Invest to Save: Report and Recommendations of the NSF-DELOS Working Group on Digital Archiving and Preservation

Digital archiving and preservation are important areas for research and development, but there is no agreed upon set of priorities or coherent plan for research in this area. Research projects in this area tend to be small and driven by particular institutional problems or concerns. As a consequence, proposed solutions from experimental projects and prototypes tend not to scale to millions of digital objects, nor do the results from disparate projects readily build on each other. It is also unclear whether it is worthwhile to seek general solutions or whether different strategies are needed for different types of digital objects and collections. The lack of coordination in both research and development means that there are some areas where researchers are reinventing the wheel while other areas are neglected. Digital archiving and preservation is an area that will benefit from an exercise in analysis, priority setting, and planning for future research. The WG aims to survey current research activities, identify gaps, and develop a white paper proposing future research directions in the area of digital preservation. Some of the potential areas for research include repository architectures and inter-operability among digital archives; automated tools for capture, ingest, and normalization of digital objects; and harmonization of preservation formats and metadata. There can also be opportunities for development of commercial products in the areas of mass storage systems, repositories and repository management systems, and data management software and tools.

Transition between terrestrial-submerged walking and swimming revealed by Early Permian amphibian trackways and a new proposal for the nomenclature of compound trace fossils

Exceptionally preserved Early Permian tetrapod trackways from the Orobic Basin (Central-Western Southern Alps) offer a unique opportunity to investigate in detail locomotion in fossil vertebrates that lived on continental European landmasses. Herein are reported the results of a study on several tetrapod trackways that display a large variety of behavioral, gait and substrate related extramorphologies. They clearly document the transition from terrestrial-underwater walking to swimming and are assigned to the compound ichnotaxon Batrachichnus C Lunichnium. The use of the "C" symbol is here introduced for the first time as nomenclatural indication of a Compound trace. Producers were probably small-sized temnospondyl or lepospondyl (microsaurs) amphibians. Comparisons with living urodelan anatomy and mechanics provide evidence for conservatism of locomotor mechanics in evolutionary history among amphibians. The derived model for locomotor kinematics in Early Permian amphibians provides a reference for interpreting transitional land-to-water trackways. The shift from walking to swimming behavior in early tetrapods, as in extant urodelan amphibians, is described as a complex balance between different dynamics

Effect of High Glucose on Ocular Surface Epithelial Cell Barrier and Tight Junction Proteins

PURPOSE. Patients with diabetes mellitus are reported to have ocular surface defects, impaired ocular surface barrier function, and a higher incidence of corneal and conjunctival infections. Tight junctions are critical for ocular surface barrier function. The present study was designed to investigate the effect of high glucose exposure on human corneal and conjunctival epithelial cell barrier function and tight junction proteins. METHODS. Human corneal and conjunctival epithelial cells were exposed to 15 mM and 30 mM glucose for 24 and 72 hours. The barrier function was measured using transepithelial electrical resistance (TEER). The cell migration was quantified using scratch assay. The cells were harvested for protein extraction and mRNA isolation. Gene and protein expression of claudins, zonula occludens (ZOs), and occludin was quantified using realtime PCR and Western blot. RESULTS. Glucose caused a significant decrease in TEER after 72 hours of exposure in both corneal and conjunctival epithelial cells. Glucose did not cause any notable change in migration of either corneal or conjunctival epithelial cells. Glucose exposure did not cause any notable change in protein expression of claudin-1, ZO-1, ZO-2, ZO-3, or occludin. On the other hand, 15 mM glucose caused an increase in gene expression of claudin-1, claudin-3, ZO-2, ZO-3, and occludin, a likely response to osmotic stress since 15 mM mannitol also caused consistently similar increase in gene expression of these proteins. CONCLUSIONS. High glucose exposure causes impairment of corneal and conjunctival epithelial cell barrier function, but this detrimental effect is not caused by a decrease in expression of tight junction proteins: claudin-1, ZO-1, ZO-2, ZO-3, and occludin

Genomic Classifier Augments the Role of Pathological Features in Identifying Optimal Candidates for Adjuvant Radiation Therapy in Patients With Prostate Cancer: Development and Internal Validation of a Multivariable Prognostic Model.

Purpose Despite documented oncologic benefit, use of postoperative adjuvant radiotherapy (aRT) in patients with prostate cancer is still limited in the United States. We aimed to develop and internally validate a risk-stratification tool incorporating the Decipher score, along with routinely available clinicopathologic features, to identify patients who would benefit the most from aRT. Patient and Methods Our cohort included 512 patients with prostate cancer treated with radical prostatectomy at one of four US academic centers between 1990 and 2010. All patients had ≥ pT3a disease, positive surgical margins, and/or pathologic lymph node invasion. Multivariable Cox regression analysis tested the relationship between available predictors (including Decipher score) and clinical recurrence (CR), which were then used to develop a novel risk-stratification tool. Our study adhered to the Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis guidelines for development of prognostic models. Results Overall, 21.9% of patients received aRT. Median follow-up in censored patients was 8.3 years. The 10-year CR rate was 4.9% vs. 17.4% in patients treated with aRT versus initial observation ( P \u3c .001). Pathologic T3b/T4 stage, Gleason score 8-10, lymph node invasion, and Decipher score \u3e 0.6 were independent predictors of CR (all P \u3c .01). The cumulative number of risk factors was 0, 1, 2, and 3 to 4 in 46.5%, 28.9%, 17.2%, and 7.4% of patients, respectively. aRT was associated with decreased CR rate in patients with two or more risk factors (10-year CR rate 10.1% in aRT v 42.1% in initial observation; P = .012), but not in those with fewer than two risk factors ( P = .18). Conclusion Using the new model to indicate aRT might reduce overtreatment, decrease unnecessary adverse effects, and reduce risk of CR in the subset of patients (approximately 25% of all patients with aggressive pathologic disease in our cohort) who benefit from this therapy

International comparison in walkable environments and hospital burden in type 2 diabetes patients

Introduction While some comparative work has provided evidence for a universally positive impact of built environment features that promote physical activity, less is known about chronic diseases and hospitalization among different social contexts and health care systems. Parallel international linkage efforts present an opportunity to study health impacts of the built environment. Objectives and Approach This study compares the impact of neighbourhood environments on health outcomes for patients with type 2 diabetes (T2D) in two countries. Neighborhood-level measures for walkable environments were derived for Canada and Wales using Geographic Information Systems. Hospitalization admissions from routine data sources and linked survey data responses (from the Welsh Health Survey and Canadian Community Health Survey) allow for the generation of population-based descriptive statistics on socio-demographic information, self-reported health, diagnostic patterns, and health care use. We examine the feasibility of investigating contextual differences in walkable environments, T2D, and hospitalization between Wales and Canada. Results Data linkage in respective privacy protecting safe havens in the Canada Research Data Centre Network (CRDCN) and the Wales Secure Anonymised Information Linkage (SAIL) Databank show promise for a comparative study, enabling parallel modelling of environmental and socio-demographic factors with hospitalization data. Both the Canadian and Welsh surveys ask respondents about their current diabetes status, allowing us to compare hospitalization rates and neighborhood effects of those who report having diabetes with the those who do not. Moreover, the linking of survey responses and similarity in geographic scale permitted consistent measurement of walkable environments across countries. Key administrative variables have been identified relating to health and behaviors, such as socio-demographic information, smoking status, and body mass index, and hospitalization metrics in both countries are commensurable. Conclusion/Implications The generation of comparable linked datasets, built environment indicators and comparative research for T2D patients will have wider implications for international assessment of the impacts of environment on chronic diseases, and the hospital burden associated with these conditions

Foot-mediated incubation: Nazca booby (Sula granti) feet as surrogate brood patches

ABSTRACT Incubation in most avian species involves transferring heat from parent to egg through a highly vascularized brood patch. Some birds, however, do not develop a brood patch. Unusual among birds, these species hold their eggs under the webs of their feet, but the role of the feet in heat transfer is uncertain. Often the webs are positioned between the feathered abdomen and the egg during incubation, suggesting that either the abdomen, the feet, or both could transfer heat to the egg. We studied heat transfer from foot webs to eggs during incubation in Nazca boobies by spatially separating the feet from the abdomen using an oversized egg. We found that feet transfer heat to eggs independently of any heat that may be transferred from the abdomen. In addition, we found that incubating boobies had significantly greater vascularization in their foot webs, measured as a percentage of web area covered by vessels, than nonincubating boobies. We also found that males, whether incubating or nonincubating, had significantly less web vascularization than females. We concluded that vascularized Nazca booby feet function in the same way during incubation that vascularized brood patches do, acting as surrogate brood patches

In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different

RATIONALE: Sputum and bronchoalveolar lavage fluid (BALF) are often obtained to elucidate the lower airway microbiota in adults. Acquiring sputum samples from children is difficult and obtaining samples via bronchoscopy in children proves challenging due to the need for anesthesia and specialized procedural expertise; therefore nasopharyngeal (NP) swabs are often used as surrogates when investigating the pediatric airway microbiota. In adults, the airway microbiota differs significantly between NP and BALF samples however, minimal data exist in children. OBJECTIVES: To compare NP and BALF samples in children undergoing clinically indicated bronchoscopy. METHODS: NP and BALF samples were collected during clinically indicated bronchoscopy. Bacterial DNA was extracted from 72 samples (36 NP/BALF pairs); the bacterial V1-V3 region of the 16S rRNA gene was amplified and sequenced on the Illumina Miseq platform. Analysis was performed using mothur software. RESULTS: Compared to NP samples, BALF had increased richness and diversity. Similarity between paired NP and BALF (intra-subject) samples was greater than inter-subject samples (P = 0.0006). NP samples contained more Actinobacteria (2.2% vs 21%; adjusted P = 1.4 × 10-6 ), while BALF contained more Bacteroidetes (29.5% vs 3.2%; adjusted P = 1.2 × 10-9 ). At the genus level several differences existed, however Streptococcus abundance was similar in both sample types (NP 37.3% vs BAL 36.1%; adjusted P = 0.8). CONCLUSION: Our results provide evidence that NP samples can be used to distinguish differences between children, but the relative abundance of organisms may differ between the nasopharynx and lower airway in pediatric patients. Studies utilizing NP samples as surrogates for the lower airway should be interpreted with caution

Median fin function during the escape response of bluegill sunfish (Lepomis macrochirus). I: Fin-ray orientation and movement

The fast-start escape response is critically important to avoid predation, and axial movements driving it have been studied intensively. Large median dorsal and anal fins located near the tail have been hypothesized to increase acceleration away from the threat, yet the contribution of flexible median fins remains undescribed. To investigate the role of median fins, C-start escape responses of bluegill sunfish (Lepomis macrochirus) were recorded by three high-speed, high-resolution cameras at 500framess–1 and the 3-D kinematics of individual dorsal and anal fin rays were analyzed. Movement and orientation of the fin rays relative to the body axis were calculated throughout the duration of the C-start. We found that: (1) timing and magnitude of angular displacement varied among fin rays based on position within the fin and (2) kinematic patterns support the prediction that fin rays are actively resisting hydrodynamic forces and transmitting momentum into the water. We suggest that regions within the fins have different roles. Anterior regions of the fins are rapidly elevated to increase the volume of water that the fish may interact with and transmit force into, thus generating greater total momentum. The movement pattern of all the fin rays creates traveling waves that move posteriorly along the length of the fin, moving water as they do so. Flexible posterior regions ultimately act to accelerate this water towards the tail, potentially interacting with vortices generated by the caudal fin during the C-start. Despite their simple appearance, median fins are highly complex and versatile control surfaces that modulate locomotor performance.Organismic and Evolutionary Biolog

Median fin function during the escape response of bluegill sunfish (Lepomis macrochirus). II: Fin-ray curvature

Although kinematic analysis of individual fin rays provides valuable insight into the contribution of median fins to C-start performance, it paints an incomplete picture of the complex movements and deformation of the flexible fin surface. To expand our analysis of median fin function during the escape response of bluegill sunfish (Lepomis macrochirus), patterns of spanwise and chordwise curvature of the soft dorsal and anal fin surfaces were examined from the same video sequences previously used in analysis of fin-ray movement and orientation. We found that both the span and chord undergo undulation, starting in the anterior region of either fin. Initiated early in Stage 1 of the C-start, the undulation travels in a postero-distal direction, reaching the trailing edge of the fins during early Stage 2. Maximum spanwise curvature typically occurred among the more flexible posterior fin rays, though there was no consistent correlation between maximum curvature and fin-ray position. Undulatory patterns suggest different mechanisms of action for the fin regions. In the anterior fin region, where the fin rays are oriented dorsoventrally, undulation is directed primarily chordwise, initiating a transfer of momentum into the water to overcome the inertia of the flow and direct the water posteriorly. Within the posterior region, where the fin rays are oriented caudally, undulation is predominantly directed spanwise; thus, the posterior fin region acts to ultimately accelerate this water towards the tail to increase thrust forces. Treatment of median fins as appendages with uniform properties does not do justice to their complexity and effectiveness as control surfaces.Organismic and Evolutionary Biolog