring dataset initiated in 1915 to show that grass cover dynamics during the 20th century were closely correlated to the Pacific decadal oscillation (PDO) index. The relationship out-performed models correlating grasses to yearly precipitation and drought indices, suggesting that ecosystem transitions attributed only to local disturbances were instead influenced by climate teleconnections. Shifts in PDO phase over time were associated with the persistent loss of core grass species and recovery of transient species, so recovery of grasses in aggregate concealed significant changes in species composition. However, the relationship between PDO and grass cover broke down after 1995; grass cover is consistently lower than PDO would predict. The decoupling of grass cover from the PDO suggests that a threshold had been crossed in which warming or land degradation overwhelmed the ability of any grass species to recover during favorable periods.

Quadrat-based monitoring of desert grassland vegetation at the Jornada Experimental Range, New Mexico, 1915-2016.

The data set covers a 101-yr period (1915-2016) of quadrat-based plant sampling at the Jornada Experimental Range in southern New Mexico. At each sampling event, a pantograph was used to record the location and perimeter of living plants within permanent quadrats. Basal area was recorded for perennial grass species, canopy cover area was recorded for shrub species, and all other perennial species were recorded as point data. The data set includes 122 1 × 1 m permanent quadrats, although not all quadrats were sampled in each year of the study and there is a gap in monitoring from 1980 to 1995. These data provide a unique opportunity to investigate changes in the plant community over 100 yr of variation in precipitation and other environmental conditions. We provide the following data and data formats: (1) the digitized maps in shapefile format; (2) a data table containing coordinates (x, y) of perennial species within quadrats, including cover area for grasses and shrubs; (3) a data table of counts of annual plant individuals per quadrat; (4) a species list indicating growth form and habit of recorded species; (5) a table of dates when each quadrat was sampled; (6) a table of the pasture each quadrat was located within (note that pasture boundaries have changed over time); (7) a table of depth to petrocalcic layer measurements taken at quadrat locations; (8) a table of particle size analysis of soil samples taken at quadrat locations; (9) a table of topographic characteristics of quadrat locations (e.g., concave or convex topography). Pantograph sampling is currently conducted at 5-yr intervals by USDA-ARS staff, and new data will be added periodically to the EDI Data Portal Repository (see section V.E.2). This information is released under the Creative Commons license-Attribution-CC BY and the consumer of these data is required to cite it appropriately in any publication that results from its use.

A case report of a congenital left subcostal hernia in a neonate.

We present an unusual case of a congenital left subcostal hernia in a female born at 39 weeks by caesarean delivery to a 39 year-old gravida(2)para(1-2)abortus(0) mother. The pregnancy was complicated by gestational diabetes, although she had normal prenatal imaging. After an uneventful caesarean delivery, the patient's initial physical examination was normal although subsequently was found to have a left subcostal hernia. During surgical evaluation, a reducible hernia was found along with left renal agenesis and no underlying masses. At 4 weeks of age, the patient's hernia was successfully repaired with no sequela. We present the first reported case of a congenital subcostal hernia, evaluation, and treatment.