TransParsCit: A Transformer-Based Citation Parser Trained on Large-Scale Synthesized Data

Accurately parsing citation strings is key to automatically building large-scale citation graphs, so a robust citation parser is an essential module in academic search engines. One limitation of the state-of-the-art models (such as ParsCit and Neural-ParsCit) is the lack of a large-scale training corpus. Manually annotating hundreds of thousands of citation strings is laborious and time-consuming. This thesis presents a novel transformer-based citation parser by leveraging the GIANT dataset, consisting of 1 billion synthesized citation strings covering over 1500 citation styles. As opposed to handcrafted features, our model benefits from word embeddings and character-based embeddings by combining the bidirectional long shortterm memory (BiLSTM) with the Transformer and Conditional Random Forest (CRF). We varied the training data size from 500 to 1M and investigated the impact of training size on the performance. We evaluated our models on standard CORA benchmark and observed an increase in F1-score as the training size increased. The best performance happened when the training size was around 220K, achieving an F1-score of up to 100% on key citation fields. To our best knowledge, this is the first citation parser trained on a largescale synthesized dataset. Project codes and documentation can be found on this GitHub repository: https://github.com/lamps-lab/Citation-Parser

Improving Multi-Touch Interactions Using Hands as Landmarks

Efficient command selection is just as important for multi-touch devices as it is for traditional interfaces that follow the Windows-Icons-Menus-Pointers (WIMP) model, but rapid selection in touch interfaces can be difficult because these systems often lack the mechanisms that have been used for expert shortcuts in desktop systems (such as keyboards shortcuts). Although interaction techniques based on spatial memory can improve the situation by allowing fast revisitation from memory, the lack of landmarks often makes it hard to remember command locations in a large set. One potential landmark that could be used in touch interfaces, however, is people’s hands and fingers: these provide an external reference frame that is well known and always present when interacting with a touch display. To explore the use of hands as landmarks for improving command selection, we designed hand-centric techniques called HandMark menus. We implemented HandMark menus for two platforms – one version that allows bimanual operation for digital tables and another that uses single-handed serial operation for handheld tablets; in addition, we developed variants for both platforms that support different numbers of commands. We tested the new techniques against standard selection methods including tabbed menus and popup toolbars. The results of the studies show that HandMark menus perform well (in several cases significantly faster than standard methods), and that they support the development of spatial memory. Overall, this thesis demonstrates that people’s intimate knowledge of their hands can be the basis for fast interaction techniques that improve performance and usability of multi-touch systems

Use of Landmarks to Improve Spatial Learning and Revisitation in Computer Interfaces

Efficient spatial location learning and remembering are just as important for two-dimensional Graphical User Interfaces (GUI) as they are for real environments where locations are revisited multiple times. Rapid spatial memory development in GUIs, however, can be difficult because these interfaces often lack adequate landmarks that have been predominantly used by people to learn and recall real-life locations. In the absence of sufficient landmarks in GUIs, artificially created visual objects (i.e., artificial landmarks) could be used as landmarks to support spatial memory development of spatial locations. In order to understand how spatial memory development occurs in GUIs and explore ways to assist users’ efficient location learning and recalling in GUIs, I carried out five studies exploring the use of landmarks in GUIs – one study that investigated interfaces of four standard desktop applications: Microsoft Word, Facebook, Adobe Photoshop, and Adobe Reader, and other four that tested artificial landmarks augmented two prototype desktop GUIs against non-landmarked versions: command selection interfaces and linear document viewers; in addition, I tested landmarks’ use in variants of these interfaces that varied in the number of command sets (small, medium, and large) and types of linear documents (textual and video). Results indicate that GUIs’ existing features and design elements can be reliable landmarks in GUIs that provide spatial benefits similar to real environments. I also show that artificial landmarks can significantly improve spatial memory development of GUIs, allowing support for rapid spatial location learning and remembering in GUIs. Overall, this dissertation reveals that landmarks can be a valuable addition to graphical systems to improve the memorability and usability of GUIs

An Interpretable Machine Learning Framework to Understand Bikeshare Demand before and during the COVID-19 Pandemic in New York City

In recent years, bikesharing systems have become increasingly popular as affordable and sustainable micromobility solutions. Advanced mathematical models such as machine learning are required to generate good forecasts for bikeshare demand. To this end, this study proposes a machine learning modeling framework to estimate hourly demand in a large-scale bikesharing system. Two Extreme Gradient Boosting models were developed: one using data from before the COVID-19 pandemic (March 2019 to February 2020) and the other using data from during the pandemic (March 2020 to February 2021). Furthermore, a model interpretation framework based on SHapley Additive exPlanations was implemented. Based on the relative importance of the explanatory variables considered in this study, share of female users and hour of day were the two most important explanatory variables in both models. However, the month variable had higher importance in the pandemic model than in the pre-pandemic model

Characterizing User Behaviors in Open-Source Software User Forums: An Empirical Study

User forums of Open Source Software (OSS) enable end-users to collaboratively discuss problems concerning the OSS applications. Despite decades of research on OSS, we know very little about how end-users engage with OSS communities on these forums, in particular, the challenges that hinder their continuous and meaningful participation in the OSS community. Many previous works are developer-centric and overlook the importance of end-user forums. As a result, end-users' expectations are seldom reflected in OSS development. To better understand user behaviors in OSS user forums, we carried out an empirical study analyzing about 1.3 million posts from user forums of four popular OSS applications: Zotero, Audacity, VLC, and RStudio. Through analyzing the contribution patterns of three common user types (end-users, developers, and organizers), we observed that end-users not only initiated most of the threads (above 96% of threads in three projects, 86% in the other), but also acted as the significant contributors for responding to other users' posts, even though they tended to lack confidence in their activities as indicated by psycho-linguistic analyses. Moreover, we found end-users more open, reflecting a more positive emotion in communication than organizers and developers in the forums. Our work contributes new knowledge about end-users' activities and behaviors in OSS user forums that the vital OSS stakeholders can leverage to improve end-user engagement in the OSS development process.Comment: 15th International Conference on Cooperative and Human Aspects of Softare Engineerin

ToSHI - Towards Secure Heterogeneous Integration: Security Risks, Threat Assessment, and Assurance

The semiconductor industry is entering a new age in which device scaling and cost reduction will no longer follow the decades-long pattern. Packing more transistors on a monolithic IC at each node becomes more difficult and expensive. Companies in the semiconductor industry are increasingly seeking technological solutions to close the gap and enhance cost-performance while providing more functionality through integration. Putting all of the operations on a single chip (known as a system on a chip, or SoC) presents several issues, including increased prices and greater design complexity. Heterogeneous integration (HI), which uses advanced packaging technology to merge components that might be designed and manufactured independently using the best process technology, is an attractive alternative. However, although the industry is motivated to move towards HI, many design and security challenges must be addressed. This paper presents a three-tier security approach for secure heterogeneous integration by investigating supply chain security risks, threats, and vulnerabilities at the chiplet, interposer, and system-in-package levels. Furthermore, various possible trust validation methods and attack mitigation were proposed for every level of heterogeneous integration. Finally, we shared our vision as a roadmap toward developing security solutions for a secure heterogeneous integration

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Biochemical and computational approach of selected phytocompounds from Tinospora crispa in the management of COVID-19

A pandemic caused by the novel coronavirus (SARS-CoV-2 or COVID-19) began in December 2019 in Wuhan, China, and the number of newly reported cases continues to increase. More than 19.7 million cases have been reported globally and about 728,000 have died as of this writing (10 August 2020). Recently, it has been confirmed that the SARS-CoV-2 main protease (Mpro) enzyme is responsible not only for viral reproduction but also impedes host immune responses. The Mpro provides a highly favorable pharmacological target for the discovery and design of inhibitors. Currently, no specific therapies are available, and investigations into the treatment of COVID-19 are lacking. Therefore, herein, we analyzed the bioactive phytocompounds isolated by gas chromatography–mass spectroscopy (GC-MS) from Tinospora crispa as potential COVID-19 Mpro inhibitors, using molecular docking study. Our analyses unveiled that the top nine hits might serve as potential anti-SARS-CoV-2 lead molecules, with three of them exerting biological activity and warranting further optimization and drug development to combat COVID-19

A comprehensive review on global contributions and recognition of pharmacy professionals amidst COVID-19 pandemic: moving from present to future

Abstract Background COVID-19, a respiratory tract infection caused by SARS-CoV-2, is a burning question worldwide as it gives rise to a pandemic situation. No specific medications are still recommended for COVID-19; however, healthcare support is crucial for ameliorating the disease condition. Pharmacists are the frontline fighters who are responsible for providing healthcare support to the COVID-19 infected patients around the world. This review endeavored to briefly rationalize the contributions of several pharmacy professionals in diverse fields along with their collaborative efforts and dedication regarding their limitations during the COVID-19 situation and view the prospects of pharmaceutical care services in the post-pandemic period. Main body of the abstract Online databases were utilized to search for scholarly articles and organizational websites, to sum up the information about the contemporary and expanded role of pharmacists. Key articles were retrieved from Google Scholar, PubMed, and Science Direct databases using terms: “COVID-19,” “novel coronavirus,” “community,” “industrial,” “hospital,” “clinical,” “recognition,” “obstacles,” “collaboration,” “SARS-CoV-2,” “healthcare,” and “outbreak” in combination with “pharmacist.” The articles were included from the inception of the pandemic to January 25, 2021. The current review found pharmacist’s global contributions and involvements with other professionals to provide healthcare services amidst COVID-19. This included testing of suspects, providing medical information, psycho-social support, debunking myths, mitigating drug shortage events, telemedicine, e-prescription, infection control, and controlling the drug supply chain. In many countries, pharmacists’ activities were much appreciated but in some countries, they were not properly acknowledged for their contributions amidst COVID-19 outbreak. They played additional roles such as participating in the antimicrobial stewardship team, improving value-added services, conducting clinical data analysis to suppress the outspread of the SARS-CoV-2. Short conclusion During the COVID-19 pandemic while the whole world is fighting against an invisible virus, the pharmacists are the earnest hero to serve their responsibilities along with additional activities. They need to be prepared and collaborate with other healthcare professionals further to meet the challenges of post-pandemic circumstances