Digital Commons Network^™

Extending Outbreak Investigation With Machine Learning And Graph Theory: Benefits Of New Tools With Application To A Nosocomial Outbreak Of A Multidrug-Resistant Organism, Andrew Atkinson, Benjamin Ellenberger, Vanja Piezzi, Tanja Kaspar, Luisa Salazar-Vizcaya, Olga Endrich, Alexander B Leichtle, Jonas Marschall

2020-Current year OA Pubs

OBJECTIVE: From January 1, 2018, until July 31, 2020, our hospital network experienced an outbreak of vancomycin-resistant enterococci (VRE). The goal of our study was to improve existing processes by applying machine-learning and graph-theoretical methods to a nosocomial outbreak investigation.

METHODS: We assembled medical records generated during the first 2 years of the outbreak period (January 2018 through December 2019). We identified risk factors for VRE colonization using standard statistical methods, and we extended these with a decision-tree machine-learning approach. We then elicited possible transmission pathways by detecting commonalities between VRE cases using a graph theoretical network analysis approach.

RESULTS: …

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 …

A Narrative Review Of Screen Time And Wellbeing Among Adolescents Before And During The Covid-19 Pandemic: Implications For The Future, Verity Yu Qing Lua, Terence B. K. Chua, Michael Y. H. Chia

Research Collection School of Social Sciences

The COVID-19 pandemic has disrupted the lives of many. In particular, during the height of the pandemic, many experienced lockdowns, which in turn increased screen time drastically. While the pandemic has been declared an endemic and most activities have been reinstated, there appears to still be elevated screen time among adolescents due to poor habits formed during the pandemic lockdowns. This paper explores the factors by which screen time affects well-being among adolescents and how the pandemic may have influenced some of these factors. For example, beyond having greater screen time, many adolescents have also reduced their physical activities and …

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 …

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 …

Smartphone Use And Daily Cognitive Failures: A Critical Examination Using A Daily Diary Approach With Objective Smartphone Measures, Andree Hartanto, Kristine Y. X. Lee, Yi Jing Chua, Frosch Y. X. Quek, Nadyannam M. Majeed

Research Collection School of Social Sciences

While smartphones have brought many benefits and conveniences to users, there is continuing debate regarding their potential negative consequences on everyday cognition such as daily cognitive failures. A few cross-sectional studies have found positive associations between smartphone use and cognitive failures. However, several research gaps remain, such as the use of cross-sectional designs, confounds related to stable individual differences, the lack of validity in self-report measures of smartphone use, memory biases in retrospective self-reports, and the lack of differentiation between smartphone checking and smartphone screen time. To simultaneously address the aforementioned shortcomings, the current study examined the within-person associations between …

Dexamethasone To Prevent Everolimus-Induced Stomatitis (Alliance Mist Trial: A221701), Kathryn J Ruddy, David Zahrieh, Jun He, Blake Waechter, Julianne L Holleran, Lionel D Lewis, Selina Chow, Jan Beumer, Matthias Weiss, Nikolaos Trikalinos, Bryan Faller, Maryam Lustberg, Hope S Rugo, Charles Loprinzi

2020-Current year OA Pubs

mTOR inhibitors such as everolimus may cause oral stomatitis, often a dose-limiting toxicity. Prior clinical research has suggested that a dexamethasone mouth rinse might help prevent and/or treat this. Alliance A221701 was a randomized phase III trial of patients initiating 10 mg daily oral everolimus that compared dexamethasone mouthwash taken preventively (initial dexamethasone group) versus therapeutically (initial placebo group) to assess two coprimary endpoints: the incidence of mTOR inhibitor-associated stomatitis (mIAS), and the area under the curve (AUC) of mIAS-associated pain over an 8-week treatment period. A Fisher's exact test was used to compare the incidences while a Wilcoxon rank-sum …

Genetic And Environmental Variation In Continuous Phenotypes In The Abcd Study®, Hermine H M Maes, Dana M Lapato, J Eric Schmitt, Monica Luciana, Marie T Banich, James M Bjork, John K Hewitt, Pamela A Madden, Andrew C Heath, Deanna M Barch, Wes K Thompson, William G Iacono, Michael C Neale

2020-Current year OA Pubs

Twin studies yield valuable insights into the sources of variation, covariation and causation in human traits. The ABCD Study® (abcdstudy.org) was designed to take advantage of four universities known for their twin research, neuroimaging, population-based sampling, and expertise in genetic epidemiology so that representative twin studies could be performed. In this paper we use the twin data to: (i) provide initial estimates of heritability for the wide range of phenotypes assessed in the ABCD Study using a consistent direct variance estimation approach, assuring that both data and methodology are sound; and (ii) provide an online resource for researchers that can …

Late-Nc Staging In Routine Neuropathologic Diagnosis: An Update, Peter T Nelson, Katherine E Schwetye, Et Al.

2020-Current year OA Pubs

An international consensus report in 2019 recommended a classification system for limbic-predominant age-related TDP-43 encephalopathy neuropathologic changes (LATE-NC). The suggested neuropathologic staging system and nomenclature have proven useful for autopsy practice and dementia research. However, some issues remain unresolved, such as cases with unusual features that do not fit with current diagnostic categories. The goal of this report is to update the neuropathologic criteria for the diagnosis and staging of LATE-NC, based primarily on published data. We provide practical suggestions about how to integrate available genetic information and comorbid pathologies [e.g., Alzheimer's disease neuropathologic changes (ADNC) and Lewy body disease]. …

Swarming Infrastructures, Jack Greatrex

Research Collection College of Integrative Studies

The first car on the roads of Malacca, a town in the British Straits Settlements colony on the Malay Peninsula, was reportedly nicknamed The Swallow. Images of the eponymous bird were painted onto the vehicle: an avian metaphor fitting for the new, emerging age of the automobile, with its associations with freedom, rapidity and the smoother flows of modern life (Hillier 1961: 99).1

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 …

Clinical Importance Of Clonal Hematopoiesis In Metastatic Gastrointestinal Tract Cancers, Bill H Diplas, Kelly Bolton, Et Al.

2020-Current year OA Pubs

IMPORTANCE: Clonal hematopoiesis (CH) has been associated with development of atherosclerosis and leukemia and worse survival among patients with cancer; however, the association with cancer therapy efficacy, in particular immune checkpoint blockade (ICB), and toxicity has not yet been established. Given the widespread use of ICB and the critical role hematopoietic stem cell-derived lymphocytes play in mediating antitumor responses, CH may be associated with therapeutic efficacy and hematologic toxicity.

OBJECTIVE: To determine the association between CH and outcomes, hematologic toxicity, and therapeutic efficacy in patients with metastatic gastrointestinal tract cancers being treated with systemic therapy, both in the first-line metastatic …

Final Findings From The Control Trial: Strategies To Reduce The Incidence And Severity Of Neratinib-Associated Diarrhea In Patients With Her2-Positive Early-Stage Breast Cancer, Arlene Chan, Ron Bose, Et Al.

2020-Current year OA Pubs

BACKGROUND: Neratinib is an irreversible pan-HER tyrosine kinase inhibitor approved for HER2-positive early-stage and metastatic breast cancer. Diarrhea is the most frequent side effect and the most common reason for early discontinuation. The phase II CONTROL trial investigated antidiarrheal prophylaxis or neratinib dose escalation (DE) for prevention of diarrhea. We present complete study results including final data for two DE strategies.

METHODS: Patients who completed trastuzumab-based adjuvant therapy received neratinib 240 mg/day for 1 year. Early cohorts investigated mandatory prophylaxis with loperamide, then additional budesonide or colestipol. Final cohorts assessed neratinib DE over the first 2 (DE1) or 4 weeks …

Lgmdd1 Natural History And Phenotypic Spectrum: Implications For Clinical Trials, Andrew R Findlay, Sarah E Robinson, Stephanie Poelker, Michelle Seiffert, Rocio Bengoechea, Conrad C Weihl

2020-Current year OA Pubs

OBJECTIVE: To delineate the full phenotypic spectrum and characterize the natural history of limb girdle muscular dystrophy type D1 (LGMDD1).

METHODS: We extracted age at clinical events of interest contributing to LGMDD1 disease burden via a systematic literature and chart review. Manual muscle testing and quantitative dynamometry data were used to estimate annualized rates of change. We also conducted a cross-sectional observational study using previously validated patient-reported outcome assessments (ACTIVLIM, PROMIS-57) and a new LGMDD1 questionnaire. Some individuals underwent repeat ACTIVLIM and LGMDD1 questionnaire assessments at 1.5 and 2.5 years.

RESULTS: A total of 122 LGMDD1 patients were included from …

Getting Dynamic Implementation To Work, Yi-Chun Chen, Richard Holden, Takashi Kunimoto, Yifei Sun, Tom Wilkening

Research Collection School Of Economics

We develop a new class of two-stage mechanisms, which fully implement any social choice function under initial rationalizability in complete information environments. We show theoretically that our Simultaneous Report (SR) mechanisms are robust to small amounts of incomplete information about the state of nature. We also highlight the robustness of the mechanisms to a wide variety of reasoning processes and behavioral assumptions. We show experimentally that a SR mechanism performs well in inducing truth-telling in both complete and incomplete information environments and that it can induce efficient investment in a two-sided hold-up problem with ex-ante investment. The SR mechanism also …

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, …

Multi-Ancestry Transcriptome-Wide Association Analyses Yield Insights Into Tobacco Use Biology And Drug Repurposing, Fang Chen, Lisa De Las Fuentes, Et Al.

2020-Current year OA Pubs

Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with …

Real-World Covid-19 Vaccine Effectiveness Against The Omicron Ba.2 Variant In A Sars-Cov-2 Infection-Naive Population, Jonathan J Lau, Chao Wu, Gaya K Amarasinghe, Et Al.

2020-Current year OA Pubs

The SARS-CoV-2 Omicron variant has demonstrated enhanced transmissibility and escape of vaccine-derived immunity. Although first-generation vaccines remain effective against severe disease and death, robust evidence on vaccine effectiveness (VE) against all Omicron infections, irrespective of symptoms, remains sparse. We used a community-wide serosurvey with 5,310 subjects to estimate how vaccination histories modulated risk of infection in infection-naive Hong Kong during a large wave of Omicron BA.2 epidemic in January-July 2022. We estimated that Omicron infected 45% (41-48%) of the local population. Three and four doses of BNT162b2 or CoronaVac were effective against Omicron infection 7 days after vaccination (VE of …

Functional And Clinical Studies Reveal Pathophysiological Complexity Of Clcn4-Related Neurodevelopmental Condition, Elizabeth E Palmer, Linda J Richards, Et Al.

2020-Current year OA Pubs

Missense and truncating variants in the X-chromosome-linked CLCN4 gene, resulting in reduced or complete loss-of-function (LOF) of the encoded chloride/proton exchanger ClC-4, were recently demonstrated to cause a neurocognitive phenotype in both males and females. Through international clinical matchmaking and interrogation of public variant databases we assembled a database of 90 rare CLCN4 missense variants in 90 families: 41 unique and 18 recurrent variants in 49 families. For 43 families, including 22 males and 33 females, we collated detailed clinical and segregation data. To confirm causality of variants and to obtain insight into disease mechanisms, we investigated the effect on …

Brainwave: A Flexible Method For Noninvasive Stimulation Of Brain Rhythms Across Species, Matthew K. Attokaren, Nuri Jeong, Lou Blanpain, Abigail L. Paulson, Kristie M. Garza, Ben Borron, Michael Walelign, Jon Willie, Annabelle C. Singer

2020-Current year OA Pubs

Rhythmic neural activity, which coordinates brain regions and neurons to achieve multiple brain functions, is impaired in many diseases. Despite the therapeutic potential of driving brain rhythms, methods to noninvasively target deep brain regions are limited. Accordingly, we recently introduced a noninvasive stimulation approach using flickering lights and sounds ("flicker"). Flicker drives rhythmic activity in deep and superficial brain regions. Gamma flicker spurs immune function, clears pathogens, and rescues memory performance in mice with amyloid pathology. Here, we present substantial improvements to this approach that is flexible, user-friendly, and generalizable across multiple experimental settings and species. We present novel open-source …

Dissecting Cell Identity Via Network Inference And In Silico Gene Perturbation, Kenji Kamimoto, Blerta Stringa, Christy M Hoffmann, Kunal Jindal, Lilianna Solnica-Krezel, Samantha A Morris

2020-Current year OA Pubs

Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks

Fa3: Fine-Grained Android Application Analysis, Yan Lin, Weng Onn Wong, Debin Gao

Research Collection School Of Computing and Information Systems

Understanding Android applications' behavior is essential to many security applications, e.g., malware analysis. Although many systems have been proposed to perform such dynamic analysis, they are limited by their applicable analysis environment (on device vs. emulator), transparency to subject apps, applicable runtime (Dalvik vs. ART), applicable system stack, or granularity. In this paper, we propose FA3 (Fine-Grained Android Application Analysis), a novel on-device, non-invasive, and fine-grained analysis platform by leveraging existing profiling mechanisms in the Android Runtime (ART) and kernel to inspect method invocations and control-flow transfers for both Java methods and third-party native libraries. FA3 embeds its tracing capability …

Effective Graph Kernels For Evolving Functional Brain Networks, Xinlei Wang, Jinyi Chen, Bing Tian Dai, Junchang Xin, Yu Gu, Ge Yu

Research Collection School Of Computing and Information Systems

The graph kernel of the functional brain network is an effective method in the field of neuropsychiatric disease diagnosis like Alzheimer's Disease (AD). The traditional static brain networks cannot reflect dynamic changes of brain activities, but evolving brain networks, which are a series of brain networks over time, are able to seize such dynamic changes. As far as we know, the graph kernel method is effective for calculating the differences among networks. Therefore, it has a great potential to understand the dynamic changes of evolving brain networks, which are a series of chronological differences. However, if the conventional graph kernel …

Identification Of Bradycardia Following Remdesivir Administration Through The Us Food And Drug Administration American College Of Medical Toxicology Covid-19 Toxic Pharmacovigilance Project, Jason M Devgun, Rongmei Zhang, Jeffrey Brent, Paul Wax, Keith Burkhart, Alison Meyn, Sharan Campleman, Stephanie Abston, Kim Aldy, Toxicology Investigators Consortium Fact Study Group

2020-Current year OA Pubs

IMPORTANCE: The rapid spread and mortality associated with COVID-19 emphasized a need for surveillance system development to identify adverse events (AEs) to emerging therapeutics. Bradycardia is a remdesivir infusion-associated AE listed in the US Food and Drug Administration-approved prescribing information.

OBJECTIVE: To evaluate the magnitude and duration of bradycardic events following remdesivir administration.

DESIGN, SETTING, AND PARTICIPANTS: A multicenter cohort study of patients with recorded heart rate less than 60 beats per minute within 24 hours after administration of a remdesivir dose was conducted between November 23, 2020, and October 31, 2021. Participants included patients hospitalized with COVID-19 at 15 …

Web Apis: Features, Issues, And Expectations: A Large-Scale Empirical Study Of Web Apis From Two Publicly Accessible Registries Using Stack Overflow And A User Survey, Neng Zhang, Ying Zou, Xin Xia, David Lo, David Lo, Shanping Li

Research Collection School Of Computing and Information Systems

With the increasing adoption of services-oriented computing and cloud computing technologies, web APIs have become the fundamental building blocks for constructing software applications. Web APIs are developed and published on the internet. The functionality of web APIs can be used to facilitate the development of software applications. There are numerous studies on retrieving and recommending candidate web APIs based on user requirements from a large set of web APIs. However, there are very limited studies on the features of web APIs that make them more likely to be used and the issues of using web APIs in practice. Moreover, users' …