Miracle-dz/UniFAR-FTUs huggingface dataset:
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Similar Structures but Different Roles – An Updated Perspective on TLR Structures

Toll-like receptors (TLRs) are pattern recognition receptors that recognize conserved structures in pathogens, trigger innate immune responses, and prime antigen-specific adaptive immunity. Elucidation of crystal structures of TLRs interacting with their ligands such as TLR1-2 with triacylated lipopeptide, TLR2-6 with diacylated lipopeptide, TLR4–MD-2 with LPS, and TLR3 with double-stranded RNA (dsRNA) have enabled an understanding of the initiation of TLR signaling. Agonistic ligands such as LPS, dsRNA, and lipopeptides induce “m” shaped TLR dimers in which C-termini converge at the center. Such central convergence is necessary to bring the two intracellular receptor TIR domains closer together and promote their dimerization, which serves as an essential step in downstream signaling. In this review, we summarize TLR ECD structures that have been reported to date with special emphasis on ligand recognition and activation mechanism.
Early Warnings of Regime Shift When the Ecosystem Structure Is Unknown

Abrupt changes in dynamics of an ecosystem can sometimes be detected using monitoring data. Using nonparametric methods that assume minimal knowledge of the underlying structure, we compute separate estimates of the drift (deterministic) and diffusion (stochastic) components of a general dynamical process, as well as an indicator of the conditional variance. Theory and simulations show that nonparametric conditional variance rises prior to critical transition. Nonparametric diffusion rises also, in cases where the true diffusion function involves a critical transition (sometimes called a noise-induced transition). Thus it is possible to discriminate noise-induced transitions from other kinds of critical transitions by comparing time series for the conditional variance and the diffusion function. Monte Carlo analysis shows that the indicators generally increase prior to the transition, but uncertainties of the indicators become large as the ecosystem approaches the transition point.
Reduced complexity single-carrier maximum-likelihood detection for decision feedback assisted space-time equalization

A novel decision-feedback (DF) aided reduced complexity maximum likelihood (ML) space-time equalizer (STE) designed for single-carrier multiple antenna assisted receivers is introduced. The proposed receiver structure is based on a recursive tree search, which is capable of achieving ML performance at a moderate computational cost and substantially outperforms the linear benchmarker based on the minimum mean-squared error (MMSE) criterion. Additionally a further complexity reduction scheme is proposed, which exploits the specific characteristics of both the wide-band channel and the proposed DF-STE
Effective thermal via and decoupling capacitor insertion for 3D system-on-package

The increased component density of a 3D system-on-package (SOP) exacerbates the thermal hotspot problem. A popular choice to mitigate the thermal issues is thermal vias (t-vias) that are used to establish thermal paths from the core of an SOP package to the heat sinks. Another major problem with SOP integration is the power supply noise coupling among various mixed signal components constituting the system. In this case, decoupling capacitors (decaps) are inserted to provide the switching currents locally. The goal of our automatic 3D SOP component placement algorithm is to determine the x/y/z location of each component while minimizing the footprint area under thermal and power supply noise constraints. In general, t-vias and decaps are typically inserted in the white space in the placement, whereas the proximity of the t-vias and decaps to the target components determines their effectiveness. Hence, our component placer considers t-via and decap insertion during the early design stage, where the component location can be flexibly changed. Related experiments demonstrate the effectiveness of our approach
Evaluation of genotypic tropism prediction tests compared with in vitro co-receptor usage in HIV-1 primary isolates of diverse subtypes.

OBJECTIVES To evaluate the sensitivity and specificity of genotypic methods for predicting the co-receptor usage of subtypes B and non-B HIV-1 primary isolates, using as gold standard the infectivity of each primary isolate in GHOST cells stably expressing HIV-1 co-receptors. METHODS Primary isolates were obtained by co-culturing either patient's peripheral blood mononuclear cells (PBMCs) or ultracentrifuged plasma with donor-activated PBMCs. In vitro co-receptor usage was determined by infecting GHOST cells. Tropism prediction, based on V3 sequences, was determined with simple rules and bioinformatic tools (Geno2pheno[coreceptor] and WebPSSM). RESULTS This study includes 102 HIV-1 primary isolates; 23 (22.5%) subtype B and 79 (77.5%) non-B genetic forms. V3 sequences were classified into six subtypes (A-G), although 32 (31.4%) were circulating recombinant forms and 21 (20.6%) were unique recombinant forms. Sixty-nine isolates were R5, 27 R5X4 and 6 X4. The highest levels of sensitivity and specificity for the detection of X4 strains among V3 sequences, between 91% and 100%, were obtained by using PSSM(x4r5), PSSM(si/nsi) and the 11/25 rule for sequences of subtypes A, B and G, but not for subtype F. Establishing the recommended cut-off for clinical settings of a 10% false positive rate for Geno2pheno, we obtained 93% specificity and 97% sensitivity. CONCLUSIONS Comparing genotypic assays for HIV-1 co-receptor use with a cell-culture phenotypic assay could provide more reliable results of sensitivity and specificity for the detection of X4 strains than comparing them with recombinant assays, considered as gold standard. In general, except for subtype F isolates, there is a good correlation for tropism prediction.
Effect of smoking history on outcome of patients diagnosed with TB and HIV

Tobacco use, infection with HIV and active tuberculosis (TB) are important public health problems worldwide. Smoking affects susceptibility to TB, with an increased risk of infection, TB disease and TB death [1, 2]. An estimated 1.1 million of the 8.6 million people who developed TB in 2012 were HIV-positive [3]. It has been estimated that smoking could cause 18 million excess cases of TB and 40 million excess deaths between 2010 and 2050 [4], but little is known about the effect of smoking on the outcomes of people receiving care for both HIV and TB. Among TB–HIV patients on antiretrovirals those who smoke(d) are more likely to have adverse TB treatment outcomes http://ow.ly/DyPqW
Optimal rejection of bounded persistent disturbances in periodic systems

The problem of optimal rejection of bounded persistent disturbances is solved in the case of linear discrete-time periodic systems. The solution consists of solving an equivalent time-invariant standard l/sup 1/ optimization problem subject to an additional constraint. This constraint ensures the causality of the resulting periodic controller. By duality theory, the problem is shown to be equivalent to a linear programming problem, which is no harder than the standard l/sup 1/ problem. <<ETX>>
A COMING OF AGE FOR GPS : A RTLINUX BASED GPS RECEIVER

The Global Positioning System, or GPS, is a key technology for both the civilian and scientific research markets. GPS provides users with precise geodetic positioning and time determination. Most GPS receivers require specialized hardware and complex software to operate. One receiver, originally designed to run in DOS, will be the focus of a code migration to RTLinux. The major aspects of the migrated code are an interrupt service routine, multiple threads, and TCP connectivity. Following the migration we noticed that not only did receiver stability increase dramatically, but also errors in positioning decreased. To provide insight into code migration from DOS to RTLinux, we will focus on the specific difficulties, discoveries, and enlightenments encountered.
Towards User-Centered Privacy Risk Detection and Quantification Framework

With the prevalence of privacy incidents and recurrent leaks, privacy protection has become a concern of users and data protection entities. Previous research in privacy risk prevention has mostly followed the "collect and prevent" philosophy, e.g., by applying anonymization techniques to the user data on the back-end. These approaches neglect the users' right to informational self-determination since the privacy risk analysis and prevention takes place once the data is out of control of the user. In this paper, we present an architecture for user-centered privacy risk detection and quantification framework based on combinatorial, and probabilistic mathematical models coupled with advanced machine learning classifiers. The framework empowers users to take informed privacy prevention actions prior to unwanted revelations.
WYSIWYG computational photography via viewfinder editing

Digital cameras with electronic viewfinders provide a relatively faithful depiction of the final image, providing a WYSIWYG experience. If, however, the image is created from a burst of differently captured images, or non-linear interactive edits significantly alter the final outcome, then the photographer cannot directly see the results, but instead must imagine the post-processing effects. This paper explores the notion of viewfinder editing, which makes the viewfinder more accurately reflect the final image the user intends to create. We allow the user to alter the local or global appearance (tone, color, saturation, or focus) via stroke-based input, and propagate the edits spatiotemporally. The system then delivers a real-time visualization of these modifications to the user, and drives the camera control routines to select better capture parameters.
Magic mirror: a new VR platform design and its applications

This paper describes a case study of VR platform Magic Mirror and its applications that are economic in development process and cost, flexible by contents and installation conditions, and that has business potential for consumer market. Magic Mirror uses video based virtual world and tangible interaction by motion tracking. Magic Mirror platform enables a user to monitor their action and to collaborate with other users of remote place within attractive interaction feedback. Magic Mirror system gives serious distance learning experience with tutoring and group collaboration. They are presented in public exhibitions and tested by exhibition visitors. They showed application potential of Magic Mirror platform in interactive game, distance learning, and entertainment field.
New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer

We focus on characterizing common and different coexpression patterns among RNAs and proteins in breast cancer tumors. To address this problem, we introduce Joint Random Forest (JRF), a novel nonparametric algorithm to simultaneously estimate multiple coexpression networks by effectively borrowing information across protein and gene expression data. The performance of JRF was evaluated through extensive simulation studies using different network topologies and data distribution functions. Advantages of JRF over other algorithms that estimate class-specific networks separately were observed across all simulation settings. JRF also outperformed a competing method based on Gaussian graphic models. We then applied JRF to simultaneously construct gene and protein coexpression networks based on protein and RNAseq data from CPTAC-TCGA breast cancer study. We identified interesting common and differential coexpression patterns among genes and proteins. This information can help to cast light on the potential disease mechanisms of breast cancer.
Silverback and the Archival Layer of OceanStore

Silverback, coupled with the OceanStore archival layer, is a backup/archival system that is designed to increase the availability of data by allowing file servers to distribute archival copies of files across an arbitrary set of servers. The system uses erasure codes as a means to recreate data in the event that one or more servers fail. As a result, files will still be available in the event of server failures, provided that a sufficient amount of the data network is still functioning. We implemented Silverback and OceanStore’s archive, and ran a performance benchmark against them.
Analyzing Plans through Image Schemas and Descriptions

We describe our efforts in building the epistemic layer of the cognitive architecture AKIRA. We assume a constructive stance: experiences, although depending also on entities that exist independently, are “constructed” (in a sense that is stronger than “framed”) by the intentionality of an observer, according to its categorical and ontological structure. Here we face directly one interesting challenge of this workshop: is it possible to relate the information expressed by an ontology with the semantic content embodied in the cognitive semantic categories?
Evidence for overfishing on pristine coral reefs: reconstructing coastal catches in the Australian Indian Ocean Territories

The fisheries statistics systems of many countries are performing poorly, often failing to report on small-scale catches, particularly from subsistence and recreational fisheries. These deficiencies, which lead to the underestimation of catches, are particularly evident in overseas territories of developed countries. This study is an attempt to remedy this for the years 1950–2010 for the Australia Indian Ocean Territories, an area from which little reporting is done. The results suggest that the Cocos (Keeling) Islands had a catch of approximately 80 t·year−1 in the 1950s (essentially subsistence based), which increased, starting in the mid-1980s to reach 250 t·year−1 in recent years, mainly due to the introduction of recreational and later commercial fishing, with signs of overexploitation since 2000. The coastal catch from Christmas Island was tentatively assessed as being higher (40–70 t·year−1) in the 1950s and 1960s than in the 2000s (<30 t·year−1). Fisheries managers in these areas should focus on determining primary target species and their vulnerability to overfishing, as well as developing island specific recreational fishing management plans.
EMDR in Competition with Fate: A Case Study in a Chinese Woman with Multiple Traumas

This paper described the application of eye movement desensitization reprocessing (EMDR) for addressing the posttraumatic stress disorder (PTSD) symptoms in a Chinese woman who had experienced multiple traumas in her childhood. EMDR is an integrative therapeutic intervention that uses a standardized eight-phase approach to treatment. It is also a proven, effective, and efficient treatment for trauma. In this client with multiple traumas, the etiological event that lay the foundation of her dysfunctional responses was reprocessed first. The successful resolution of this event allowed the positive treatment effects to transfer to other traumatic events of a similar theme. This case also illustrates the importance of identifying a culturally appropriate positive cognition (PC) in contributing to the success of the treatment.
Hybrid Cellular / WLAN Networks with Wireless Offloading : A Novel Communication Paradigm

The exploitation of already deployed wireless local area networks (WLAN)s (e.g., WiFi access points (AP)s) has attracted considerable attention, as an efficient and pract ical method to improve the performance of wireless networks. In t his paper, we propose a novel communication paradigm to satisfy the performance demands of the future wireless networks:a hybrid Cellular-WLAN network architecture with wireless offloadi ng. In contrast to the commonly adopted practice of the WiFi offloading, where the WLAN APs have a wired backhaul (e.g., Digital Subscriber Line), we propose a wireless offloading approach, wh ere the WLAN APs will share their wireless cellular broadband connection with other users. These users will select their s erving node, i.e., the macro-cell base station or a WLAN AP, based on a certain selection criterion, originating a challenging research field, where interfering effects and wireless resources limitations play a dominant role. Important performance metrics of the proposed hybrid scheme -as the outage probability and the avera ge signal-to-interference-plus noise ratio (SINR)are theo retically studied and closed form expressions are derived for the sing leuser case with multiple interferers, considering both identical and non-identical fading channels. Furthermore, consideringa multicell network scenario the proposed hybrid scheme is optimiz ed for minimizing the intercell interference. Moreover, based on the general multi-cellular hybrid WLAN/Celullar concept, we present a novel scheme for achieving frequency reuse one wit hin a single macro-cell, under specific performance criteria an d constraints, that guarantee the overall cell’s or the individual user’s quality-of-service requirements. We consider two optimization problems that aim at the overall cell’s SINR maximization or at the minimum user’s SINR maximization and we propose a fast greedy solution for both of them. Numerical results and simulations showed that the proposed wireless architectur e may offer significant performance gains in the presence of multi ple interferers, compared to a conventional cellular network.
Predicting Youth Participation in Extracurricular Recreational Activities: Relationships with Individual, Parent, and Family Characteristics

The importance of participating in extracurricular activities for adolescents and youth has been extensively investigated and confirmed, yet much less is known about what influences youth to participate and parents to enroll their child in different types of programs. This study of 216 sixth-grade youth collected comprehensive histories of extracurricular activity participation and investigated relationships with individual (gender, preschool experience), familial (parent in home, siblings, income), and parental characteristics (mother and father working hours, occupational status, educational level) to determine the extent to which each of these variables predicted youth involvement. The degree of participation in extracurricular activities was measured as both breadth (number of activities) and time (frequency of participation). Participation patterns were determined for four types of activity programs (team sports, individual sports, performing arts, community clubs, and activities) and composite measures of the extent of involvement were also scrutinized. The findings revealed strong differences between males and females and also between the four types of activities in terms of which factors were important predictors of participation. These data provide implications for learning more about the types of participants who are most likely to participate in different recreational programs, and for using this information to better design and market such programs. The data in this study provides detailed information about who is most likely to seek and participate in these programs. In addition, it is reasonable to posit that certain types of activity programs might be better able to attract and retain youth with certain interests and backgrounds. The information presented in this research is informative about which characteristics best predict participation in which types of activity programs. This is deemed to be a major benefit to agencies and other providers, especially with a population that has been generally regarded to be a more challenging constituency with lower rates of participation.
A Comparison of Cabin Safety Awareness among Airline Passengers in Taiwan and Mainland China

This article compares the effect of cabin safety education on passengers' cabin safety awareness in knowledge, attitude, and behavior (KAB) in Taiwan and Mainland China, primarily for passengers that cross the Taiwan Strait. Evidence reveals that passengers from both sides of the Taiwan Strait need to be taught about safety before they fly. Passengers from both sides of the Taiwan Strait were surveyed at two Taiwan airports, the Taoyuan International Airport and the Taipei Municipal Airport. The Structural Equation Modeling (SEM) technique is used for data analysis. The results show that cabin safety education positively affects Taiwan passengers' cabin safety knowledge, attitude, and behavior. Safety education that involves accurate utilization of emergency equipment procedures, situational awareness, and responses is recommended. Although the cabin safety education positively affects Mainland China passengers' attitude and behavior, it does not have a strong effect on the aspect of knowledge. Emergency equipment procedures and regulations are needed content for cabin safety education for Mainland China passengers. The findings also indicate that Taiwan passengers' cabin safety knowledge will positively affect their behavior; therefore, the knowledge-behavior consistency is supported. The attitude-behavior and the knowledge-attitude consistency correlation are both supported as well. However, the relationships among Mainland China passengers' cabin safety knowledge, attitude, and behavior are not consistent. Passengers' demographic data indicate that the Mainland China passengers' educational level, age, and number of flights could be major factors in this inconsistency.
Models Used in the Online Learning Environment

The inter-human communication is a continuous process: a person receives, decodes and interprets messages (according to his/her own semantics) and encodes information in his/her answers. In 1954, Schramm and Osgood defined the circular communication model, according to which feedback is the most important. Communication is described as a continuous process consisting in messages sending and receiving feedback. Starting from the circular communication model, it is proposed a model of communication that can be used in the online learning environment.
A visual context-aware multimodal system for spoken language processing

Recent psycholinguistic experiments show that acoustic and syntactic aspects of online speech processing are inﬂuenced by visual context through cross-modal inﬂuences. During interpretation of speech, visual context seems to steer speech processing and vice versa. We present a real-time multimodal sys-tem motivated by these ﬁndings that performs early integration of visual contextual information to recognize the most likely word sequences in spoken language utterances. The system ﬁrst acquires a grammar and a visually grounded lexicon from a “show-and-tell” procedure where the training input consists of camera images consisting of sets of objects paired with verbal object descriptions. Given a new scene, the system generates a dynamic visually-grounded language model and drives a dynamic model of visual attention to steer speech recognition search paths towards more likely word sequences.