Digital Commons Network^™

Serial Recombineering Cloning To Build Selectable And Tagged Genomic P[Acman] Bac Clones For Selection Transgenesis And Functional Gene Analysis Using Drosophila Melanogaster, Koen J T Venken, Nick Matinyan, Yezabel Gonzalez, Herman A Dierick

Faculty, Staff and Students Publications

Transgenes with genomic DNA fragments that encompass genes of interest are the gold standard for complementing null alleles in rescue experiments in the fruit fly Drosophila melanogaster. Of particular interest are genomic DNA clones available as bacterial artificial chromosomes (BACs) or fosmids from publicly available genomic DNA libraries. Genes contained within BAC and fosmid clones can be easily modified by recombineering cloning to insert peptide or protein tags to localize, visualize, or manipulate gene products, and to create point mutations or deletions for structure-function analysis of the inserted genes. However, since transgenesis efficiency is inversely correlated with transgene size, obtaining …

Multiplexed Transgenic Selection And Counterselection Strategies To Expedite Genetic Manipulation Workflows Using Drosophila Melanogaster, Koen J T Venken, Nick Matinyan, Yezabel Gonzalez, Herman A Dierick

Faculty, Staff and Students Publications

We recently described a set of four selectable and two counterselectable markers that provide resistance and sensitivity, respectively, against their corresponding drugs using the model organism Drosophila melanogaster. The four selectable markers provide animal resistance against G418 sulfate, Puromycin HCl, Blasticidin S, or Hygromycin B, while the two counterselection markers make animals sensitive to Ganciclovir/Acyclovir, or 5-Fluorocytosine. Unlike classical phenotypic markers, visual or fluorescent, which require extensive screening progeny of a genetic cross for desired genotypes, resistance and sensitivity markers eliminate this laborious procedure by directly selecting for, or counterselecting against, the desired genotypes. We demonstrated the usefulness of …

A Next-Generation Approach To Mental Health Outcomes: Treatment, Time, And Trajectories, Mario Montelongo, Jaehoon Lee, Edward Poa, Robert Boland, Katrina A Rufino, Michelle Patriquin, Hyuntaek Oh

Staff and Researcher Publications

Over the last several decades, inpatient psychiatric length of stay (LOS) has been greatly reduced to the detriment of patients. Latent variable mixture modeling, can be used to improve the quality of care for patients by identifying unobserved subgroups and optimize treatment variables, including LOS. This study had three objectives (1) to replicate the findings made by Oh et al. in a distinct sample, (2) to examine demographic differences related to inpatient treatment trajectories, and (3) to relate additional variables to each trajectory. We collected data on six key mental illness factors and information on felonies, misdemeanors, history of stopping …

Pediatric Rhabdomyosarcoma Incidence And Survival In The United States: An Assessment Of 5656 Cases, 2001–2017, Matthew T Mcevoy, David A Siegel, Shifan Dai, Mehmet Fatih Okcu, Mark Zobeck, Rajkumar Venkatramani, Philip J Lupo

Faculty, Staff and Students Publications

BACKGROUND: While rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents, past epidemiology studies of this malignancy used data that covered

METHODS: Incidence and survival were assessed for pediatric patients diagnosed with RMS during 2003-2017 and 2001-2016, respectively. Both demographic and clinical variables were evaluated. Age-adjusted incidence rates, average annual percent change (AAPC), and 5-year relative survival (RS) were calculated, all with corresponding 95% confidence intervals (CIs). Cox regression models were used to evaluate the impact of demographic and clinical variables on survival.

RESULTS: We identified 5656 primary RMS cases in USCS during 2003-2017. The age-adjusted …

Molecular Mechanisms Regulating Wound Repair: Evidence For Paracrine Signaling From Corneal Epithelial Cells To Fibroblasts And Immune Cells Following Transient Epithelial Cell Treatment With Mitomycin C, Sonali Pal-Ghosh, Beverly A Karpinski, Himani Datta Majumdar, Trisha Ghosh, Julie Thomasian, Stephen R Brooks, Andrew P Sawaya, Maria I Morasso, Kaitlin K Scholand, Cintia S De Paiva, Jeremias G Galletti, Mary Ann Stepp

Faculty, Staff and Students Publications

In this paper, we use RNAseq to identify senescence and phagocytosis as key factors to understanding how mitomyin C (MMC) stimulates regenerative wound repair. We use conditioned media (CM) from untreated (CMC) and MMC treated (CMM) human and mouse corneal epithelial cells to show that corneal epithelial cells indirectly exposed to MMC secrete elevated levels of immunomodulatory proteins including IL-1α and TGFβ1 compared to cells exposed to CMC. These factors increase epithelial and macrophage phagocytosis and promote ECM turnover. IL-1α supplementation can increase phagocytosis in control epithelial cells and attenuate TGFβ1 induced αSMA expression by corneal fibroblasts. Yet, we show …

Factors Affecting Adherence To Intranasal Treatment For Allergic Rhinitis: A Qualitative Study, Meha G Fox, Lauren M Cass, Kevin J Sykes, Emily L Cummings, Scott N Fassas, Rohit Nallani, Josh B Smith, Alexander G Chiu, Jennifer A Villwock

Faculty, Staff and Students Publications

OBJECTIVE: To determine the facilitators of and barriers to adherence to use of intranasal pharmacotherapy (daily intranasal corticosteroids and/or antihistamine, and nasal saline irrigation [NSI]), for allergic rhinitis (AR).

METHODS: Patients were recruited from an academic tertiary care rhinology and allergy clinic. Semi-structured interviews were conducted after the initial visit and/or 4-6 weeks following treatment. Transcribed interviews were analyzed using a grounded theory, inductive approach to elucidate themes regarding patient adherence to AR treatment.

RESULTS: A total of 32 patients (12 male, 20 female; age 22-78) participated (seven at initial visit, seven at follow-up visit, and 18 at both). Memory …

Confucius, Wisdom, And Political Participation: Benevolence And Timeliness In The Analects, Sydney Morrow, Shane Ryan

Research Collection School of Social Sciences

This paper aims to address when the wise person should participate in politics. The question is addressed through engagement with the Analects. Rather than provide interpretations of key terms in the Analects, we provide an account of wisdom that draws from themes in the Analects. The case is made that the wise person is committed to participating in politics primarily because of the connection between wisdom and benevolence (ren 仁 in the Analects). We address challenges to the Confucian approach from the Zhuangzi concerning the potential harms of political participation. General political disengagement is not considered exemplary on the Confucian …

Disentangling The Effects Of Smartphone Screen Time, Checking Frequency, And Problematic Use On Executive Function: A Structural Equation Modelling Analysis, Wei Xing Toh, Wee Qin Ng, Hwajin Yang, Sujin Yang

Research Collection School of Social Sciences

The pervasiveness of smartphone engagement among young adults has attracted growing interest regarding its impact on cognitive processes. However, research on the relation between smartphone use and executive function (EF)—a set of adaptive, goal-directed control processes—remains inconclusive due to imprecise estimation of EF dimensions and inconsistent operationalisation of smartphone use in past studies. Therefore, we examined how two indices of smartphone use—screen time and checking frequency—would predict EF (common EF, shifting-specific-, and working-memory-specific components), using a latent-variable approach based on a comprehensive battery of EF tasks. We also examined the moderating role of problematic smartphone use in the link between …

Effects Of Positive Reappraisal And Self-Distancing On The Meaningfulness Of Everyday Negative Events, Clement Yong Hao Lau, William Tov

Research Collection School of Social Sciences

Current work on meaning-making has primarily focused on major negative life events such as trauma and loss, leaving common daily adversities unexplored. This study aimed to examine how utilizing meaning-making strategies such as positive reappraisal and self-distancing (in isolation or in combination) can facilitate an adaptive processing of these daily negative experiences. Overall meaning and facets of meaning (coherence, purpose, and significance/mattering) were assessed at both global and situational levels. Results suggested that positive reappraisal was generally effective for enhancing situational meaning but not under all conditions. Specifically, when negative experiences were high on emotional intensity, reflecting on the experience …

The City Never Sleeps: But When Will Investment Banks Wake Up To The Climate Crisis?, Theodor Florian Cojoianu, Andrea G. F. Hoepner, Fabiola I. Schneider, Michael Urban, Anh Vu, Dariusz Wojcik

Research Collection College of Integrative Studies

Using a global dataset of over 840,000 equity, bond and syndicated loan investment banking deals, we build the fossil fuel investment brokerage profile of financial centres worldwide between 2000 and 2018. We also study whether city-level fossil fuel divestment commitments and country-level green banking policies impact the profile of fossil fuel financial centres over our study timeframe. We find that several financial centres shift their fossil fuel investment brokerage profiles substantially, including the asset classes in which they are active. However, we do not find any evidence that this is driven by city-level divestment commitments. In contrast, we find that …

What Are The Relationships Between Public Transit And Gentrification Progress? An Empirical Study In The New York-Northern New Jersey-Long Island Areas, Yefu Chen, Hao Xi, Junfeng Jiao

Research Collection College of Integrative Studies

Transit-oriented development has been a widely accepted tool among transportation planning practitioners; however, there are concerns about the risk of increasing residential property values leading to gentrification or displacements. Therefore, it is critical to provide precise investigations of the relationships between public transit and gentrification. Although numerous studies have explored this topic, few have discussed these relationships based on detailed measurements of gentrification from a regional perspective. This study aims to fill the research gap by measuring the gentrification subcategories through a hierarchical definition based on data in the New York–Northern New Jersey–Long Island areas and applying the transit desert …

Urban Air Mobility (Uam) Flight Path: Literature Review And Conceptual Design Of Uam Corridor Virtual Lane System Using “Tracks”, Immanuel Bankole

Student Works

As the Urban Air Mobility (UAM) industry grows and becomes more popular, most of the conversations in the public domain are focused on the (electric Vertical Take-off and Landing) eVTOL aircraft and the physical infrastructure that will support these eVTOL aircraft. However, there is a lack of research on UAM traffic management and flight paths taken by aircraft between locations.

The United States (U.S.) Federal Aviation Administration has proposed the use of corridors to minimize the interaction between UAM operations and traditional air traffic as eVTOL aircraft perform flight activities. The government also acknowledges the need for additional structures (such …

Missed Opportunities In The Diagnosis Of Tuberculosis Meningitis, Niamh Simmons, Margaret A Olsen, Joanna Buss, Thomas C Bailey, Carlos Mejia-Chew

2020-Current year OA Pubs

BACKGROUND: Tuberculosis meningitis (TBM) has high mortality and morbidity. Diagnostic delays can impact TBM outcomes. We aimed to estimate the number of potentially missed opportunities (MOs) to diagnose TBM and determine its impact on 90-day mortality.

METHODS: This is a retrospective cohort of adult patients with a central nervous system (CNS) TB

RESULTS: Of 893 patients with TBM, median age at diagnosis was 50 years (interquartile range, 37-64), 61.3% were male, and 35.2% had Medicaid as primary payer. Overall, 407 (45.6%) had a prior hospital or ED visit with an MO code. In-hospital 90-day mortality was not different between those …

Knockout Of Tsc2 In Nav1.8+ Neurons Predisposes To The Onset Of Normal Weight Obesity, Jennifer M Brazill, David Shin, Kristann Magee, Anurag Majumdar, Ivana R Shen, Valeria Cavalli, Erica L Scheller

2020-Current year OA Pubs

OBJECTIVE: Obesity and nutrient oversupply increase mammalian target of rapamycin (mTOR) signaling in multiple cell types and organs, contributing to the onset of insulin resistance and complications of metabolic disease. However, it remains unclear when and where mTOR activation mediates these effects, limiting options for therapeutic intervention. The objective of this study was to isolate the role of constitutive mTOR activation in Nav1.8-expressing peripheral neurons in the onset of diet-induced obesity, bone loss, and metabolic disease.

METHODS: In humans, loss of function mutations in tuberous sclerosis complex 2 (TSC2) lead to maximal constitutive activation of mTOR. To mirror this in …

Primary Central Nervous System Germ Cell Tumors In Children And Young Adults: A Review Of Controversies In Diagnostic And Treatment Approach, Kee Kiat Yeo, Sumanth Nagabushan, Girish Dhall, Mohamed S Abdelbaki

2020-Current year OA Pubs

Primary central nervous system (CNS) germ cell tumors (GCT) are a rare heterogenous group of cancers, arising most commonly in the second decade of life. Through several clinical trials conducted around the world by various groups, the treatment approach for CNS GCT has advanced substantially with generally improved overall outcomes. In recent years, the goal of clinical trials has been focused on reduction of the radiotherapy burden and minimization of long-term toxicity. This review summarizes the current diagnostic and treatment regimens for CNS GCT, examines the controversies associated with these approaches, gaps in contemporary knowledge, and underscores the challenges we …

First-Principles Calculations On The Electronic Structure, Mechanical, Vibrational, And Thermal Properties Of The Ca₃Bin Antiperovskite Alloy, Reem Maher Mohamad

Theses

Antiperovskites are the counterparts of perovskites. They have diverse properties that make them physically rich and technologically relevant. In the recent years, the alkaline earth based antiperovskites, especially the ones with small semiconductor bandgap, have captured tremendous attention due to their properties which make them efficient to be used in optoelectronic and thermoelectric applications. In this thesis, we are shading light on the alkaline antiperovskite ����₃������ due to its narrow bandgap. Thus, it can be considered as a promising candidate for thermoelectric and optoelectronic applications. Specifically, it is used to harvest waste thermal energy into electricity at low …

The Impact Of School-Based Intervention For Overweight And Obese 9-13-Year-Olds On Anthropometry, Nutrition Knowledge, Attitudes, Selfefficacy And Dietary Behaviors, Sara Zuarub

Dissertations

Childhood obesity has emerged as a significant public health concern in the United Arab Emirates (UAE). The study evaluated the effects of school-based nutrition education on knowledge, attitude, dietary practices, self-efficacy, and anthropometric measurements of overweight and obese school children aged 9-13 years. Additionally, the parents' perceptions on factors contributing to childhood obesity were examined. A 6-month intervention program based on Social Cognitive Theory (SCT) was undertaken by children from 36 public schools located in Dubai and Sharjah emirates, UAE. The overweight/obese school children (n = 403) were classified into three categories, including two intervention groups (1 and 2) and …

Heat Transfer In Mini-Channel Heat Exchanger With Smooth And Pin-Fins Surfaces, Mohammed Molham Daadoua

Theses

This research aims to investigate heat transfer of single-phase and two-phase fluids in mini-channel heat exchanger with smooth and pin-fins surfaces. The main goal of the study is to develop a high-performance heat exchanger for thermal management in various processing applications. This research is carried out using computational fluid dynamics (CFD) modeling and experimentations. The proposed method is to use enhanced structured pin-fins surfaces in a mini-channel heat exchanger to improve heat transfer. The pin-fin microchannel heat exchanger is investigated using a CFD method with single-phase fluid (water, air). The experimental investigations are conducted using single-phase and two-phase fluid involving …

An Empirical Study Of Package Management Issues Via Stack Overflow, Syful Islam, Raula Kula, Christoph Treude, Bodin Chinthanet, Takashi Ishio, Kenichi Matsumoto

Research Collection School Of Computing and Information Systems

The package manager (PM) is crucial to most technology stacks, acting as a broker to ensure that a verified dependency package is correctly installed, configured, or removed from an application. Diversity in technology stacks has led to dozens of PMs with various features. While our recent study indicates that package management features of PM are related to end-user experiences, it is unclear what those issues are and what information is required to resolve them. In this paper, we have investigated PM issues faced by end-users through an empirical study of content on Stack Overflow (SO). We carried out a qualitative …

Solving Large-Scale Pursuit-Evasion Games Using Pre-Trained Strategies, Shuxin Li, Xinrun Wang, Youzhi Zhang, Wanqi Xue, Jakub Cerny, Bo An

Research Collection School Of Computing and Information Systems

Pursuit-evasion games on graphs model the coordination of police forces chasing a fleeing felon in real-world urban settings, using the standard framework of imperfect-information extensive-form games (EFGs). In recent years, solving EFGs has been largely dominated by the Policy-Space Response Oracle (PSRO) methods due to their modularity, scalability, and favorable convergence properties. However, even these methods quickly reach their limits when facing large combinatorial strategy spaces of the pursuit-evasion games. To improve their efficiency, we integrate the pre-training and fine-tuning paradigm into the core module of PSRO -- the repeated computation of the best response. First, we pre-train the pursuer's …

Bidding Graph Games With Partially-Observable Budgets, Guy Avni, Ismael Jecker, Dorde Zikelic

Research Collection School Of Computing and Information Systems

Two-player zero-sum graph games are a central model, which proceeds as follows. A token is placed on a vertex of a graph, and the two players move it to produce an infinite play, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In bidding games, however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as fullinformation games. In this work we initiate the study of partial-information bidding games: we study bidding games in which …

Learning Control Policies For Stochastic Systems With Reach-Avoid Guarantees, Dorde Zikelic, Mathias Lechner, A. Thomas Henzinger, Krishnendu Chatterjee

Research Collection School Of Computing and Information Systems

We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p ∈ [0,1] over the infinite time horizon in general Lipschitz continuous systems. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees …

Quantization-Aware Interval Bound Propagation For Training Certifiably Robust Quantized Neural Networks, Mathias Lechner, Dorde Zikelic, Krishnendu Chatterjee, A. Thomas Henzinger, Daniela Rus

Research Collection School Of Computing and Information Systems

We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training …

Alignment-Enriched Tuning For Patch-Level Pre-Trained Document Image Models, Lei Wang, Jiabang He, Xing Xu, Ning Liu, Hui Liu

Research Collection School Of Computing and Information Systems

Alignment between image and text has shown promising im provements on patch-level pre-trained document image mod els. However, investigating more effective or finer-grained alignment techniques during pre-training requires a large amount of computation cost and time. Thus, a question natu rally arises: Could we fine-tune the pre-trained models adap tive to downstream tasks with alignment objectives and achieve comparable or better performance? In this paper, we pro pose a new model architecture with alignment-enriched tuning (dubbed AETNet) upon pre-trained document image models, to adapt downstream tasks with the joint task-specific super vised and alignment-aware contrastive objective. Specifically, weintroduce an extra …

Learning Relation Prototype From Unlabeled Texts For Long-Tail Relation Extraction, Yixin Cao, Jun Kuang, Ming Gao, Aoying Zhou, Yonggang Wen, Tat-Seng Chua

Research Collection School Of Computing and Information Systems

Relation Extraction (RE) is a vital step to complete Knowledge Graph (KG) by extracting entity relations from texts. However, it usually suffers from the long-tail issue. The training data mainly concentrates on a few types of relations, leading to the lack of sufficient annotations for the remaining types of relations. In this paper, we propose a general approach to learn relation prototypes from unlabeled texts, to facilitate the long-tail relation extraction by transferring knowledge from the relation types with sufficient training data. We learn relation prototypes as an implicit factor between entities, which reflects the meanings of relations as well …

Learning Comprehensive Global Features In Person Re-Identification: Ensuring Discriminativeness Of More Local Regions, Jiali Xia, Jianqiang Huang, Shibao Zheng, Qin Zhou, Bernt Schiele, Xian-Sheng Hua, Qianru Sun

Research Collection School Of Computing and Information Systems

Person re-identification (Re-ID) aims to retrieve person images from a large gallery given a query image of a person of interest. Global information and fine-grained local features are both essential for the representation. However, global embedding learned by naive classification model tends to be trapped in the most discriminative local region, leading to poor evaluation performance. To address the issue, we propose a novel baseline network that learns strong global feature termed as Comprehensive Global Embedding (CGE), ensuring more local regions of global feature maps to be discriminative. In this work, two key modules are proposed including Non-parameterized Local Classifier …

Online Hyperparameter Optimization For Class-Incremental Learning, Yaoyao Liu, Yingying Li, Bernt Schiele, Qianru Sun

Research Collection School Of Computing and Information Systems

Class-incremental learning (CIL) aims to train a classification model while the number of classes increases phase-by-phase. An inherent challenge of CIL is the stability-plasticity tradeoff, i.e., CIL models should keep stable to retain old knowledge and keep plastic to absorb new knowledge. However, none of the existing CIL models can achieve the optimal tradeoff in different data-receiving settings—where typically the training-from-half (TFH) setting needs more stability, but the training-from-scratch (TFS) needs more plasticity. To this end, we design an online learning method that can adaptively optimize the tradeoff without knowing the setting as a priori. Specifically, we first introduce the …

Real-Time Hierarchical Map Segmentation For Coordinating Multi-Robot Exploration, Tianze Luo, Zichen Chen, Budhitama Subagdja, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Coordinating a team of autonomous agents to explore an environment can be done by partitioning the map of the environment into segments and allocating the segments as targets for the individual agents to visit. However, given an unknown environment, map segmentation must be conducted in a continuous and incremental manner. In this paper, we propose a novel real-time hierarchical map segmentation method for supporting multi-agent exploration of indoor environments, wherein clusters of regions of segments are formed hierarchically from randomly sampled points in the environment. Each cluster is then assigned with a cost-utility value based on the minimum cost possible …

Safe Delivery Of Critical Services In Areas With Volatile Security Situation Via A Stackelberg Game Approach, Tien Mai, Arunesh Sinha

Research Collection School Of Computing and Information Systems

Vaccine delivery in under-resourced locations with security risks is not just challenging but also life threatening. The COVID pandemic and the need to vaccinate added even more urgency to this issue. Motivated by this problem, we propose a general framework to set-up limited temporary (vaccination) centers that balance physical security and desired (vaccine) service coverage with limited resources. We set-up the problem as a Stackelberg game between the centers operator (defender) and an adversary, where the set of centers is not fixed a priori but is part of the decision output. This results in a mixed combinatorial and continuous optimization …

A Fair Incentive Scheme For Community Health Workers, Avinandan Bose, Tracey Li, Arunesh Sinha, Tien Mai

Research Collection School Of Computing and Information Systems

Community health workers (CHWs) play a crucial role in the last mile delivery of essential health services to under-served populations in low-income countries. Many non-governmental organizations (NGOs) provide training and support to enable CHWs to deliver health services to their communities, with no charge to the recipients of the services. This includes monetary compensation for the work that CHWs perform, which is broken down into a series of well-defined tasks. In this work, we partner with a NGO D-Tree International to design a fair monetary compensation scheme for tasks performed by CHWs in the semi-autonomous region of Zanzibar in Tanzania, …