A Tool for Interactive Data Visualization: Application to Over 10,000 Brain Imaging and Phantom MRI Data Sets

In this paper we propose a web-based approach for quick visualization of big data from brain magnetic resonance imaging (MRI) scans using a combination of an automated image capture and processing system, nonlinear embedding, and interactive data visualization tools. We draw upon thousands of MRI scans captured via the COllaborative Imaging and Neuroinformatics Suite (COINS). We then interface the output of several analysis pipelines based on structural and functional data to a t-distributed stochastic neighbor embedding (t-SNE) algorithm which reduces the number of dimensions for each scan in the input data set to two dimensions while preserving the local structure of data sets. Finally, we interactively display the output of this approach via a web-page, based on data driven documents (D3) JavaScript library. Two distinct approaches were used to visualize the data. In the first approach, we computed multiple quality control (QC) values from pre-processed data, which were used as inputs to the t-SNE algorithm. This approach helps in assessing the quality of each data set relative to others. In the second case, computed variables of interest (e.g., brain volume or voxel values from segmented gray matter images) were used as inputs to the t-SNE algorithm. This approach helps in identifying interesting patterns in the data sets. We demonstrate these approaches using multiple examples from over 10,000 data sets including (1) quality control measures calculated from phantom data over time, (2) quality control data from human functional MRI data across various studies, scanners, sites, (3) volumetric and density measures from human structural MRI data across various studies, scanners and sites. Results from (1) and (2) show the potential of our approach to combine t-SNE data reduction with interactive color coding of variables of interest to quickly identify visually unique clusters of data (i.e., data sets with poor QC, clustering of data by site) quickly. Results from (3) demonstrate interesting patterns of gray matter and volume, and evaluate how they map onto variables including scanners, age, and gender. In sum, the proposed approach allows researchers to rapidly identify and extract meaningful information from big data sets. Such tools are becoming increasingly important as datasets grow larger

The Grizzly, September 25, 2003

The State of Iraq: Critical, but not Hopeless says Trudy Rubin • Family Day Celebrates Students\u27 Second Home • The Journey of a Lifetime • Aftermath of Isabel: A Photo Essay • SERV Serves Students During Campus Emergencies • Opinions: Common Sentiments About the Common Experience; UC Fashion: Mood-Based; People Want to Know the Real Truth; WTO Talks Collapse: Possibly a Good Thing; Out of the Middle East: Part 3 • Collegeville\u27s Hot Spots • Playwriting Debut • Meet the Star Among Us • London Living: A Warm City • The Outhouse Revisited: A Review • Field Hockey: Young Sets School Record in 5-0 win • Men\u27s Soccer: Continuing to Battle Against Tough Competition • UC Football: Albright Stomps the Bearshttps://digitalcommons.ursinus.edu/grizzlynews/1542/thumbnail.jp

Relational victimization, friendship, and adolescents' hypothalamic–pituitary–adrenal axis responses to an in vivo social stressor

Adolescents’ peer experiences may have significant associations with biological stress-response systems, adding to or reducing allostatic load. This study examined relational victimization as a unique contributor to reactive hypothalamic–pituitary–adrenal (HPA) axis responses as well as friendship quality and behavior as factors that may promote HPA recovery following a stressor. A total of 62 adolescents (ages 12–16; 73% female) presenting with a wide range of life stressors and adjustment difficulties completed survey measures of peer victimization and friendship quality. Cortisol samples were collected before and after a lab-based interpersonally themed social stressor task to provide measures of HPA baseline, reactivity, and recovery. Following the stressor task, adolescents discussed their performance with a close friend; observational coding yielded measures of friends’ responsiveness. Adolescents also reported positive and negative friendship qualities. Results suggested that higher levels of adolescents’ relational victimization were associated with blunted cortisol reactivity, even after controlling for physical forms of victimization and other known predictors of HPA functioning (i.e., life stress or depressive symptoms). Friendship qualities (i.e., low negative qualities) and specific friendship behaviors (i.e., high levels of responsiveness) contributed to greater HPA regulation; however, consistent with theories of rumination, high friend responsiveness in the context of high levels of positive friendship quality contributed to less cortisol recovery. Findings extend prior work on the importance of relational victimization and dyadic peer relations as unique and salient correlates of adaptation in adolescence

The Grizzly, November 6, 2003

Ursinus to Take its Place in the Future • Sticks and Stones: Hate Speech on Campus • Students Bug Out after Insect Invasion • Election Day: Mud Slinging and Politics • Look Back at October: Breast Cancer Month • Opinions: OCD: Harmless Passions or Medical Disorder?; Struggling with OCD, the Disorder; Finding Ways to Cope with the Parting of a Pet; Rush Limbaugh: Another Conservative Hypocrite; Pot Smoking Equals Lower Stamina?; Registering Online: An Extreme Inconvenience • Poet Comes to U.C. • Careers in Criminology and Investigation • Meet Dr. Kozusko: The New Shakespeare Professor • Perceptions of Greeks in the Media, UC • Greek Life Fifty Years Ago • Rushing: Is it for You? • Despite Loss, UC Football Team Remains Hopeful • UC XC Competes in Centennial Conference Championship • UC XC Holds 18th Annual Bear Pack Run 5K • Athletic Profile: Katie Dougherty • Women\u27s Rugby Team Makes History • UC Soccer Updateshttps://digitalcommons.ursinus.edu/grizzlynews/1547/thumbnail.jp

The Grizzly, October 9, 2003

Choose to Reuse: Recycling at Ursinus • Volunteer Program Breaks the Bank • Get Registered to Get Out the Vote • Meet the Democratic Candidates for President • A Look at the Response to Rape at Ursinus • Opinions: How Safe do we Feel?; Out of the Middle East: End of a Journey; Text Messaging Behind Your S.O.\u27s Back; New Addiction: AIM; Domo Arigato, Dr. Roboto • Guster: Having Fun Being Young • Halloween Fun Around Collegeville • The Eger Gateway • Field Hockey Still Undefeated in Conference Play • Ursinus XC Takes on Div. 1 and 2 Opponents • Volleyball Splits First C.C Matches • Women\u27s Soccer Continues to Impress • Men\u27s Soccer Trying to Battle • Josh Kemp: Changing the Record Bookshttps://digitalcommons.ursinus.edu/grizzlynews/1544/thumbnail.jp

Anarcho-Environmentalists: Ascetics of Late Modernity

This article explores experiences of environmental activism from the viewpoint of members of a radical environment group. It is based on data collected during eight months of participant observation and through semistructured interviews with ten core members and two ex-members. Working on personal feelings, attitudes, beliefs, and behaviors (self-work) was central to the strategy for social change employed by this group. Drawing on Weber's sociology of religion, this article explores the way the high expectation the activists had of themselves matched Weber's typification of the rationally active ascetic. It is argued that asceticism is an enduring element of Western culture that takes different forms in response to historical conditions. In this case, we see a form of secular asceticism that responds to the conditions of late modernity

Risks Involved in the Use of Enrofloxacin for Salmonella Enteritidis or Salmonella Heidelberg in Commercial Poultry

The objectives of the present study were to evaluate the risks involved in the use of Enrofloxacin for Salmonella Enteritidis (SE) or Salmonella Heidelberg (SH) in commercial poultry and determine the effects of a probiotic as an antibiotic alternative. Two experiments were conducted to evaluate the risks involved in the use of Enrofloxacin for SE or SH in commercial poultry. Exp 1 consisted of 2 trials. In each trial, chickens were assigned to one of three groups; control + SE challenged; Enrofloxacin 25 mg/kg + SE; Enrofloxacin 50 mg/kg + SE. Chickens received Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, all groups received fresh water without any treatment. All chickens were orally gavaged with 107 cfu/chick of SE at 7 days of age and euthanized on 8 days of age. In Exp 2, turkey poults were assigned to one of the three groups; control + SH; probiotic + SH; Enrofloxacin 50 mg/kg + SH. Poults received probiotic or Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, poults received fresh water without any treatment. Poults were orally gavaged with 107 cfu/poult of SH at 7 days of age. Poults were weighted and humanely killed 24 h post-SH challenge to evaluate serum concentration of FITC-D to evaluate intestinal permeability, metagenomics and SH infection. In both trials of Exp 1, chickens treated with Enrofloxacin were more susceptible to SE organ invasion and intestinal colonization when compared with control non-treated chickens (P < 0.05). In Exp 2, poults treated with 50 mg/kg of Enrofloxacin showed an increase in body weight, however, this group also showed an increase in SH susceptibility, intestinal permeability and lower proportion of Firmicutes and Bacteroidetes, but with control group had the highest proportion of Proteobacteria. In contrast, poults that received the probiotic had the highest proportion of Firmicutes and Bacteroidetes, but lowest Proteobacteria. The results of the present study suggest that prophylactic utilization of Enrofloxacin at 5 times the recommended dose in poultry, increases the susceptibility to salmonellae infections, and confirms probiotics may be a

The Grizzly, November 13, 2003

The Power of Puppets: Spiral Q at Ursinus • Registration Frustration • Philly Re-elects John Street as Mayor • First Injectable Male Contraceptive • Campus Connection: Spotlight on NYU and Student Suicide • Rush Begins at Ursinus • Cellphones Used to Cheat: Will This Technology Tempt Students at Ursinus? • Opinions: John Street: A Better Choice for Philadelphia Mayor; Die in Peace or Stay Alive?; Careers over Children; Why You Should Vote • Academy of Sportfighting • Networking for Holidays • Halloween Extravaganzas: Frightful Night for the Senior Class; Smoking Party • Musical Performances in UC History • Myrin Library now Recycles! • Field Hockey\u27s Season Cut Short • Women\u27s Soccer Team has a Record Breaking Season • UC Football: Skid Continueshttps://digitalcommons.ursinus.edu/grizzlynews/1548/thumbnail.jp

The Grizzly, October 16, 2003

Feeling Drained for a Good Cause: Omega Chi Blood Drive • CAB Laugh-off Left Students Rolling in the Aisles • UC in the City Program Announces Easier Access to Philly • Political Pagemakers: Democratic Candidates for President • California Recall Circus has its Star • Club Spotlight: Forensics • Opinions: UC in the City: An Attempt to Fight the Boredom; California Recall Election Democracy at its Best; Video Games as Government Training Tools; Flu Season is Near; Legal BAC Should Still be Lower; Myrin Library: Use It • On the Verge Review: Memorable • Believe it or Not: A Tree in the End Zone • Meet Dr. Zwerling • Job Fair Success • 2003 Homecoming Court • Women\u27s Rugby: A Tough and Spirited Group of Ladies • Field Hockey Team Remains Undefeated in Conference • Men\u27s Soccer Continues to Face Tough Losses • Volleyball 2-3 in Conference Play • Sue Hadfield Named Head Swimming Coachhttps://digitalcommons.ursinus.edu/grizzlynews/1545/thumbnail.jp

The Grizzly, September 18, 2003

Senate Debates Future of Pell Grants • Presidential Address on Iraq • Downloading a Lawsuit • Working for the Weekend • How Accessible is Ursinus College? • Time of the Month not Every Month • Doors Close on an Urban Myth: Elevator Danger • Opinions: Zack\u27s: Not Always a Good Alternative; Have you Thanked Your Cleaning Staff Today?; The Negative Side of Reality TV; Out of the Middle East: Part Two • Nonsense! • An Off-campus Opportunity: Southlander • Potions, Pills and Prescriptions: Careers in the Pharmaceutical Industry • Dance with the Best! • Dave Matthews\u27 Experience: From the Eyes of UC Students • Student Profile: Jennifer Cackowski Challenged at Frankfurt Consulate • Price Comparison: Gas Prices • Bears Defense Crushes Catholic • Volleyball Team Continues Streaky Play • UC Cross Country Battles Elements and Competition • Women\u27s Soccer Team off to Best Start Ever • Men\u27s Soccer: Continuing to Fight • Field Hockey: Bears Lose Tough Onehttps://digitalcommons.ursinus.edu/grizzlynews/1541/thumbnail.jp