Topics in Matrix Sampling Algorithms

We study three fundamental problems of Linear Algebra, lying in the heart of various Machine Learning applications, namely: 1)"Low-rank Column-based Matrix Approximation". We are given a matrix A and a target rank k. The goal is to select a subset of columns of A and, by using only these columns, compute a rank k approximation to A that is as good as the rank k approximation that would have been obtained by using all the columns; 2) "Coreset Construction in Least-Squares Regression". We are given a matrix A and a vector b. Consider the (over-constrained) least-squares problem of minimizing ||Ax-b||, over all vectors x in D. The domain D represents the constraints on the solution and can be arbitrary. The goal is to select a subset of the rows of A and b and, by using only these rows, find a solution vector that is as good as the solution vector that would have been obtained by using all the rows; 3) "Feature Selection in K-means Clustering". We are given a set of points described with respect to a large number of features. The goal is to select a subset of the features and, by using only this subset, obtain a k-partition of the points that is as good as the partition that would have been obtained by using all the features. We present novel algorithms for all three problems mentioned above. Our results can be viewed as follow-up research to a line of work known as "Matrix Sampling Algorithms". [Frieze, Kanna, Vempala, 1998] presented the first such algorithm for the Low-rank Matrix Approximation problem. Since then, such algorithms have been developed for several other problems, e.g. Graph Sparsification and Linear Equation Solving. Our contributions to this line of research are: (i) improved algorithms for Low-rank Matrix Approximation and Regression (ii) algorithms for a new problem domain (K-means Clustering).Comment: PhD Thesis, 150 page

11. Changes in Adolescent and Young Adult (AYA) Relationship Status during COVID19: Data from a 30 Country Sexual and Reproductive Health Study

This article is made available for unrestricted research re-use and secondary analysis in any form or be any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Purpose: Important milestones - including romantic/sexual relationship development - were impacted by COVID19 mitigation measures. We examined self-reported change in relationship status before, during and after COVID among AYA who participated in a 30-country survey. Methods: Data were drawn from the International Sexual Health And REproductive Health Survey (I-SHARE-1), a multi-country, cross-sectional, online study conducted to assess the impact of the pandemic on adult sexual health across the globe. Participants were recruited through local, regional, and national networks (e.g. listservs of professional organizations and international health organizations, social media, etc.) of each country’s research team. We drew a subsample of AYA (N=7527 18-26 years; 32.3% of the total sample; 60.1% female, 86.1% cisgender, 77.1% heterosexual). We examined 5 categories of relationship status change: 1) unpartnered pre/post; 2) unpartnered pre, new partner post; 3) same partner pre/post; 4) partnered pre, broke up, unpartnered post; 5) partnered pre, broke up, new partner post. Random intercept mixed effects multinomial regression (gllamm; Stata 17.0; all p<.05) adjusted for country-level clustering was used to understand how demographic (age, gender identity, sexual identity, employment status during COVID, mental health, distancing or isolation during COVID) and country-level predictors (income group, Oxford Stringency Index [national response to COVID], Palma Ratio [country-income inequality) and Gender Inequality Index (country-gender inequality) were associated with relationship change. Results: 15% of AYA had no partner pre/post COVID, 5% were unpartnered pre-COVID with new partner post. 63.3% had the same partner pre/post, whereas 11.3% had a partner pre-COVID, but broke up and had no new partner post-COVID. Less than 5% had a new partner post-COVID after breaking up with their pre-COVID partner. Of those who broke up with their partner, the majority ended during (44.4%) or after (26.6%) COVID-lockdowns, and one-third thought social distancing precipitated the relationship’s end. Older (RRR=0.86-0.91), female (RRR=0.32-0.63) and transgender AYA (RRR=0.10-0.37) all had a lower risk, and sexual minority AYA had a higher risk (RRR=1.35-1.51), of being in all status categories compared to being in the same relationship before-and-after COVID. Higher mental health scores were linked to lower probability of being unpartnered pre/post as compared to being partnered pre/post (RRR=0.89-0.82). Social-distancing was associated with a lower risk for pre-COVID unpartnered individuals finding new post-COVID relationships (RRR=0.76) or of partnered individuals breaking up, while ever being in isolation was associated with higher risk of being unpartnered pre/post (RRR=1.20). Higher country income was associated with being unpartered pre-COVID (RRR=0.08-0.12) and higher risk of having a pre-COVID relationship break-up (RRR=1.32). Unpartnered individuals in countries with higher lockdown stringency had a greater probability of finding a new post-COVID relationship (RRR=1.13). Conclusions: COVID measures were associated with AYA relationships both initiating and ending. Strategies for relationship development/support should be included as part of preparation for future public health emergencies

Efficient, high-throughput transfection of human embryonic stem cells

INTRODUCTION: Genetic manipulation of human embryonic stem cells (hESC) has been limited by their general resistance to common methods used to introduce exogenous DNA or RNA. Efficient and high throughput transfection of nucleic acids into hESC would be a valuable experimental tool to manipulate these cells for research and clinical applications. METHODS: We investigated the ability of two commercially available electroporation systems, the Nucleofection(® )96-well Shuttle(® )System from Lonza and the Neon™ Transfection System from Invitrogen to efficiently transfect hESC. Transfection efficiency was measured by flow cytometry for the expression of the green fluorescent protein and the viability of the transfected cells was determined by an ATP catalyzed luciferase reaction. The transfected cells were also analyzed by flow cytometry for common markers of pluripotency. RESULTS: Both systems are capable of transfecting hESC at high efficiencies with little loss of cell viability. However, the reproducibility and the ease of scaling for high throughput applications led us to perform more comprehensive tests on the Nucleofection(® )96-well Shuttle(® )System. We demonstrate that this method yields a large fraction of transiently transfected cells with minimal loss of cell viability and pluripotency, producing protein expression from plasmid vectors in several different hESC lines. The method scales to a 96-well plate with similar transfection efficiencies at the start and end of the plate. We also investigated the efficiency with which stable transfectants can be generated and recovered under antibiotic selection. Finally, we found that this method is effective in the delivery of short synthetic RNA oligonucleotides (siRNA) into hESC for knockdown of translation activity via RNA interference. CONCLUSIONS: Our results indicate that these electroporation methods provide a reliable, efficient, and high-throughput approach to the genetic manipulation of hESC

A Transient Sub-Eddington Black Hole X-ray Binary Candidate in the Dust Lanes of Centaurus A

We report the discovery of a bright X-ray transient, CXOU J132527.6-430023, in the nearby early-type galaxy NGC 5128. The source was first detected over the course of five Chandra observations in 2007, reaching an unabsorbed outburst luminosity of 1-2*10^38 erg/s in the 0.5-7.0 keV band before returning to quiescence. Such luminosities are possible for both stellar-mass black hole and neutron star X-ray binary transients. Here, we attempt to characterize the nature of the compact object. No counterpart has been detected in the optical or radio sky, but the proximity of the source to the dust lanes allows for the possibility of an obscured companion. The brightness of the source after a >100 fold increase in X-ray flux makes it either the first confirmed transient non-ULX black hole system in outburst to be subject to detailed spectral modeling outside the Local Group, or a bright (>10^38 erg/s) transient neutron star X-ray binary, which are very rare. Such a large increase in flux would appear to lend weight to the view that this is a black hole transient. X-ray spectral fitting of an absorbed power law yielded unphysical photon indices, while the parameters of the best-fit absorbed disc blackbody model are typical of an accreting ~10 Msol black hole in the thermally dominant state.Comment: 8 pages, 6 figures, accepted for publication in Ap

Human PrimPol is a highly error-prone polymerase regulated by single-stranded DNA binding proteins

PrimPol is a recently identified polymerase involved in eukaryotic DNA damage tolerance, employed in both re-priming and translesion synthesis mechanisms to bypass nuclear and mitochondrial DNA lesions. In this report, we investigate how the enzymatic activities of human PrimPol are regulated. We show that, unlike other TLS polymerases, PrimPol is not stimulated by PCNA and does not interact with it in vivo. We identify that PrimPol interacts with both of the major single-strand binding proteins, RPA and mtSSB in vivo. Using NMR spectroscopy, we characterize the domains responsible for the PrimPol-RPA interaction, revealing that PrimPol binds directly to the N-terminal domain of RPA70. In contrast to the established role of SSBs in stimulating replicative polymerases, we find that SSBs significantly limit the primase and polymerase activities of PrimPol. To identify the requirement for this regulation, we employed two forward mutation assays to characterize PrimPol's replication fidelity. We find that PrimPol is a mutagenic polymerase, with a unique error specificity that is highly biased towards insertion-deletion errors. Given the error-prone disposition of PrimPol, we propose a mechanism whereby SSBs greatly restrict the contribution of this enzyme to DNA replication at stalled forks, thus reducing the mutagenic potential of PrimPol during genome replication

The Grizzly, December 6, 1994

Beetlemania Hits Ursinus • Strassburger Appointed President • Unrest in the Baltics Continues • Ursinus Birthday Card Unveiled • Jeffrey Dahmer Dead • Philadelphia Teen Slain as Result of Inner City Rivalries • Lectures, Friendships, and Giving Up Shop • The Holidays Mean More Than Just Christmas • Alumna Spotlight: The Life of a Doctor • The Java Trench: More Than Just Coffee • Indigo Girls Delight Philly Fans • Intramural Updatehttps://digitalcommons.ursinus.edu/grizzlynews/1349/thumbnail.jp

word~river literary review (2009)

wordriver is a literary journal dedicated to the poetry, short fiction and creative nonfiction of adjuncts and part-time instructors teaching in our universities, colleges, and community colleges. Our premier issue was published in Spring 2009. We are always looking for work that demonstrates the creativity and craft of adjunct/part-time instructors in English and other disciplines. We reserve first publication rights and onetime anthology publication rights for all work published. We define adjunct instructors as anyone teaching part-time or full-time under a semester or yearly contract, nationwide and in any discipline. Graduate students teaching under part-time contracts during the summer or who have used up their teaching assistant time and are teaching with adjunct contracts for the remainder of their graduate program also are eligible.https://digitalscholarship.unlv.edu/word_river/1002/thumbnail.jp