Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of exosomal HIV-1 Tat expression on the human cellular proteome

HIV-1 exists in a latent form in all infected patients. When antiretroviral therapy is stopped, viral replication resumes. The HIV-1 Tat protein is a potent activator of viral transcription. Our previous work has demonstrated that exosomal formulations of Tat can reverse HIV-1 latency in primary CD4+ T lymphocytes isolated from long term antiretroviral treated individuals suggesting a potential role for Tat as a therapeutic HIV-1 Latency Reversal Agent (LRA). Here, we employed the label-free proteomic approach for profiling the proteomic changes associated with exosomal Tat production in human cell lines. Comparative proteomic analysis revealed that >30% peptides were differentially expressed in abundance in the Tat-expressing cell line compared with relevant controls. As expected, many of the known Tat-interactor proteins were upregulated. Tat expression also led to the upregulation of antioxidant proteins suggesting Tat-mediates an oxidative burst. Gene ontology and pathway analyses of these differentially expressed proteins showed enrichment of extracellular vesicular exosome and spliceosome localized proteins and proteins involved with transcriptional and translational mechanisms. Our work suggests that HIV-1 Tat expression leads to perturbations in cellular protein expression. In vivo administration of Tat using HIV/SIV animal models needs to be performed to assess the physiologic significance of Tat-induced proteomic changes prior to developing HIV-1 Tat as an LRA.
Static and Mobile Target kk-Coverage in Wireless Rechargeable Sensor Networks

Energy remains a major hurdle in running computation-intensive tasks on wireless sensors. Recent efforts have been made to employ a Mobile Charger (MC) to deliver wireless power to sensors, which provides a promising solution to the energy problem. Most of previous works in this area aim at maintaining perpetual network operation at the expense of high operating cost of MC. In the meanwhile, it is observed that due to the low cost of wireless sensors, they are usually deployed at high density so there is abundant redundancy in their coverage in the network. For such networks, it is possible to take advantage of the redundancy to reduce the energy cost. In this paper, we relax the strictness of perpetual operation by allowing some sensors to temporarily run out of energy while still maintaining target $k$k-coverage in the network at lower cost of MC. We first establish a theoretical model to analyze the performance improvements under this new strategy. Then, we organize sensors into load-balanced clusters for target monitoring by a distributed algorithm. Next, we propose a charging algorithm named $\lambda$λ-GTSP Charging Algorithm to determine the optimal number of sensors to be charged in each cluster to maintain $k$k-coverage in the network and derive the route for MC to charge them. We further generalize the algorithm to encompass mobile targets as well. Our extensive simulation results demonstrate significant improvements of network scalability and cost saving that MC can extend charging capability over 2-3 times with a reduction of 40 percent of moving cost without sacrificing the network performance.
Using the D3 library for web-mapping in an SDI environment

This paper is about different worlds, and how we try to unite them. One of these worlds is the world of National Atlases: collections of complex, high quality maps presenting a nation to the geographically interested. The second is the world of National Spatial Infrastructures: highly organised, standardised and institutionalised large collections of spatial data and services. In the paper we describe the two worlds and their fundamental differences and we present the theoretical framework in which these worlds could be united. We introduce a test bed we are using to try out the theoretical framework in a real-life use case. In the architecture of that test bed we introduce a National Atlas Services layer and describe how we have created an Atlas Map Viewer component, using the Open Web Platform. We conclude by commenting on the results thusfar and taking a look into future developments.
Modeling and improving performance of write out-of-place storage technologies

of the Thesis Modeling and Improving Performance of Write Out-of-Place Storage Technologies by Mansour Shafaei Moghaddam Doctor of Philosophy in Computer Engineering Northeastern University, February 2018 Dr. Peter Desnoyers, Advisor For years data access rate and capacity growth for storage devices were directly correlated as putting more number of bits in tracks would increase both. This correlation, however, was changed a few years ago with the introduction of write out-of-place technologies such as NAND flash and Shingled Magnetic Recording (SMR). NAND flash devices offer orders of magnitude faster data access by replacing the magnetic technology with CMOS. Shingled magnetic recording increases the capacity of conventional HDDs by partially overlapping adjacent tracks in them. Despite the benefits that each of these technologies offers, they both suffer from the fact that data updates (writes) in these devices can not be done in-place. A data page in a flash-based storage device must be in a clean state before an update can be applied to it. On the other hand, random writes in an SMR drive corrupt the data on the next track(s) in shingling direction. Due to these limitations in writes, drives from both technologies need translation layers to move valid data around inside the drive in order to prevent such service interrupts or data corruptions. In this thesis I study these two technologies from the translation layer perspective to 1) model their performance characteristics and 2) to provide better algorithms to improve their performance: Modeling SMR drives is a challenge, requiring an array of approaches including both existing disk modeling techniques as well as new techniques for inferring internal translation layer algorithms. I present the first predictive simulation model of a generally-available drive-managed SMR disk which is derived from external measurements. The available model can predict mean latency within a few percent, and with an RMS cumulative latency error of 25% or less for most workloads tested. These variations, although not small, are in most cases less than three times the drive-todrive variation seen among seemingly identical drives. ‘I also propose a track-based static
Spatio-temporal variation in oxidative status regulation in a small mammal

Life-history allocation trade-offs are dynamic over time and space according to the ecological and demographical context. Fluctuations in food availability can affect physiological trade-offs like oxidative status regulation, reflecting the balance between pro-oxidant production and antioxidant capacity. Monitoring the spatio-temporal stability of oxidative status in natural settings may help understanding its importance in ecological and evolutionary processes. However, few studies have yet conducted such procedures in wild populations. Here, we monitored individual oxidative status in a wild eastern chipmunk (Tamias striatus) population across the 2017 summer active period and over three study sites. Oxidative damage (MDA: Malondialdehyde levels) and non-enzymatic antioxidant levels (FRAP: Ferric reducing antioxidant power and HASC: Hypochlorous acid shock capacity) were quantified across time and space using assays optimized for small blood volumes. Our results showed an increase in oxidative damage mirrored by a decrease in FRAP throughout the season. We also found different antioxidant levels among our three study sites for both markers. Our results also revealed the effects of sex and body mass on oxidative status. Early in the active season, females and individuals with a greater body mass had higher oxidative damage. Males had higher HASC levels than females throughout the summer. This study shows that oxidative status regulation is a dynamic process that requires a detailed spatial and temporal monitoring to yield a complete picture of possible trade-offs between pro-oxidant production and antioxidant capacity.
"More Interaction, More Story, More Lore": Motivations Related to Game-centric Transmedia

Transmedia research has in the past been mainly interested in defining transmedia and examining transmedia franchises that have their starting point in movies and TVseries. However, there are multiple transmedia constellations that have a game as their starting point and this paper concentrates on two of those, Defiance (Trion Worlds, 2013) and Quantum Break (Remedy Entertainment, 2016). The survey data from these two examples was analyzed by using constructivist grounded theoryinformed approach in order to find out what motivates audiences to consume or avoid game-centric transmedia. Ten categories related to consuming game-centric transmedia and five categories related to avoiding it emerged from the data. The motivations to consume gamecentric transmedia had a strong focus on narrative aspects. The results differ from earlier transmedia audience studies and suggest the need for more game-centric transmedia audience studies, where the core text is a game instead of a television show.
Grounding Human-To-Vehicle Advice for Self-Driving Vehicles

Recent success suggests that deep neural control networks are likely to be a key component of self-driving vehicles. These networks are trained on large datasets to imitate human actions, but they lack semantic understanding of image contents. This makes them brittle and potentially unsafe in situations that do not match training data. Here, we propose to address this issue by augmenting training data with natural language advice from a human. Advice includes guidance about what to do and where to attend. We present the first step toward advice giving, where we train an end-to-end vehicle controller that accepts advice. The controller adapts the way it attends to the scene (visual attention) and the control (steering and speed). Attention mechanisms tie controller behavior to salient objects in the advice. We evaluate our model on a novel advisable driving dataset with manually annotated human-to-vehicle advice called Honda Research Institute-Advice Dataset (HAD). We show that taking advice improves the performance of the end-to-end network, while the network cues on a variety of visual features that are provided by advice. The dataset is available at https://usa.honda-ri.com/HAD.
Game Streaming Revisited: Some Observations on Marginal Practices and Contexts

The focus of this paper is on the spectating phenomenon of live streaming gameplay, which has been described as “marginal. ” After reviewing important non-gaming factors capable of bringing game streaming from the analytical margins to the center, we discuss the larger context in which game streaming is embedded, plus its implications. Data were gathered via in-depth interviews with game stream viewers, analyses of game streaming-related forum posts, and an online survey. According to our observations, game streaming should not be viewed as only a game-related phenomenon or extended gameplay practice, but also as a type of cross-media entertainment involving multiple media consumption characteristics—a form of stage performance, a space for social interaction, and as entertainment similar to hosted variety shows and reality television. Consumers tend to move among multiple streaming activities serving assorted media functions in search of entertainment, with their identities changing according to personal time restrictions and social situations.
Responsible genetic genealogy

The scientific development of forensic genetic genealogy (FGG), which couples genetic analysis with investigation of publicly available genealogy information, has successfully transformed law enforcement investigations by solving more than 50 cases over the last 18 months in the United States. However, use of FGG by law enforcement has preceded widespread development of best practices to protect the genetic privacy of private citizens who have voluntarily submitted samples to genealogy databases. Absent best practices, use of FGG could lead to compromised cases, diminished use, or the loss of this new investigative tool. Public support for FGG could be jeopardized and confidence in forensic DNA analysis could be undermined. As the custodian of a national law enforcement DNA database (CODIS), the U.S. Federal Bureau of Investigation (FBI) is looked to by many in the law enforcement and forensic DNA communities for guidance, and its efforts often influence the global community. The emergence of FGG suggests that further discussions on privacy, genomics, and the use of genealogy by law enforcement would be beneficial. Accordingly, the FBI seeks to engage the scientific and bioethics communities in such a dialogue.
Middle-aged Players' Memorable Experiences with Pokémon GO

As the first location-based augmented reality game to gain mainstream popularity, Pokémon GO also reached an older demographic of players that have traditionally played less and whose play experiences are under-researched. In this article, we present the findings of a qualitative survey study (n=349) focusing on the middleaged (40–65-year-old) Pokémon GO players’ memorable experiences from the time when the game’s popularity was at its peak and its player base likely most diverse. We analyzed the open-ended survey responses with thematic analysis, resulting in 7 categories and 88 thematic codes. The categories constructed were Game Play & Game Content, People & Sociability, Location, Circumstances & Context, Negative Events, Feelings and Other Codes. Through our analysis and findings, we provide insights to understand the play experiences of middle-aged players through Pokémon GO. These findings also capture the memorable moments of a massive, unique social phenomenon at its peak from the perspective of a traditionally overlooked demographic.
A Typology of Rumble

Rumble is a feature of most modern games published for home consoles, yet no existing studies on rumble and haptic feedback consider its various manifestations and functions in digital games. Likewise, analytical frameworks for understanding digital games tend to overlook rumble as a significant component of the game object or experience. Building on analyses of nine games from the PlayStation family of home consoles, this paper explores rumble as a two-level semiotic structure, consisting of a feedback source and (a) level(s) of operation. The two components are suggested as the base for a typology that accounts for the specific feedback source – environment, object, interface, or body – and its specific levels of operation as ludic, dramatic, technical, or an overlap of any of these. We present examples of each type to discuss the uses, applications, and limitations of the framework in relation to both analysis and design.
Sound Opinions: Creating a Virtual Tool for Sound Art Installations through Sentiment Analysis of Critical Reviews

The author presents Sound Opinions, a custom software tool that uses sentiment analysis to create sound art installations and music compositions. The software runs inside the NodeRed.js programming environment. It scrapes text from web pages, pre-processes it, performs sentiment analysis via a remote API, and parses the resulting data for use in external digital audio programs. The sentiment analysis itself is handled by IBM’s Watson Tone Analyzer. The author has used this tool to create an interactive multimedia installation, titled Critique. Sources of criticism of a chosen musical work are analyzed and the negative or positive statements about that composition work to warp and change it. This allows the audience to only hear the work through the lens of its critics, and not in the original form that its creator intended.
Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production.

Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria, and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N-metabolism-related genes to fertilization differed in archaea, bacteria, and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, alpha-, beta-, gamma-, and delta Proteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes. This article is protected by copyright. All rights reserved.
Higher underestimation of tumour size post-neoadjuvant chemotherapy with breast magnetic resonance imaging (MRI)—A concordance comparison cohort analysis

Objectives The aim of this study was to evaluate the diagnostic accuracy of breast MRI for detecting residual tumor and the tumor size whether it would be affected after neoadjuvant chemotherapy. Methods Total 109 patients with NAC and 682 patients without NAC were included in this retrospective study. Measurement of the largest diameter of tumors at pathology was chosen as gold standard and compared with preoperative breast MRI. A concordance threshold of ±25% of maximal tumor size was used. The accuracy of MRI was graded as concordant, underestimation, or overestimation rate. Further subgroup analysis with tumor stages, histologic subgroups and intrinsic subtypes was performed. Results The post-NAC MRI was associated with 92.5% sensitivity, 55.2% specificity, 85.1% positive predictive value, 72.7% negative predictive value, and overall 82.6% accuracy for detecting residual tumor. In determining tumor size, the overall concordance rates of the non-NAC group and the NAC group were 43.5% and 41.3%, respectively (p = 0.678). But the overestimation rate and underestimation rate were 26.6% and 32.1% for NAC group, and 52.9% and 3.5% for the non-NAC group (p<0.001). While in the subgroups analysis, the concordance rate of the NAC group (26.7%) was lower than that of the non-NAC group (82.1%) at T3 stage (p<0.001). There were no statistically significant differences between different tumor histologic subgroups and intrinsic subtypes. Conclusions The overall accuracy of MRI in predicting tumor size was not affected by NAC; however, it tends to underestimate tumor size after NAC, especially in patients with T3 lesions and above.
A Smo/Gli Multitarget Hedgehog Pathway Inhibitor Impairs Tumor Growth

Pharmacological Hedgehog (Hh) pathway inhibition has emerged as a valuable anticancer strategy. A number of small molecules able to block the pathway at the upstream receptor Smoothened (Smo) or the downstream effector glioma-associated oncogene 1 (Gli1) has been designed and developed. In a recent study, we exploited the high versatility of the natural isoflavone scaffold for targeting the Hh signaling pathway at multiple levels showing that the simultaneous targeting of Smo and Gli1 provided synergistic Hh pathway inhibition stronger than single administration. This approach seems to effectively overcome the drug resistance, particularly at the level of Smo. Here, we combined the pharmacophores targeting Smo and Gli1 into a single and individual isoflavone, compound 22, which inhibits the Hh pathway at both upstream and downstream level. We demonstrate that this multitarget agent suppresses medulloblastoma growth in vitro and in vivo through antagonism of Smo and Gli1, which is a novel mechanism of action in Hh inhibition.
Process Monitoring and Data Mining with Chemical Process Historical Databases

xiv Chapter 1 Introduction . 1 1.1 Background . 1 1.2 Dissertation Motivation . 5 1.3 Research Aims . 8 1.4 Publications and Presentations . 9 1.5 Dissertation Contributions . 10 1.6 Dissertation Structure . 11 1.7 References . 12 Chapter 2 Data Preprocessing. 16 2.1 Data Pretreatment. 16 2.1.1 Outlier removal . 17 2.1.2 Data normalization . 17 2.1.3 Missing data approximation . 18 2.2 Multiway Unfolding. 18 2.3 Dynamic Time Warping (DTW) . 20 2.3.1 Synchronization of batch trajectories with DTW . 21 2.3.2 Iterative synchronization of multivariate batch process data . 26 2.4 Synthetic Minority Over-sampling Technique (SMOTE) . 28 2.5 References . 31 Chapter 3 Data Mining Techniques . 32 3.1 Data Mining Approach . 33 3.2 Dimensionality Reduction (DR) . 34 3.2.1 Principal component analysis (PCA) . 35 3.2.2 Independent component analysis (ICA) . 36 3.2.3 Kernel principal component analysis (KPCA) . 39 3.2.4 Isomap . 41 3.2.5 Spectral embedding (SE) . 42 3.3 Data Clustering . 44 3.3.1 K-means clustering . 44 3.3.2 DBSCAN . 45 3.3.3 Balanced iterative reducing and clustering using hierarchies (BIRCH) . 48
Epidermal hepcidin is required for neutrophil response to bacterial infection

Novel approaches for adjunctive therapy are urgently needed for complicated infections and patients with compromised immunity. Necrotizing fasciitis (NF) is a destructive skin and soft tissue infection. Despite treatment with systemic antibiotics and radical debridement of necrotic tissue, lethality remains high. The key iron regulatory hormone hepcidin was originally identified as a cationic antimicrobial peptide (AMP), but its putative expression and role in the skin, a major site of AMP production, have never been investigated. We report here that hepcidin production is induced in the skin of patients with group A Streptococcus (GAS) NF. In a GAS-induced NF model, mice lacking hepcidin in keratinocytes failed to restrict systemic spread of infection from an initial tissue focus. Unexpectedly, this effect was due to its ability to promote production of the CXCL1 chemokine by keratinocytes, resulting in neutrophil recruitment. Unlike CXCL1, hepcidin is resistant to degradation by major GAS proteases and could therefore serve as a reservoir to maintain steady-state levels of CXCL1 in infected tissue. Finally, injection of synthetic hepcidin at the site of infection can limit or completely prevent systemic spread of GAS infection, suggesting that hepcidin agonists could have a therapeutic role in NF.