Quantitative measurements in 3-dimensional datasets of mouse lymph nodes resolve organ-wide functional dependencies

Deep tissue imaging has become state of the art in biology, but now the problem is to quantify spatial information in a global, organ-wide context. Although access to the raw data is no longer a limitation, the computational tools to extract biologically useful information out of these large data sets is still catching up. In many cases, to understand the mechanism behind a biological process, where molecules or cells interact with each other, it is mandatory to know their mutual positions. We illustrate this principle here with the immune system. Although the general functions of lymph nodes as immune sentinels are well described, many cellular and molecular details governing the interactions of lymphocytes and dendritic cells remain unclear to date and prevent an in-depth mechanistic understanding of the immune system. We imaged ex vivo lymph nodes isolated from both wild-type and transgenic mice lacking key factors for dendritic cell positioning and used software written in MATLAB to determine the spatial distances between the dendritic cells and the internal high endothelial vascular network. This allowed us to quantify the spatial localization of the dendritic cells in the lymph node, which is a critical parameter determining the effectiveness of an adaptive immune response.

I want to be my own person: the meaning-making and psychosocial processes of legacy students at Bucknell University

This study examined the meaning-making and psychosocial processes of five female legacy students at Bucknell University, each of whom having had at least one parent graduate from the institution. With a research philosophy, design, and methodology rooted in qualitative inquiry and phenomenology, inductive data analysis led to three primary categories that underscored legacy identity development. The first, Paradox of Influence and Identity, revealed through six themes nuanced experiences of separation-individuation. Second, Teaching and Learning, comprised of five themes, illuminated the impact of family — and of Bucknell parent alumni in particular — on their children’s internal working models. Lastly, Bucknell — the Environmental Contextand the five themes grouped therein highlighted the contributions of University community members, and of the campus culture and climate itself, to the co-construction of psychosocial formation. A tentative outline of grounded theory was offered, which explored categorical relationships; Paradox of Influence and Identity emerged as thedominant phenomenon, informing and being reinforced by the data of Teaching and Learning and Bucknell — the Environmental Context. Provisional intervention strategies for student affairs practice, in the contexts of academics, residential life, and career development, were discussed. Further, triangulated research is needed to substantiate and evolve the findings and theoretical model of this thesis.

Object-Oriented Legacy System Trace-based Logic Testing

When reengineering legacy systems, it is crucial to assess if the legacy behavior has been preserved or how it changed due to the reengineering effort. Ideally if a legacy system is covered by tests, running the tests on the new version can identify potential differences or discrepancies. However, writing tests for an unknown and large system is difficult due to the lack of internal knowledge. It is especially difficult to bring the system to an appropriate state. Our solution is based on the acknowledgment that one of the few trustable piece of information available when approaching a legacy system is the running system itself. Our approach reifies the execution traces and uses logic programming to express tests on them. Thereby it eliminates the need to programatically bring the system in a particular state, and handles the test-writer a high-level abstraction mechanism to query the trace. The resulting system, called TESTLOG, was used on several real-world case studies to validate our claims.

How does spatial extent of fMRI datasets affect independent component analysis decomposition?

Spatial independent component analysis (sICA) of functional magnetic resonance imaging (fMRI) time series can generate meaningful activation maps and associated descriptive signals, which are useful to evaluate datasets of the entire brain or selected portions of it. Besides computational implications, variations in the input dataset combined with the multivariate nature of ICA may lead to different spatial or temporal readouts of brain activation phenomena. By reducing and increasing a volume of interest (VOI), we applied sICA to different datasets from real activation experiments with multislice acquisition and single or multiple sensory-motor task-induced blood oxygenation level-dependent (BOLD) signal sources with different spatial and temporal structure. Using receiver operating characteristics (ROC) methodology for accuracy evaluation and multiple regression analysis as benchmark, we compared sICA decompositions of reduced and increased VOI fMRI time-series containing auditory, motor and hemifield visual activation occurring separately or simultaneously in time. Both approaches yielded valid results; however, the results of the increased VOI approach were spatially more accurate compared to the results of the decreased VOI approach. This is consistent with the capability of sICA to take advantage of extended samples of statistical observations and suggests that sICA is more powerful with extended rather than reduced VOI datasets to delineate brain activity.

Computational Techniques for Spatial Logistic Regression with Large Datasets

In epidemiological work, outcomes are frequently non-normal, sample sizes may be large, and effects are often small. To relate health outcomes to geographic risk factors, fast and powerful methods for fitting spatial models, particularly for non-normal data, are required. We focus on binary outcomes, with the risk surface a smooth function of space. We compare penalized likelihood models, including the penalized quasi-likelihood (PQL) approach, and Bayesian models based on fit, speed, and ease of implementation. A Bayesian model using a spectral basis representation of the spatial surface provides the best tradeoff of sensitivity and specificity in simulations, detecting real spatial features while limiting overfitting and being more efficient computationally than other Bayesian approaches. One of the contributions of this work is further development of this underused representation. The spectral basis model outperforms the penalized likelihood methods, which are prone to overfitting, but is slower to fit and not as easily implemented. Conclusions based on a real dataset of cancer cases in Taiwan are similar albeit less conclusive with respect to comparing the approaches. The success of the spectral basis with binary data and similar results with count data suggest that it may be generally useful in spatial models and more complicated hierarchical models.

Characterization of legacy organic carbon in a culturally eutrophic lake : the role of the historic carbon deposition in the time course and extent of lake recovery

The time course of lake recovery after a reduction in external loading of nutrients is often controlled by conditions in the sediment. Remediation of eutrophication is hindered by the presence of legacy organic carbon deposits, that exert a demand on the terminal electron acceptors of the lake and contribute to problems such as internal nutrient recycling, absence of sediment macrofauna, and flux of toxic metal species into the water column. Being able to quantify the timing of a lake’s response requires determination of the magnitude and lability, i.e., the susceptibility to biodegradation, of the organic carbon within the legacy deposit. This characterization is problematic for organic carbon in sediments because of the presence of different fractions of carbon, which vary from highly labile to refractory. The lability of carbon under varied conditions was tested with a bioassay approach. It was found that the majority of the organic material found in the sediments is conditionally-labile, where mineralization potential is dependent on prevailing conditions. High labilities were noted under oxygenated conditions and a favorable temperature of 30 °C. Lability decreased when oxygen was removed, and was further reduced when the temperature was dropped to the hypolimnetic average of 8° C . These results indicate that reversible preservation mechanisms exist in the sediment, and are able to protect otherwise labile material from being mineralized under in situ conditions. The concept of an active sediment layer, a region in the sediments in which diagenetic reactions occur (with nothing occurring below it), was examined through three lines of evidence. Initially, porewater profiles of oxygen, nitrate, sulfate/total sulfide, ETSA (Electron Transport System Activity- the activity of oxygen, nitrate, iron/manganese, and sulfate), and methane were considered. It was found through examination of the porewater profiles that the edge of diagenesis occurred around 15-20 cm. Secondly, historical and contemporary TOC profiles were compared to find the point at which the profiles were coincident, indicating the depth at which no change has occurred over the (13 year) interval between core collections. This analysis suggested that no diagenesis has occurred in Onondaga Lake sediment below a depth of 15 cm. Finally, the time to 99% mineralization, the t99, was viewed by using a literature estimate of the kinetic rate constant for diagenesis. A t99 of 34 years, or approximately 30 cm of sediment depth, resulted for the slowly decaying carbon fraction. Based on these three lines of evidence , an active sediment layer of 15-20 cm is proposed for Onondaga Lake, corresponding to a time since deposition of 15-20 years. While a large legacy deposit of conditionally-labile organic material remains in the sediments of Onondaga Lake, it becomes clear that preservation, mechanisms that act to shield labile organic carbon from being degraded, protects this material from being mineralized and exerting a demand on the terminal electron acceptors of the lake. This has major implications for management of the lake, as it defines the time course of lake recovery following a reduction in nutrient loading.

Analysis of independent microarray datasets of renal biopsies identifies a robust transcript signature of acute allograft rejection

Transcriptomics could contribute significantly to the early and specific diagnosis of rejection episodes by defining 'molecular Banff' signatures. Recently, the description of pathogenesis-based transcript sets offered a new opportunity for objective and quantitative diagnosis. Generating high-quality transcript panels is thus critical to define high-performance diagnostic classifier. In this study, a comparative analysis was performed across four different microarray datasets of heterogeneous sample collections from two published clinical datasets and two own datasets including biopsies for clinical indication, and samples from nonhuman primates. We characterized a common transcriptional profile of 70 genes, defined as acute rejection transcript set (ARTS). ARTS expression is significantly up-regulated in all AR samples as compared with stable allografts or healthy kidneys, and strongly correlates with the severity of Banff AR types. Similarly, ARTS were tested as a classifier in a large collection of 143 independent biopsies recently published by the University of Alberta. Results demonstrate that the 'in silico' approach applied in this study is able to identify a robust and reliable molecular signature for AR, supporting a specific and sensitive molecular diagnostic approach for renal transplant monitoring.

Reading Our Land Use Legacy in Groundwater: Nitrate Dynamics in the Judith River Watershed

Elevated nitrate in groundwater is common is agricultural areas where fertilizer has been added at high rates for decades. Within the Judith River Wastershed, high native soil fertility allowed for dryland wheat production without N fertilization until the 1980s, yet elevated nitrate levels were frequently observed in shallow aquifers. Dr. Stephanie Ewing presents results for soil, groundwater and surface water analyses from a hydrologically isolated strath terrace near Moccasin, MT. In context of this uniquely well constrained field setting, these observed data, along with land use history and a simple mass balance model, revel the long term development and perturbation of native soil fertility with cultivation.

Legislative Legacy: Big Changes in Legislative Article of 1972 Constitution -- Jerry Loendorf, Arlyne Reichert & Rich Bechtel “In the Crucible of Change”

The fulcrum upon which were leveraged many of the dramatic progressive changes in Montana that are documented "In the Crucible of Change" series was the lead up to, preparation, writing and adoption of the 1972 Montana Constitution. As Montana citizens exhibited their concern over the dysfunctional state government in MT under its 1889 Constitution, one of the areas that stood out as needing serious change was the Montana Legislature. Meeting for only sixty calendar days every two years, the Legislature regularly tried to carry off the subterfuge of stopping the wall clock at 11:59 PM on the sixtieth day and placing a shroud over it so they could continue to conduct business as if it were still the 60th day. Lawyers hired by the Anaconda Company drafted most bills that legislators wanted to have introduced. Malapportionment, especially in the State Senate where each county had one Senator regardless of their population, created a situation where Petroleum County with 800 residents had one senator while neighboring Yellowstone County with 80,000 people also had one senator -- a 100-1 differential in representation. Reapportionment imposed by rulings of the US Supreme Court in the mid-1960s created great furor in rural Montana to go along with the previous dissatisfaction of the urban centers. Stories of Anaconda Company “thumbs up – thumbs down” control of the votes were prevalent. Committee meeting and votes were done behind closed doors and recorded votes were non-existent except for the nearly meaningless final tally. People were in the dark about the creation of laws that affected their daily lives. It was clear that change in the Legislature had to take the form of change in the Constitution and, because it was not likely that the Legislature would advance Constitutional amendments on the subject, a convention seemed the only remedy. Once that Convention was called and went to work, it became apparent that the Legislative Article provided both opportunity for change and danger that too dramatic a change might sink the whole new document. The activities of the Legislative Committee and the whole Convention when acting upon Legislative issues provides one of the more compelling stories of change. The story of the Legislative Article of the Montana Constitution is discussed in this episode by three major players who were directly involved in the effort: Jerry Loendorf, Arlyne Reichert and Rich Bechtel. Their recollections of the activities surrounding the entire Constitutional Convention and specifically the Legislative Article provide an insider’s perspective of the development of the entire Constitution and the Legislative portion which was of such a high degree of interest to the people of Montana during the important period of progressive change documented “In the Crucible of Change.” Jerry Loendorf, who served as Chair of the Legislative Committee at the 1972 Montana Constitutional Convention, received a BA from Carroll College in 1961 and a JD from the University of Montana Law School in 1964. Upon graduation he served two years as a law clerk for the Montana Supreme Court after which he was for 34 years a partner in the law firm of Harrison, Loendorf & Posten, Duncan. In addition to being a delegate to the Constitutional Convention, Jerry served on the Board of Labor Appeals from 2000 to 2004. He was designated a Montana Special Assistant Attorney General to represent the state in federal court on the challenge to the results of the ratification election of Montana's Constitution in 1972. Jerry served on the Carroll College Board of Directors in the late 1960s and then again as a member of the Board of Trustees of Carroll College from 2001 to 2009. He has served on the Board of Directors of the Rocky Mountain Development Council since 1970 and was on the board of the Helena YMCA from 1981 to 1987. He also served on the board of the Good Samaritan Ministries from 2009 to 2014. On the business side, Jerry was on the Board of Directors of Valley Bank to Helena from 1980 to 2005. He is a member of the American Bar Association, State Bar of Montana, the First Judicial District Bar Association, and the Montana Trial Lawyers Association. Carroll College awarded Jerry the Warren Nelson Award 1994 and the Insignias Award in 2007. At Carroll College, Jerry has funded the following three scholarship endowments: George C and Helen T Loendorf, Gary Turcott, and Fr. William Greytek. Arlyne Reichert, Great Falls Delegate to the Constitutional Convention and former State Legislator, was born in Buffalo, NY in 1926 and attended University of Buffalo in conjunction with Cadet Nurses Training during WWII. She married a Montanan in Great Falls in 1945 and was widowed in 1968. She is mother of five, grandmother of seven, great-grandmother of four. Arlyne was employed by McLaughlin Research Institute in Great Falls for 23 years, serving as Technical Editor of Transplantation Journal in 1967, retiring as Assistant Director in 1989. In addition to being a state legislator (1979 Session) and a delegate to the 1972 Montana Constitutional Convention, she has filled many public roles, including Cascade County Study Commissioner (1974), MT Comprehensive Health Council, US Civil Rights Commission MT Advisory Committee, MT Capitol Restoration Committee, and Great Falls Public Library Trustee. Arlyne has engaged in many non-profit activities including League of Women Voters (State & Local Board Officer – from where her interest in the MT Constitutional change developed), Great Falls Public Radio Association (President & Founder), American Cancer Society (President Great Falls Chapter), Chair of MT Rhodes Scholarship Committee, and Council Member of the National Civic League. She also served a while as a Television Legislative Reporter. Arlyne has been recipient of numerous awards, the National Distinguished Citizens Award from the National Municipal League, two Women of Achievement Awards from Business & Professional Women, the Salute to Women Award by YWCA, Heritage Preservation Award from Cascade County Historical Society and the State of Montana, and the Heroes Award from Humanities Montana. She remains active, serving as Secretary-Treasurer of Preservation Cascade, Inc., and as Board Member of the McLaughlin Research Institute. Her current passion is applied to the preservation/saving of the historic 10th Street Bridge that crosses the Missouri River in Great Falls. Rich Bechtel of Helena was born in Napa, California in 1945 and grew up as an Air Force brat living in such places as Bitberg, Germany, Tripoli, Libya, and Sevilla, Spain. He graduated from Glasgow High School and the University of Montana. Rich was a graduate assistant for noted Montana History professor Professor K. Ross Toole, but dropped out of graduate school to pursue a real life in Montana politics and government. Rich has had a long, varied and colorful career in the public arena. He currently is the Director of the Office of Taxpayer Assistance & Public Outreach for MT’s Department of Revenue. He previously held two positions with the National Wildlife Federation in Washington, DC (Sr. Legislative Representative [1989-91] and Sr. Legislative Representative for Wildlife Policy [2004-2006]). While in Washington DC, he also was Assistant for Senator Lee Metcalf (D-MT), 1974-1976; Federal-State Coordinator for State of Montana, 1976-1989; Director of the Western Governors’ Association Washington Office, 1991-2000; and Director of Federal Affairs for Governor Kitzhaber of Oregon, 2001- 2003. Earlier in Montana Government, between 1971 and 1974, Rich was Research Analyst for MT Blue Ribbon Commission on Postsecondary Education, Legislative Consultant and Bill Drafter for MT Legislative Council, Research Analyst for the MT Constitutional Convention Commission where he provided original research on legislatures, as well as Researcher/Staff for the MT Constitutional Convention Legislative Committee, from where he drafted the various provisions of the Legislative Article and the majority and minority reports on behalf of the Committee members. Rich has represented Montana’s Governor on a trade and cultural mission to Republic of China and participated in US-German Acid Rain Committee sessions in Germany and with European Economic Community environmental officials in Belgium. He is married to Yvonne Seng (Ph.D.) - T’ai Chi apprentice; author and birder.