Miracle-dz/UniFAR-FTUs huggingface dataset:
Networks as vectors of their motif frequencies and 2-norm distance as a measure of similarity CS 322 Project Writeup

Previous studies have uncovered a list of interesting properties that exist in real networks by comparing them to synthetic networks. However, there has been less focus on comparing real networks to other real networks. How do Autonomous Systems routing networks compare to social networks? How can we tell that one biological network looks different from other biological networks? How can we quantify how similar two networks are? One way to capture the difference between two networks is to define an ”appropriate” notion of distance. This project proposes using the 2-norm distance between vectors to capture network similarity. In particular, we present the results of using the 2-norm distance as a measure of similarity in two cases: a) when networks are represented as 4 dimensional vectors based on their 2x2 stochastic Kronecker initiator matrices, b) when networks are represented as 8 dimensional vectors based on the frequencies of their 3and 4-size motifs. We show that the motif frequencies are able to capture the similarity among the following classes of networks in our data set: road networks, AS routing networks, biological networks, p2p networks, social networks, citation networks, collaboration networks and item co-purchasing networks.
Time-varying cortical connectivity by adaptive multivariate estimators applied to a combined foot-lips movement

In this paper we propose the use of an adaptive multivariate approach to define time-varying multivariate estimators based on the directed transfer function (DTF) and the partial directed coherence (PDC). DTF and PDC are frequency-domain estimators that are able to describe interactions between cortical areas in terms of the concept of Granger causality. Time-varying DTF and PDC were obtained by the adaptive recursive fit of an MVAR model with time- dependent parameters, by means of a generalized recursive least-square (RLS) algorithm, taking into consideration a set of EEG epochs. Such estimators are able to follow rapid changes in the connectivity between cortical areas during an experimental task. We provide an application to the cortical estimations obtained from high resolution EEG data, recorded from a group of healthy subject during a combined foot-lips movement, and present the time-varying connectivity patterns resulting from the application of both DTF and PDC. Two different cortical networks were detected, one constant across the task and the other evolving during the preparation of the joint movement.
HotSwap: correct and efficient controller upgrades for software-defined networks

Like any complex software, SDN programs must be updated periodically, whether to migrate to a new controller platform, repair bugs, or address performance issues. Nowadays, SDN operators typically perform such upgrades by stopping the old controller and starting the new one---an approach that wipes out all installed flow table entries and causes substantial disruption including losing packets, increasing latency, and even compromising correctness. This paper presents HotSwap, a system for upgrading SDN controllers in a disruption-free and correct manner. HotSwap is a hypervisor (sitting between the switches and the controller) that maintains a history of network events. To upgrade from an old controller to a new one, HotSwap bootstraps the new controller (by replaying the history) and monitors its output (to determine which parts of the network state may be reused with the new controller). To ensure good performance, HotSwap filters the history using queries specified by programmers. We describe our design and preliminary implementation of HotSwap, and present experimental results demonstrating its effectiveness for managing upgrades to third-party controller programs.
The DigitalDesk calculator: tangible manipulation on a desk top display

Today’s electronic desktop is quite separate from the physical desk of the user. Electronic documents lack many useful properties of paper, and paper lacks useful properties of electronic documents. Instead of making the electronic desktop more like the physical desk, this work attempts the opposite: to give the physical desk electronic properties and merge the two desktops into one. This paper describes a desk with a computer-controlled camera and projector above it. The camera sees where the user is pointing, and it reads portions of documents that are placed on the desk. The projector displays feedback and electronic objects onto the desk surface. This DigitalDesk adds electronic features to physical paper, and it adds physical features to electronic documents. The system allows the user to interact with paper and electronic objects by touching them with a bare finger (digit). Instead of “direct” manipulation with a mouse, this is tactile manipulation with a finger. The Digi-talDesk Calculator is a prototype example of a simple application that can benefit from the interaction techniques enabled by this desktop. The paper begins by discussing the motivation behind this work, then describes the Digi-talDesk, tactile manipulation, and the calculator prototype. It then discusses implementation details and ends with ideas for the future of tactile manipulation.
“IF EVERYONE COPIES ME, THAILAND WILL BE SO MUCH BETTER OFF”: THE POWER OF VERBAL IRONY IN YOUTH CONVERSATION

This paper explores the types of verbal irony employed by resilient youth in spontaneous conversation and examines how they use this irony to navigate potentially challenging psychosocial terrain. We documented and analyzed instances of irony in the spontaneous speech of adolescent participants in an international, ecological study of resilience using quasi-naturalistic and participatory visual methods. We found irony to be co-constructively utilized by the youths we studied. They spontaneously used many types of irony to mute criticism and avoid embarrassment. These resilient youth, who were thriving under adverse circumstances, used irony in a positive way to facilitate affiliation with their friends and family.
FORMATION OF ARROWHEAD COMPLEXES WITH HEAVY MEROMYOSIN IN A VARIETY OF CELL TYPES

Heavy meromyosin (HMM) forms characteristic arrowhead complexes with actin filaments in situ. These complexes are readily visualized in sectioned muscle. Following HMM treatment similar complexes appear in sectioned fibroblasts, chondrogenic cells, nerve cells, and several types of epithelial cells. Thin filaments freshly isolated from chondrogenic cells also bind HMM and form arrowhead structures in negatively stained preparations. HMM-filament complexes are prominent in the cortex of a variety of normal metaphase and Colcemid-arrested metaphase cells. There is no detectable binding of HMM with other cellular components such as microtubules, 100-A filaments, tonofilaments, membranes, nuclei, or collagen fibrils. The significance of HMM-filament binding is discussed in view of the finding that arrowhead complexes form in types of cells not usually thought to contain actin filaments.
Hidden Cliques and the Certification of the Restricted Isometry Property

Compressed sensing is a technique for finding sparse solutions to underdetermined linear systems. This technique relies on properties of the sensing matrix such as the restricted isometry property. Sensing matrices that satisfy this property with optimal parameters are mainly obtained via probabilistic arguments. Deciding whether a given matrix satisfies the restricted isometry property is a nontrivial computational problem. Indeed, it is shown in this paper that restricted isometry parameters cannot be approximated in polynomial time within any constant factor under the assumption that the hidden clique problem is hard. In addition, on the positive side, an improvement on the brute-force enumeration algorithm for checking the restricted isometry property is proposed.
Ultrastructural analysis of the root canal walls after simultaneous irrigation of different sodium hypochlorite concentration and 0.2% chlorhexidine gluconate

To determine whether sodium hypochlorite (NaOCl) with 0.2% chlorhexidine gluconate (CHX) leads to colour change and precipitate formation, and to ultrastructurally analyse the dentine surface after simultaneous irrigation with 0.5% NaOCl and 0.2% CHX. Four tubes in which 5ml of different NaOCl concentrations and 5ml 0,2% CHX were placed, were observed every 15 minutes in the first two hours and after 7 days. Mixture solutions were centrifuged at 800 rpm/4 min. A precipitate is observed under light‐microscopy. Thirty‐five single‐rooted teeth were instrumented using crown‐down technique with irrigation: Positive control: distilled water, Negative control: 0,5% NaOCl+15% EDTA, Experimental group: identical to the negative control, then canals were treated with 0.5% NaOCl+0.2% CHX. The longitudinal root sections were observed under scanning‐electron‐microscopy. The amount of debris was assessed with 5/score‐system, and the results were analysed using the Mann‐Whitney U test (p < 0.001). Change in colour was noticed immediately after the merger and it did not change with time. Mixture solutions showed considerable turbidity, but precipitate was observed only after centrifugation. Statistical analysis showed a significant difference in the dentinal wall purity when comparing the cervical and middle root canal thirds between the experimental and negative control group. The difference was also observed between the cervical and middle thirds compared to the apical third of the root canal within these groups. Interaction between NaOCl and CHX, as well as the creation of precipitates, depends not only on the concentration of NaOCl, but also on the concentration of CHX. Microsc. Res. Tech. 75:1099–1103, 2012. © 2012 Wiley Periodicals, Inc.
The Reduction of Anti-Gay Bias through Interpersonal Contact: The Moderating Roles of HIV Stigma and Motivation to Respond without Prejudice.

The intergroup contact effect is well-documented in the research literature (for a meta-analysis see Pettigrew & Tropp, 2006). Although researchers have identified a few moderators of the contact effect, the constraints under which the contact effect is optimally effective are not well understood. The current research explored two individual difference measures related to anti-gay attitudes, AIDS stigma and motivation to respond without prejudice (internal and external motivation), as potential moderators of the contact effect on heterosexual men’s attitudes towards gay men. Results indicated that increased external motivation and AIDS stigma hinder the benefits of contact for anti-gay attitudes. Implications of these findings for understanding how intergroup contact serves as a prejudice-reduction technique are discussed. INDEX WORDS: Anti-Gay Bias, AIDS Stigma, Motivation THE REDUCTION OF ANTI-GAY BIAS THROUGH INTERPERSONAL CONTACT: THE MODERATING ROLES OF HIV STIGMA AND MOTIVATION TO RESPOND WITHOUT PREJUDICE
Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism

The plant parasitic beet cyst nematode Heterodera schachtii induces syncytial feeding structures in Arabidopsis roots. The feeding structures form strong sink tissues that have been suggested to be metabolically highly active. In the present study, metabolic profiling and gene targeted expression analyses were performed in order to study the local and systemic effects of nematode infection on the plant host. The results showed increased levels of many amino acids and phosphorylated metabolites in syncytia, as well as high accumulation of specific sugars such as 1-kestose that do not accumulate naturally in Arabidopsis roots. A correlation-based network analysis revealed highly activated and coordinated metabolism in syncytia compared to non-infected control roots. An integrated analysis of the central primary metabolism showed a clear coherence of metabolite and transcript levels, indicating transcriptional regulation of specific pathways. Furthermore, systemic effects of nematode infection were demonstrated by correlation-based network analysis as well as independent component analysis. 1-kestose, raffinose, α,α-trehalose and three non-identified analytes showed clear systemic accumulation, indicating future potential for diagnostic and detailed metabolic analyses. Our studies open the door towards understanding the complex remodelling of plant metabolism in favour of the parasitizing nematode.
Foot protein isoforms are expressed at different times during embryonic chick skeletal muscle development

We have investigated the time course of expression of the alpha and beta triad junctional foot proteins in embryonic chick pectoral muscle. The level of [3H]ryanodine binding in muscle homogenates is low until day E20 of embryonic development, then increases dramatically at the time of hatching reaching adult levels by day N7 posthatch. The alpha and beta foot protein isoforms increase in abundance concomitantly with [3H]ryanodine binding. Using foot protein isoform-specific antibodies, the alpha foot protein is detected in a majority of fibers in day E10 muscle, while the beta isoform is first observed at low levels in a few fibers in day E15 muscle. A high molecular weight polypeptide, distinct from the alpha and beta proteins, is recognized by antifoot protein antibodies. This polypeptide is observed in day E8 muscle and declines in abundance with continued development. It appears to exist as a monomer and does not bind [3H]ryanodine. In contrast, the alpha isoform present in day E10 muscle and the beta isoform in day E20 muscle are oligomeric and bind [3H]ryanodine suggesting that they may exist as functional calcium channels in differentiating muscle. Comparison of the intracellular distributions of the alpha foot protein, f-actin, the heavy chain of myosin and titin in day E10 muscle indicates that the alpha foot protein is expressed during myofibril assembly and Z line formation. The differential expression of the foot protein isoforms in developing muscle, and their continued expression in mature muscle, is consistent with these proteins making different functional contributions. In addition, the expression of the alpha isoform during the time of organization of a differentiated muscle morphology suggests that foot proteins may participate in events involved in muscle differentiation.
Functional Adaptive Model Estimation

In this article we are interested in modeling the relationship between a scalar, Y, and a functional predictor, X(t). We introduce a highly flexible approach called functional adaptive model estimation (FAME), which extends generalized linear models (GLMs), generalized additive models (GAMs), and projection pursuit regression (PPR) to handle functional predictors. The FAME approach can model any of the standard exponential family of response distributions that are assumed for GLM or GAM while maintaining the flexibility of PPR. For example, standard linear or logistic regression with functional predictors, as well as far more complicated models, can easily be applied using this approach. We use a functional principal components decomposition of the predictor functions to aid visualization of the relationship between X(t) and Y. We also show how the FAME procedure can be extended to deal with multiple functional and standard finite-dimensional predictors, possibly with missing data. We illustrate the FAME approach on simulated data, as well as on the prediction of arthritis based on bone shape. We end with a discussion of the relationships between standard regression approaches, their extensions to functional data, and FAME.
Molecular Differences between Sporadic Serrated and Conventional Colorectal Adenomas

Purpose: The purpose is to compare the molecular characteristics of serrated adenomas (SAs) with those of conventional adenomas (CADs) and hyperplastic polyps (HPs). Experimental Design: We evaluated the proliferative activity and molecular alterations in 47 SAs (25 pure-type and 22 mixed-type), 71 CADs, and 23 HPs. Results: The proliferative activity of SAs, as evaluated by Ki-67 expression, was intermediate between CADs and HPs. There was no significant difference in the incidence of KRAS or p53 mutations between the three histological groups. In the microsatellite instability (MSI) analysis, 21% of SAs (9 of 43) showed MSI at two or more loci (MSI-H); corresponding values were 5% of CADs (3 of 64) and 8% of HPs (1 of 13; SAs versus CADs, P = 0.0125). MSI-H was more likely to be found in pure-type SAs (36%; 8 of 22) than in mixed-type SAs (5%; 1 of 21; P = 0.0212). Loss of hMLH-1 expression was found in 8 of 9 SAs with MSI-H. The incidence of BRAF or KRAS mutations was 36 and 15% of SAs, respectively; the combined incidence of BRAF and KRAS mutations occurred in 49% of SAs. However, there was no significant difference in the incidence of BRAF or KRAS mutations between SAs with and without MSI-H. Conclusions: Genetic instability is more frequently implicated in the tumorigenesis of SAs, especially pure-type SAs, than in that of CADs. In contrast, activation of the Ras/Raf/MEK/MAP kinase cascade by BRAF or KRAS mutation, independently of the genetic instability, may be associated with the progression of about half of SAs.
On Scan Chain Diagnosis for Intermittent Faults

Diagnosis is increasingly important, not only for individual analysis of failing ICs, but also for high-volume test response analysis which enables yield and test improvement. Scan chain defects constitute a significant fraction of the overall digital defect universe, and hence it is well justified that scan chain diagnosis has received increasing research attention in recent years. In this paper, we address the problem of scan chain diagnosis for intermittent faults. We show that the conventional scan chain test pattern is likely to miss an intermittent fault, or inaccurately diagnose it. We propose an improved scan chain test pattern which we show to be effective. Subsequently, we demonstrate that the conventional bound calculation algorithm is likely to produce wrong results in the case of an intermittent fault. We propose a new lowerbound calculation method which does generate correct and tight bounds, even for an intermittence probability as low as 10%.
Charity and the Great Hunger in Ireland: The Kindness of Strangers

Introduction 1. 'Apparitions of death and disease': Official responses to the famine 2. 'Some great and terrible calamity': Relief efforts from near and nfar 3. 'A labour of love': Quaker charity 4. 'An ocean of benevolence': The general relief committee of New York 5. 'Arise ye dead of Skibbereen': Leading by example 6. 'This cruel calamity of scarcity': The role of the Catholic Church 7. 'How good people are! ' The involvement of women 8. 'A gloomy picture of human misery': The role of the British Relief Association 9. 'The brotherhood of mankind': Donations to the British Relief Association 10. 'Without distinction of creed or party, nation or colour': American aid 11. 'The most barbaric nation': Evangelicals and charity Conclusion: 'Thousands have by this means been saved' Notes Appendix Bibliography Index
Incorporating set-based control within the singularity-robust multiple task-priority inverse kinematics

Inverse kinematics is an active research domain in robotics since several years due to its importance in multiple robotics application. Among the various approaches, differential inverse kinematics is widely used due to the possibility to real-time implementation. Redundant robotic systems exhibit more degrees of freedom than those strictly required to execute a given end-effector task, in such a case, multiple tasks can be handled simultaneously in, e.g, a task-priority architecture. This paper addresses the systematic extension of the multiple tasks singularity robust solution, also known as Null-space Based Behavioral control, to the case of set-based control tasks, i.e, tasks for which a range, rather than a specific value, is assigned. This is the case for several variables such as, for example, mechanical joint limits of robotic arms as well as obstacle avoidance for any kind of robots. Numerical validation are provided to support the solution proposed.
Moisture Sensitivity of Hot Mix Asphalt (HMA) Mixtures in Nebraska - Phase II

As a consequential effort to the previous NDOR research project (P-564) on moisture damage, this report presents outcomes from this project incorporated with the previous project. Performance changes and fundamental material characteristics associated with moisture damage due to various anti-stripping additives in asphalt mixtures are studied through various experimental approaches and a numerical simulation. Three additives (i.e., one reference additive, hydrated lime, and two alternative additives: fly ash and cement) are investigated by adding them into two types of mixes (SP2 for low-traffic-volume roadways and SP5 for high-traffic- volume roadways) where two different asphalt binders (PG 64-22 for the SP2 mix and PG 70-28 for the SP5) are used. Two asphalt concrete mixture scale performance tests, the AASHTO T-283 and the APA under water, and two local-scale mixture constituent tests, the boiling water test (ASTM D 3625) and the pull-off test, are conducted to characterize the effects of binder-specific anti-stripping additives on the binder-aggregate bonding potential in mixtures. The pull-off tensile strength tests are then numerically modeled through the finite element technique incorporated with the cohesive zone modeling approach to seek more fundamental scientific insights into the effect of each anti-stripping additive on the overall moisture damage resistance. Results from laboratory tests and numerical simulations indicate that the SP5 mixtures, where high-quality aggregates and polymer-modified binder are used, are fairly self-resistant to moisture damage without treating any anti-stripping additive and do not show any visible sensitivity among additives, whereas the effects of additives and their sensitivity are significant in the SP2 mixes that use the unmodified binder PG 64-22 and low-quality aggregates. With the limited amount of test data, hydrated lime seems to perform slightly better than other additives, particularly with longer moisture-conditioning time. Fly ash contributes to reducing moisture damage by improving binder-aggregate interfacial properties, which are validated from the integrated experimental-computational evaluation.
Influence of Aluminium and EGCG on Fibrillation and Aggregation of Human Islet Amyloid Polypeptide

The abnormal fibrillation of human islet amyloid polypeptide (hIAPP) has been implicated in the development of type II diabetes. Aluminum is known to trigger the structural transformation of many amyloid proteins and induce the formation of toxic aggregate species. The (−)-epigallocatechin gallate (EGCG) is considered capable of binding both metal ions and amyloid proteins with inhibitory effect on the fibrillation of amyloid proteins. However, the effect of Al(III)/EGCG complex on hIAPP fibrillation is unclear. In the present work, we sought to view insight into the structures and properties of Al(III) and EGCG complex by using spectroscopic experiments and quantum chemical calculations and also investigated the influence of Al(III) and EGCG on hIAPP fibrillation and aggregation as well as their combined interference on this process. Our studies demonstrated that Al(III) could promote fibrillation and aggregation of hIAPP, while EGCG could inhibit the fibrillation of hIAPP and lead to the formation of hIAPP amorphous aggregates instead of the ordered fibrils. Furthermore, we proved that the Al(III)/EGCG complex in molar ratio of 1 : 1 as Al(EGCG)(H2O)2 could inhibit the hIAPP fibrillation more effectively than EGCG alone. The results provide the invaluable reference for the new drug development to treat type II diabetes.