The Archives Unleashed Project: Technology, Process, and Community to Improve Scholarly Access to Web Archives

The Archives Unleashed project aims to improve scholarly access to web archives through a multi-pronged strategy involving tool creation, process modeling, and community building -- all proceeding concurrently in mutually --reinforcing efforts. As we near the end of our initially-conceived three-year project, we report on our progress and share lessons learned along the way. The main contribution articulated in this paper is a process model that decomposes scholarly inquiries into four main activities: filter, extract, aggregate, and visualize. Based on the insight that these activities can be disaggregated across time, space, and tools, it is possible to generate "derivative products", using our Archives Unleashed Toolkit, that serve as useful starting points for scholarly inquiry. Scholars can download these products from the Archives Unleashed Cloud and manipulate them just like any other dataset, thus providing access to web archives without requiring any specialized knowledge. Over the past few years, our platform has processed over a thousand different collections from over two hundred users, totaling around 300 terabytes of web archives.This research was supported by the Andrew W. Mellon Foundation, the Social Sciences and Humanities Research Council of Canada, as well as Start Smart Labs, Compute Canada, the University of Waterloo, and York University. We’d like to thank Jeremy Wiebe, Ryan Deschamps, and Gursimran Singh for their contributions

Content-Based Exploration of Archival Images Using Neural Networks

We present DAIRE (Deep Archival Image Retrieval Engine), an image exploration tool based on latent representations derived from neural networks, which allows scholars to "query" using an image of interest to rapidly find related images within a web archive. This work represents one part of our broader effort to move away from text-centric analyses of web archives and scholarly tools that are direct reflections of methods for accessing the live web. This short piece describes the implementation of our system and a case study on a subset of the GeoCities web archive.This research was supported in part by the Andrew W. Mellon Foundation and the Social Sciences and Humanities Research Council of Canada

pop-1 Encodes an HMG box protein required for the specification of a mesoderm precursor in Early C. elegans embryos

AbstractIn C. elegans embryogenesis, the MS blastomere produces predominantly mesodermal cell types, while its sister E generates only endodermal tissue. We show that a maternal gene, pop-1, is essential for the specification of MS fate and that a mutation in pop-1 results in MS adopting an E fate. Previous studies have shown that the maternal gene skn-1 is required for both MS and E development and that skn-1 encodes a transcription factor. We show here that the pop-1 gene encodes a protein with an HMG box similar to the HMG boxes in the vertebrate lymphoid-specifictranscriptional regulators TCF-1 and LEF-1. We propose that POP-1 and SKN-1 function together in the early embryo to allow MS-specific differentiation

Photographing and Sketching my Way Through Europe

STEP Category: Education AbroadThis poster is an overall summary of my study abroad trip to Europe containing a sample of my drawings and photographs.The Ohio State University Second-year Transformational Experience Program (STEP)Academic Major: Landscape Architectur

Female Sex Development and Reproductive Duct Formation Depend on Wnt4a in Zebrafish.

In laboratory strains of zebrafish, sex determination occurs in the absence of a typical sex chromosome and it is not known what regulates the proportion of animals that develop as males or females. Many sex determination and gonad differentiation genes that act downstream of a sex chromosome are well conserved among vertebrates, but studies that test their contribution to this process have mostly been limited to mammalian models. In mammals, WNT4 is a signaling ligand that is essential for ovary and Müllerian duct development, where it antagonizes the male-promoting FGF9 signal. Wnt4 is well conserved across all vertebrates, but it is not known if Wnt4 plays a role in sex determination and/or the differentiation of sex organs in nonmammalian vertebrates. This question is especially interesting in teleosts, such as zebrafish, because they lack an Fgf9 ortholog. Here we show that wnt4a is the ortholog of mammalian Wnt4, and that wnt4b was present in the last common ancestor of humans and zebrafish, but was lost in mammals. We show that wnt4a loss-of-function mutants develop predominantly as males and conclude that wnt4a activity promotes female sex determination and/or differentiation in zebrafish. Additionally, both male and female wnt4a mutants are sterile due to defects in reproductive duct development. Together these results strongly argue that Wnt4a is a conserved regulator of female sex determination and reproductive duct development in mammalian and nonmammalian vertebrates

A color flow tract in ultrasound-guided random renal core biopsy predicts complications

OBJECTIVES: To determine patient and procedural risk factors for major complications in ultrasound (US)-guided random renal core biopsy. METHODS: Random renal biopsies performed by radiologists in the US department at a single institution between 2014 and 2018 were retrospectively reviewed. The patient\u27s age, sex, race, and estimated glomerular filtration rate (eGFR) were recorded. The biopsy approach, needle gauge, length of cores, number of throws, and presence of a color flow tract were recorded. Outcome data included minor and major complications. Associations between variables were tested with χ RESULTS: A total of 231 biopsies (167 native and 64 allografts) were reviewed. There was no significant difference in the sex, age, race, or eGFR between native and allograft groups. The overall rate for any complication was 18.2%, with a 4.3% rate of major complications, which was significantly greater in native compared to allograft biopsies (6% versus 0%; P = .045). A risk analysis in native biopsies only showed that major complications were significantly associated with a low eGFR such that patients with stage 4 or 5 kidney disease had higher odds of complications (odds ratio [95% confidence interval]: stage 4, 9.405 [1.995-44.338]; P = .0393; stage 5, 10.749 [2.218-52.080]; P = .0203) than patients with normal function (eGFR \u3e60 mL/min). The presence of a color flow tract portended a 10.7 times greater risk of having any complication (95% confidence interval, 4.595-24.994; P \u3c .001). Other procedural factors were not significantly associated with complications. CONCLUSIONS: There is an increased risk of major complications in US-guided random native kidney biopsy in patients with a low eGFR (\u3c30 mL/min) and a patent color flow tract in the immediate postbiopsy setting

Development of highly intensified cell culture perfusion media and process with tremendous productivity potential, while having a low cell bleed requirement for maintaining an overall high yield

Process intensification leveraging perfusion offers immense opportunities for yield improvement over fed-batch processes for the production of monoclonal antibodies. In the context of continuous processing, the goal is to achieve highly intensified perfusion processes that allow substantial footprint reduction and enable flexible adaptation in new facilities. Developing a productive and efficient perfusion process requires not only the application of the “push-to-low” concept for reducing the perfusion rate requirement, but also requires in-depth mechanistic development of medium formulations in order to decrease byproduct waste generation, reduce unproductive cell growth and increase productivity. Specifically reducing the usage of cell bleed is particularly desirable for improving the overall yield, since as much as 30% of the generated product may be lost through the use of cell bleed. In this work, we share case studies of perfusion medium development studying classical components such as vitamins and salts that can be manipulated to have profound effect for controlling the cell growth and reducing the use of cell bleed. In one case, the cell bleed rate was reduced down to as low as zero, while still being able to maintain a highly viable culture. Furthermore, in some cases, significant increase in the cell specific productivity (qp) was achieved when the perfusion culture was switched to a growth suppressed mode. In one example, the qp increased from 30 pg/cell/day to as high as 115 pg/cell/day when the cell growth was arrested. This led to increased daily volumetric productivities of 3 to 5 g/L/day compared to the control of 1 g/L/day. Cell cycle analysis of the arrested culture by flow cytometry also revealed an induced state of elevated cell population in the G0/G1 phase, which is generally considered as the most productive state of the cell cycle. In order to integrate the cell growth control strategy described herein, a two stage perfusion concept is designed where the first stage focuses on rapid accumulation of cells to reach the target cell density, and the second stage switches to a slow growth, yet highly productive and viable perfusion culture

OSSOS III - Resonant Trans-Neptunian Populations: Constraints from the first quarter of the Outer Solar System Origins Survey

The first two observational sky "blocks" of the Outer Solar System Origins Survey (OSSOS) have significantly increased the number of well-characterized observed trans-Neptunian objects (TNOs) in Neptune's mean motion resonances. We describe the 31 securely resonant TNOs detected by OSSOS so far, and we use them to independently verify the resonant population models from the Canada-France Ecliptic Plane Survey (CFEPS; Gladman et al. 2012), with which we find broad agreement. We confirm that the 5:2 resonance is more populated than models of the outer Solar System's dynamical history predict; our minimum population estimate shows that the high eccentricity (e>0.35) portion of the resonance is at least as populous as the 2:1 and possibly as populated as the 3:2 resonance. One OSSOS block was well-suited to detecting objects trapped at low libration amplitudes in Neptune's 3:2 resonance, a population of interest in testing the origins of resonant TNOs. We detected three 3:2 objects with libration amplitudes below the cutoff modeled by CFEPS; OSSOS thus offers new constraints on this distribution. The OSSOS detections confirm that the 2:1 resonance has a dynamically colder inclination distribution than either the 3:2 or 5:2 resonances. Using the combined OSSOS and CFEPS 2:1 detections, we constrain the fraction of 2:1 objects in the symmetric mode of libration to be 0.2-0.85; we also constrain the fraction of leading vs. trailing asymmetric librators, which has been theoretically predicted to vary depending on Neptune's migration history, to be 0.05-0.8. Future OSSOS blocks will improve these constraints.Comment: Accepted for publication in A