The Electronic Lab Notebook: Piloting a Research Data Management Tool at Cornell University

The maintenance of laboratory records in the digital age can be a complicated and continuously evolving task, yet clear, consistent documentation is critical for tracking, sharing and reproducing research. One tool that can be used to manage and organize such records is an Electronic Lab Notebook (ELN). The Cornell University Library and Cornell’s Academic Technologies Group are currently engaged in a joint pilot program to determine the feasibility of offering a campus-wide ELN service. The pilot, which began in January and runs through June 2013, involves ELN use in research and classroom labs. Shown here are key features of the product being trialed and an early look at the interest and feedback of researchers using the ELN

Composition and biomass of phytoplankton assemblages in coastal Antarctic waters: A comparison of chemotaxonomic and microscopic analyses

We describe the distribution of phytoplanktonic community composition and biomass from the Western Antarctic Peninsula coast (between 64° and 68° S) using 2 analytical techniques: microscopy and HPLC of photosynthetic pigments. Phytoplankton biomass was estimated as chlorophyll a (chl a) by HPLC and chemotaxonomic quantification of microalgae biomass was performed by multiple regression analysis of pigment concentrations. For the estimation of chl a: diagnostic pigment ratios, it was found of primary importance to differentiate between phytoplankton assemblages within the study area. Three assemblages were differentiated according to their total standing stock and analyzed independently. Phytoplankton biomass was also estimated as carbon (C) concentration by microscopic analysis of cell abundance and biovolumes. Microscopy and chemotaxonomy give a high level of agreement for phytoplankton characterization, showing an on/offshore gradient, with high diatom and cryptophyte biomass in coastal waters, and a mixed assemblage with low biomass in open waters. This gradient was not observed in total cell abundance, indicating that the biomass gradient is controlled by cell size. Microscopy also showed shifts in diatom species throughout the area. C and chl a biomass estimates for the individual microalgae groups were strongly correlated for cryptophytes, chlorophytes and most diatoms, but did poorly for dinoflagellates, prymnesiophytes and chrysophytes. From this study, we conclude that both microscopy and chemotaxonomy can be used to accurately characterize phytoplankton assemblages, but some limitations are present in both techniques. Based on phytoplankton C concentrations, we estimated an average in situ growth rate of 0.28 d-1. In situ cell C:chl a ratios had high variability (from 40 to 220) and were non-linearly related to sample growth rates. Significant differences were found among average C:chl a ratios of low (1 μg chl a l-1), with values of 112 and 74 μg C μg-1 chl a, respectively. In addition, our results support the hypothesis that C quotas of diatoms and other microalgae do not differ greatly from each other, as previously believed.Facultad de Ciencias Naturales y Muse

Composition and biomass of phytoplankton assemblages in coastal Antarctic waters: A comparison of chemotaxonomic and microscopic analyses

We describe the distribution of phytoplanktonic community composition and biomass from the Western Antarctic Peninsula coast (between 64° and 68° S) using 2 analytical techniques: microscopy and HPLC of photosynthetic pigments. Phytoplankton biomass was estimated as chlorophyll a (chl a) by HPLC and chemotaxonomic quantification of microalgae biomass was performed by multiple regression analysis of pigment concentrations. For the estimation of chl a: diagnostic pigment ratios, it was found of primary importance to differentiate between phytoplankton assemblages within the study area. Three assemblages were differentiated according to their total standing stock and analyzed independently. Phytoplankton biomass was also estimated as carbon (C) concentration by microscopic analysis of cell abundance and biovolumes. Microscopy and chemotaxonomy give a high level of agreement for phytoplankton characterization, showing an on/offshore gradient, with high diatom and cryptophyte biomass in coastal waters, and a mixed assemblage with low biomass in open waters. This gradient was not observed in total cell abundance, indicating that the biomass gradient is controlled by cell size. Microscopy also showed shifts in diatom species throughout the area. C and chl a biomass estimates for the individual microalgae groups were strongly correlated for cryptophytes, chlorophytes and most diatoms, but did poorly for dinoflagellates, prymnesiophytes and chrysophytes. From this study, we conclude that both microscopy and chemotaxonomy can be used to accurately characterize phytoplankton assemblages, but some limitations are present in both techniques. Based on phytoplankton C concentrations, we estimated an average in situ growth rate of 0.28 d-1. In situ cell C:chl a ratios had high variability (from 40 to 220) and were non-linearly related to sample growth rates. Significant differences were found among average C:chl a ratios of low (1 μg chl a l-1), with values of 112 and 74 μg C μg-1 chl a, respectively. In addition, our results support the hypothesis that C quotas of diatoms and other microalgae do not differ greatly from each other, as previously believed.Facultad de Ciencias Naturales y Muse

Convergence: Integrating diverse perspectives to provide a single point of service

Poster presented at Research Data Access and Preservation Summit, 22-24 March 2012, New Orleans, LA.In response to an increased awareness of the data management needs of researchers, Cornell’s Research Data Management Service Group (RDMSG) was created with the goal of making it as simple as possible for researchers to obtain the data management services they require. As more libraries get involved in data management, there are several different service models emerging, with some institutions establishing dedicated staff whose main responsibility it is to work with researchers on research data management and others using existing library staff. An example of another possible model, the RDMSG is a cross-disciplinary virtual group that relies on representatives from various service groups on campus to do the work of consulting with researchers on data management planning. With representatives from Cornell University Libraries (CUL), Cornell Information Technologies (CIT), the Center for Advanced Computing (CAC), and Cornell Institute for Social and Economic Research (CISER), the RDMSG consultant pool includes staff from both business and mission driven departments, as well as having very different backgrounds and areas of expertise. The diverse perspectives of the consultants is both a strength and a challenge for the group. In order to provide consistent high quality consultations, the group developed a set of operating principles to guide all consultants in their interactions with researchers. Developing best practices allowed the group to reach consensus on what kinds of interactions were desirable, and to focus their efforts on providing that level of research data management service. We will discuss our experience working as a cross-disciplinary group, including the advantages and disadvantages both expected and unexpected that we’ve encountered. We will also summarize our activities to date and offer some best practices for providing research data management services

Composition and biomass of phytoplankton assemblages in coastal Antarctic waters: A comparison of chemotaxonomic and microscopic analyses

We describe the distribution of phytoplanktonic community composition and biomass from the Western Antarctic Peninsula coast (between 64° and 68° S) using 2 analytical techniques: microscopy and HPLC of photosynthetic pigments. Phytoplankton biomass was estimated as chlorophyll a (chl a) by HPLC and chemotaxonomic quantification of microalgae biomass was performed by multiple regression analysis of pigment concentrations. For the estimation of chl a: diagnostic pigment ratios, it was found of primary importance to differentiate between phytoplankton assemblages within the study area. Three assemblages were differentiated according to their total standing stock and analyzed independently. Phytoplankton biomass was also estimated as carbon (C) concentration by microscopic analysis of cell abundance and biovolumes. Microscopy and chemotaxonomy give a high level of agreement for phytoplankton characterization, showing an on/offshore gradient, with high diatom and cryptophyte biomass in coastal waters, and a mixed assemblage with low biomass in open waters. This gradient was not observed in total cell abundance, indicating that the biomass gradient is controlled by cell size. Microscopy also showed shifts in diatom species throughout the area. C and chl a biomass estimates for the individual microalgae groups were strongly correlated for cryptophytes, chlorophytes and most diatoms, but did poorly for dinoflagellates, prymnesiophytes and chrysophytes. From this study, we conclude that both microscopy and chemotaxonomy can be used to accurately characterize phytoplankton assemblages, but some limitations are present in both techniques. Based on phytoplankton C concentrations, we estimated an average in situ growth rate of 0.28 d-1. In situ cell C:chl a ratios had high variability (from 40 to 220) and were non-linearly related to sample growth rates. Significant differences were found among average C:chl a ratios of low (1 μg chl a l-1), with values of 112 and 74 μg C μg-1 chl a, respectively. In addition, our results support the hypothesis that C quotas of diatoms and other microalgae do not differ greatly from each other, as previously believed.Facultad de Ciencias Naturales y Muse

Cardiopoietic cell therapy for advanced ischemic heart failure: results at 39 weeks of the prospective, randomized, double blind, sham-controlled CHART-1 clinical trial

Cardiopoietic cells, produced through cardiogenic conditioning of patients' mesenchymal stem cells, have shown preliminary efficacy. The Congestive Heart Failure Cardiopoietic Regenerative Therapy (CHART-1) trial aimed to validate cardiopoiesis-based biotherapy in a larger heart failure cohort

Research Data Management Service Group 2016-2017 Report

Dates covered: July 2016 through June 2017.This report summarizes the 2016-2017 activities of the Research Data Management Service Group, a collaborative, campus-wide organization that links Cornell University faculty, staff and students with data management services to meet their research needs

Identification of a Recurrent Microdeletion at 17q23.1q23.2 Flanked by Segmental Duplications Associated with Heart Defects and Limb Abnormalities

Segmental duplications, which comprise ∼5%–10% of the human genome, are known to mediate medically relevant deletions, duplications, and inversions through nonallelic homologous recombination (NAHR) and have been suggested to be hot spots in chromosome evolution and human genomic instability. We report seven individuals with microdeletions at 17q23.1q23.2, identified by microarray-based comparative genomic hybridization (aCGH). Six of the seven deletions are ∼2.2 Mb in size and flanked by large segmental duplications of >98% sequence identity and in the same orientation. One of the deletions is ∼2.8 Mb in size and is flanked on the distal side by a segmental duplication, whereas the proximal breakpoint falls between segmental duplications. These characteristics suggest that NAHR mediated six out of seven of these rearrangements. These individuals have common features, including mild to moderate developmental delay (particularly speech delay), microcephaly, postnatal growth retardation, heart defects, and hand, foot, and limb abnormalities. Although all individuals had at least mild dysmorphic facial features, there was no characteristic constellation of features that would elicit clinical suspicion of a specific disorder. The identification of common clinical features suggests that microdeletions at 17q23.1q23.2 constitute a novel syndrome. Furthermore, the inclusion in the minimal deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome