Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Time Lapse Microscopy of Highly Pure Hepatic Stellate Cells

Hepatic stellate cells (HSC) are the main effector cells for liver fibrosis. We aimed at optimizing HSC isolation by an additional step of fluorescence-activated cell sorting (FACS) via a UV laser. HSC were isolated from livers of healthy mice and animals subjected to experimental fibrosis. HSC isolation by iohexol- (Nycodenz) based density centrifugation was compared to a method with subsequent FACS-based sorting. We assessed cellular purity, viability, morphology, and functional properties like proliferation, migration, activation marker, and collagen expression. FACS-augmented isolation resulted in a significantly increased purity of stellate cells (>99%) compared to iohexol-based density centrifugation (60–95%), primarily by excluding doublets of HSC and Kupffer cells (KC). Importantly, this method is also applicable to young animals and mice with liver fibrosis. Viability, migratory properties, and HSC transdifferentiation in vitro were preserved upon FACS-based isolation, as assessed using time lapse microscopy. During maturation of HSC in culture, we did not observe HSC cell division using time lapse microscopy. Strikingly, FACS-isolated, differentiated HSC showed very limited molecular and functional responses to LPS stimulation. In conclusion, isolating HSC from mouse liver by additional FACS significantly increases cell purity by removing contaminations from other cell populations especially KC, without affecting HSC viability, migration, or differentiation.
Self-organization in mobile ad hoc networks: the approach of Terminodes

The Terminodes project is designing a wide-area mobile ad hoc network which is meant to be used in a public environment; in our approach, the network is run by users themselves. We give a global description of the building blocks used by the basic operation of the network; they all rely on various concepts of self-organization. Routing uses a combination of geography-based information and local MANET-like protocols. Terminode positioning is obtained by either GPS or a relative positioning method. Mobility management uses self-organized virtual regions. Terminodes employ a form of virtual money called nuglets as an incentive to collaborate. Lastly, we discuss directions for providing some level of security.
Can PCM Benefit GPU? Reconciling Hybrid Memory Design with GPU Massive Parallelism for Energy Efficiency

In recent studies, phase changing memory (PCM) has shown promising energy efficiency for systems with a modest level of parallelism. But it remains an open question whether it can benefit GPU-like massively parallel systems. This work conducts the first systematic investigation into this question. It empirically shows that contrary to the promising results shown before on CPU, the previous designs of PCM-based memory result in significant degradation to the energy efficiency of GPU computing. It reveals that the fundamental reason comes from a mismatch between those designs and the massive parallelism in GPU. It further shows that fixing the mismatch requires innovations in both hardware and software support. It introduces a set of new hardware features and a novel compiler-directed data placement scheme to address the issues. Working hand-in-hand, they tap into the full potential of hybrid memory for GPU, yielding 15.6% and 40.1% energy saving on average comparing to pure DRAM and pure PCM respectively, and keeping performance loss less than 3.9%.
Intimal Hyperplasia in Loop-Injured Carotid Arteries Is Attenuated in Transglutaminase 2-Null Mice

Arterial restenosis frequently develops after open or endovascular surgery due to intimal hyperplasia. Since tissue transglutaminase (TG2) is known to involve in fibrosis, wound healing, and extracellular matrix remodeling, we examined the role of TG2 in the process of intimal hyperplasia using TG2-null mice. The neointimal formation was compared between TG2-null and wild-type (C57BL/6) mice by two different injury models; carotid ligation and carotid loop injury. In ligation model, there was no difference in intimal thickness between two groups. In loop injury model, intimal hyperplasia developed in both groups and the intimal/medial area ratio was significantly reduced in TG2-null mice (P = 0.007). TG2 was intensely stained in neointimal cells in 2 weeks. In situ activity of TG2 in the injured arteries steadily increased until 4 weeks compared to uninjured arteries. Taken together, intimal hyperplasia was significantly reduced in TG2-null mice, indicating that TG2 has an important role in the development of intimal hyperplasia. This suggests that TG2 may be a novel target to prevent the arterial restenosis after vascular surgery. Graphical Abstract
Deep Specifications and Certified Abstraction Layers

Modern computer systems consist of a multitude of abstraction layers (e.g., OS kernels, hypervisors, device drivers, network protocols), each of which defines an interface that hides the implementation details of a particular set of functionality. Client programs built on top of each layer can be understood solely based on the interface, independent of the layer implementation. Despite their obvious importance, abstraction layers have mostly been treated as a system concept; they have almost never been formally specified or verified. This makes it difficult to establish strong correctness properties, and to scale program verification across multiple layers. In this paper, we present a novel language-based account of abstraction layers and show that they correspond to a strong form of abstraction over a particularly rich class of specifications which we call deep specifications. Just as data abstraction in typed functional languages leads to the important representation independence property, abstraction over deep specification is characterized by an important implementation independence property: any two implementations of the same deep specification must have contextually equivalent behaviors. We present a new layer calculus showing how to formally specify, program, verify, and compose abstraction layers. We show how to instantiate the layer calculus in realistic programming languages such as C and assembly, and how to adapt the CompCert verified compiler to compile certified C layers such that they can be linked with assembly layers. Using these new languages and tools, we have successfully developed multiple certified OS kernels in the Coq proof assistant, the most realistic of which consists of 37 abstraction layers, took less than one person year to develop, and can boot a version of Linux as a guest.
Development of a Natural Model of Cutaneous Leishmaniasis: Powerful Effects of  Vector Saliva and Saliva Preexposure on the Long-Term Outcome of Leishmania major Infection in the Mouse Ear Dermis

We have developed a model of cutaneous leishmaniasis due to Leishmania major that seeks to mimic the natural conditions of infection. 1,000 metacyclic promastigotes were coinoculated with a salivary gland sonicate (SGS) obtained from a natural vector, Phlebotomus papatasii, into the ear dermis of naive mice or of mice preexposed to SGS. The studies reveal a dramatic exacerbating effect of SGS on lesion development in the dermal site, and a complete abrogation of this effect in mice preexposed to salivary components. In both BALB/c and C57Bl/6 (B/6) mice, the dermal lesions appeared earlier, were more destructive, and contained greater numbers of parasites after infection in the presence of SGS. Furthermore, coinoculation of SGS converted B/6 mice into a nonhealing phenotype. No effect of SGS was seen in either IL-4– deficient or in SCID mice. Disease exacerbation in both BALB/c and B/6 mice was associated with an early (6 h) increase in the frequency of epidermal cells producing type 2 cytokines. SGS did not elicit type 2 cytokines in the epidermis of mice previously injected with SGS. These mice made antisaliva antibodies that were able to neutralize the ability of SGS to enhance infection and to elicit IL-4 and IL-5 responses in the epidermis. These results are the first to suggest that for individuals at risk of vector-borne infections, history of exposure to vector saliva might influence the outcome of exposure to transmitted parasites.
The Effects of Video Games and Religious Reminders on Prosociality

Religious primes have been shown to increase prosocial intentions (Shariff, 2016), whereas prosocial video games tend to increase both prosocial intentions and behaviors (Greitemeyer & Osswald, 2010). The aim of this study was to see whether or not these two predictors could work better in tandem to increase prosociality. It was hypothesized that both types of predictors would increase prosocial intentions on their own, that both types of predictors would work together to further increase prosocial intentions, and that this interaction would be moderated by personal religiosity. Participants were randomly assigned to read religious or nonreligious passages, and then randomly assigned to play either a prosocial or neutral video game. Afterwards, they were given the opportunity sign up to volunteer at bottle/coin drives to support their community, and participation was recorded. Results showed that empathy, humility, and overall gamer identity were associated with greater prosocial intentions, but neither prosocial reminder increased prosocial intentions or behaviors.
Joint mobility and routing for lifetime elongation in wireless sensor networks

Although many energy efficient/conserving routing protocols have been proposed for wireless sensor networks, the concentration of data traffic towards a small number of base stations remains a major threat to the network lifetime. The main reason is that the sensor nodes located near a base station have to relay data for a large part of the network and thus deplete their batteries very quickly. The solution we propose in this paper suggests that the base station be mobile; in this way, the nodes located close to it change over time. Data collection protocols can then be optimized by taking both base station mobility and multi-hop routing into account. We first study the former, and conclude that the best mobility strategy consists in following the periphery of the network (we assume that the sensors are deployed within a circle). We then consider jointly mobility and routing algorithms in this case, and show that a better routing strategy uses a combination of round routes and short paths. We provide a detailed analytical model for each of our statements, and corroborate it with simulation results. We show that the obtained improvement in terms of network lifetime is in the order of 500%.
RLIMS-P : Literature-based curation of protein phosphorylation information

Annotation of protein phosphorylation information has been the focus of many biological knowledge bases. To support the literature-based curation of phosphorylation information, an information extraction (IE) system, named RLIMS-P, has been developed, which extracts protein phosphorylation information from biomedical literature. The system has been recently redesigned as RLIMS-P v2 and a new online curator website has been developed. The new website offers improvements for curation functionalities, including PubMed-style keyword search of extracted information, multiple views of retrieved information and their downloading, editing of automatically gathered information, and entity normalization. Curators from Phospho.ELM, Protein Ontology (PRO), and BioGrid were recruited to test the website in the BioCreative Track 5 User Interactive Task (IAT). We expect the new website can be a useful tool for biocurators to search relevant literature and annotate phosphorylation information. Final results from the current evaluation test will be presented at the workshop. Introduction The reversible phosphorylation of proteins is central to the regulation of most aspects of cell function. The flow of molecular information through signaling pathways frequently depends on protein phosphorylation mediated by specific kinases that recognize and phosphorylate specific sites in the target proteins (1). In many cases, deregulation of the kinase-substrate network has been linked to disease, including cancer (2). Given its relevancy, protein phosphorylation has been an active research area as well as the focus of curation in multiple knowledgebase, such as
Differences in admission rates and outcomes between men and women presenting to emergency departments with coronary syndromes

Background: Previous studies examining sex-related differences in the treatment of coronary artery disease have focused on patients in hospital. We sought to examine sex-related differences at an earlier point in care — presentation to the emergency department. Methods: We collected data on ambulatory care and hospital admissions for 54 134 patients (44% women) who presented to an emergency department in Alberta between July 1998 and March 2001 because of acute myocardial infarction, unstable angina, stable angina or chest pain. We used logistic regression and Cox regression analyses to determine sex-specific associations between the likelihood of discharge from the emergency department or coronary revascularization within 1 year and 1-year mortality after adjusting for age, comorbidities and socioeconomic factors. Results: Following the emergency department visit, 91.3% of patients with acute myocardial infarction, 87.4% of those with unstable angina, 40.7% of those with stable angina and 19.8% of those with chest pain were admitted to hospital. Women were more likely than men to be discharged from the emergency department: adjusted odds ratio (and 95% confidence interval [CI]) 2.25 (1.75–2.90) for acute myocardial infarction, 1.71 (1.45–2.01) for unstable angina, 1.33 (1.15–1.53) for stable angina and 1.46 (1.36–1.57) for chest pain. Women were less likely than men to undergo coronary revascularization within 1 year: adjusted odds ratio (and 95% CI) 0.65 (0.57–0.73) for myocardial infarction, 0.39 (0.35–0.44) for unstable angina, 0.35 (0.29–0.42) for stable angina and 0.32 (0.27–0.37) for chest pain. Female sex had no impact on 1-year mortality among patients with acute myocardial infarction; it was associated with a decreased 1-year mortality among patients with unstable angina, stable angina and chest pain: adjusted hazard ratio (and 95% CI) 0.60 (0.46–0.78), 0.60 (0.46–0.78) and 0.74 (0.63–0.87) respectively. Interpretation: Women presenting to the emergency department with coronary syndromes are less likely than men to be admitted to an acute care hospital and to receive coronary revascularization procedures. These differences do not translate into worse outcomes for women in terms of 1-year mortality.
An Empirical Comparison of Logit Choice Models with Discrete versus Continuous Representations of Heterogeneity

Currently, there is an important debate about the relative merits of models with discrete and continuous representations of consumer heterogeneity. In a recent JMR study, Andrews, Ansari, and Currim (2002; hereafter AAC) compared metric conjoint analysis models with discrete and continuous representations of heterogeneity and found no differences between the two models with respect to parameter recovery and prediction of ratings for holdout profiles. Models with continuous representations of heterogeneity fit the data better than models with discrete representations of heterogeneity. The goal of the current study is to compare the relative performance of logit choice models with discrete versus continuous representations of heterogeneity in terms of the accuracy of household-level parameters, fit, and forecasting accuracy. To accomplish this goal, the authors conduct an extensive simulation experiment with logit models in a scanner data context, using an experimental design based on AAC and other recent simulation studies. One of the main findings is that models with continuous and discrete representations of heterogeneity recover household-level parameter estimates and predict holdout choices about equally well except when the number of purchases per household is small, in which case the models with continuous representations perform very poorly. As in the AAC study, models with continuous representations of heterogeneity fit the data better.
An Acknowledgement Control Approach for Performance Improvement of TCP in Wireless Cellular Network Environment

We present a simple method for improving TCP performance in wireless cellular networks. In our proposed method, a TCP receiver does not send one ACK, but multiple ACKs when the packet loss rate exceeds the predefined threshold. Since the major applications of current Internet are to download the Web documents from the fixed servers to the wireless terminal, proposed method only requires changes at the wireless terminal side for performance improvement. Then, TCP becomes robust against radio link errors. We present an analytical method, and show that sending two ACKs for each packet is sufficient to improve TCP performance.
Investigating Experience: Temporal Coherence and Empirical Knowledge Representation

This thesis investigates the idea of artificial intelligence as an agent making sense of its experience, illustrating some of the benefits of representing knowledge as predictions of future experience. Experience is here defined as the temporal sequence of sensations and actions that are the inputs and outputs of the agent. One characteristic of this sequence is that it can have temporal coherence: what is experienced in a short period of time is likely to be consistent. The first part of this thesis examines how an agent with dynamic memory can take advantage of the temporal coherence of its experience. Results in a simple prediction task and the more complex problem of Computer Go show how such an agent can dramatically improve on the performance of the best stationary solutions. The prediction task is then used to illustrate how temporal coherence can provide a natural testbed for meta-learning. In the second part of the thesis, the frameworks of predictive representations and options are adapted for use in knowledge representation. The traditional approach to knowledge representation for artificial intelligence uses the framework of formal logic, in which knowledge is dissociated from experience. The knowledge representation presented here is defined in terms of experience, predictions and time. This kind of representation is defined in this thesis as an empirical knowledge representation. Using objects as a case study, the final chapter shows how an empirical knowledge representation makes it possible to represent even abstract concepts in terms of experience.
A formant-trajectory model and its usage in comparing coarticulatory effects in dysarthric and normal speech

Dysarthria is a diverse group of motor speech disorders that typically are associated with impaired intelligibility. As part of a project to develop augmentative communication technologies for intelligibility enhancement of dysarthric speech, a quantitative method is proposed for measuring the relative contributions to impaired intelligibility of vowels of three factors: First, target shift: Dysarthric speakers may have spectral targets that differ from those of normal speakers. Second, coarticulation: The degree of contextual influence on articulation may be greater in dysarthric speech than in normal speech. Third, random variability: Dysarthric speakers may articulate the same phoneme in the same context with more variability. The method is based on a linear model of formant trajectories of vowels in consonant contexts. The results from analysis of a dysarthric and a normal speech sample showed surprisingly similar target values, but increased coarticulation and random variability for the dysarthric sample.
Kerr/cft Correspondence in Diverse Dimensions

It was proposed recently that the near-horizon states of an extremal four-dimensional Kerr black hole could be identified with a certain chiral conformal field theory whose Virasoro algebra arises as an asymptotic symmetry algebra of the near-horizon Kerr geometry. Supportive evidence for the proposed duality came from the equality of the microscopic entropy of the CFT, calculated by means of the Cardy formula, and the Bekenstein-Hawking entropy of the extremal Kerr black hole. In this paper we examine the proposed Kerr/CFT correspondence in a broader context. In particular, we show that the microscopic entropy and the Bekenstein-Hawking entropy agree also for the extremal Kerr-AdS metric in four dimensions, and also for the extremal Kerr-AdS metrics in dimensions 5, 6 and 7. General formulae for all higher dimensions are also presented.
Simulating Java Commercial Throughput Workload : A Case Study

Commercial throughput workloads are very important and significantly different from SPECcpu benchmarks. We present our study on the simulation methodology for one such workload, SPECjbb2000. Our result shows that the CPI correlates well with transaction throughput, thus can be used as a valid performance metric in simulation. We investigate t h applicability of SimPoint technique to SPECjbb2000. It is shown that cluster analysis of BBV can successfully identify phases. With only a small nu mber of clusters we can reap most of the benefits of suc h analysis. It is observed that a stationary main ph ase dominates the execution of the benchmark. Employin g the Standardized Time Series technique in discrete event simulation theory, we propose a method to accurately measure the CPI for the main phase with only one checkpoint. The error in the result can be quantified with a confidence interval. Moreover, t he simulation automatically stops when the user’s accuracy requirement is met.
Unpacking the Links between Interpersonal Relationship Features and Depression in Adolescence and Young Adulthood

ii Acknowledgments. iv List of Tables . vii List of Figures . viii Chapter 1: General Introduction . 1 Chapter 2: Study 1 – Interpersonal Relationships and Major Depressive Disorder Symptoms: Exploring Selection vs. Socialization Using a Developmental Cascade Approach . 7 Introduction . 8 Methods . 16 Results . 23 Discussion . 27 Chapter 3: Study 2 – Associations between Parent, Sibling, Peer, and Romantic Partner Support and Symptoms of Depression in the First Year of College . 46 Introduction . 48 Methods . 53 Results . 57 Discussion . 61 Chapter 4: General Discussion. 81 References . 86
Distance-vector routing protocols for networks with unidirectional link

We first introduce a simple distance-vector protocol for routing in networks having unidirectional links. The protocol can be seen as an adaptation for these networks of the strategy as used in the popular RIP protocol. The protocol comprises two main algorithms, one for collecting "from" information, and the other one for generating and propagating "to" information. However, the traditional RIP approach has been a "busy" one because of the periodic sending of routing information even after the network has reached a stable state. We make further improvements on the simple protocol to get a message-thrifty variant. A routing information message is sent only when there is a change to the topology or when a link changes cost and only those affected entries need to be sent around.