Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Analysis of the UBA Domain of X-linked Inhibitor of Apoptosis Protein Reveals Different Surfaces for Ubiquitin-Binding and Self-Association

Background Inhibitor of apoptosis proteins (IAPs) belong to a pivotal antiapoptotic protein family that plays a crucial role in tumorigenesis, cancer progression, chemoresistance and poor patient-survival. X-linked inhibitor of apoptosis protein (XIAP) is a prominent member of IAPs attracting intense research because it has been demonstrated to be a physiological inhibitor of caspases and apoptosis. Recently, an evolutionarily conserved ubiquitin-associated (UBA) domain was identified in XIAP and a number of RING domain-bearing IAPs. This has placed the IAPs in the group of ubiquitin binding proteins. Here, we explore the three-dimensional structure of the XIAP UBA domain (XIAP-UBA) and how it interacts with mono-ubiquitin and diubiquitin conjugates. Principal Findings The solution structure of the XIAP-UBA domain was determined by NMR spectroscopy. XIAP-UBA adopts a typical UBA domain fold of three tightly packed α-helices but with an additional N-terminal 310 helix. The XIAP-UBA binds mono-ubiquitin as well as Lys48-linked and linear-linked diubiquitins at low-micromolar affinities. NMR analysis of the XIAP-UBA–ubiquitin interaction reveals that it involves the classical hydrophobic patches surrounding Ile44 of ubiquitin and the conserved MGF/LV motif surfaces on XIAP-UBA. Furthermore, dimerization of XIAP-UBA was observed. Mapping of the self-association surface of XIAP-UBA reveals that the dimerization interface is formed by residues in the N-terminal 310 helix, helix α1 and helix α2, separate from the ubiquitin-binding surface. Conclusion Our results provide the first structural information of XIAP-UBA and map its interaction with mono-ubiquitin, Lys48-linked and linear-linked diubiquitins. The notion that XIAP-UBA uses different surfaces for ubiquitin-binding and self-association provides a plausible model to explain the reported selectivity of XIAP in binding polyubiquitin chains with different linkages.
Pricing What is Priceless: A Status Report on Non-Market Valuation of Environmental Resources

This paper provides a selective overview of the modeling and estimates of the economic values of environmental resources. Travel cost, hedonic property values, contingent valuation and household production models are discussed and evaluated. Two new approaches - calibrated models and conjoint analysis - are compared with existing methods. For each class of models the review identifies some of the current research issues and potential areas for linking the results to policy.
When forgiving enhances psychological well-being: the role of interpersonal commitment.

The present research addresses the question of when and why forgiving might enhance psychological well-being. The authors predict that forgiving is associated with enhanced well-being but that this association should be more pronounced in relationships of strong rather than weak commitment. This hypothesis received good support in Studies 1-3. Studies 2 and 3 addressed the issue of why forgiving might be associated with psychological well-being, revealing that this association was reduced after controlling for psychological tension (i.e., a psychological state of discomfort due to conflicting cognitions and feelings). Study 4 revealed that in the context of marital relationships, tendencies toward forgiving one's spouse exhibited a more pronounced association with psychological well-being than did tendencies to forgive others in general.
WIPP: Wi-Fi Compass for Indoor Passive Positioning with Decimeter Accuracy

In recent decades, the proliferation of smart phones, tablets, and wireless networks has fostered a growing interest in indoor passive positioning. The Wi-Fi-based passive positioning systems can provide Location-Based Services (LBSs) to the third party such as market and security departments. Most of the existing systems are based on the Receive Signal Strength Indication (RSSI) information, which are generally time-consuming and susceptible to environmental change. To overcome this problem, we propose the Wi-Fi compass for indoor passive positioning system (WIPP), an Angle of Arrival (AOA) based passive positioning system using the existing commodity Wi-Fi network. In this paper, we first propose a new algorithm for the joint estimation of AOA and Time of Arrival (TOA) measurements based on the fine-grained Channel State Information (CSI), which is collected by an off-the-shelf Wi-Fi device equipped with only three antennas. Second, we use the affinity propagation clustering algorithm to identify the direct signal path from the target to each Wi-Fi Access Point (AP). Finally, we deploy the WIPP in an actual indoor environment to conduct the performance comparison with the well-known radio-frequency (RF) based system for locating and tracking users inside buildings (RADAR), as well as the conventional passive positioning system using the AOA solely. The experimental results show that the WIPP is able to achieve the median positioning error 0.7 m, which is much lower than the ones by the RADAR system and the conventional system using the AOA solely.
Performance Evaluation of Radio Map Construction Methods for Wi-Fi Positioning Systems

A radio map is a collection of signal fingerprints labeled with their collected locations. It is known that the performance of a fingerprint-based positioning systems is closely related to the precision and accuracy of the underlying radio maps. However, little has been studied on the performance of radio maps in relation to the fingerprint collection methods and the radio map models, which determine the accuracy and precision of radio maps, respectively. This paper evaluates the performance of various radio map construction methods in both indoor and outdoor environments. Four radio map construction methods, i.e., a point-by-point manual calibration, a walking survey, a semisupervised learning-based method, and an unsupervised learning-based method, have been compared. We also evaluate the performance of various types of radio map models that represent the characteristics of collected fingerprints. To demonstrate the importance of the radio map model, a new model named signal fluctuation matrix (SFM) was developed, and its performance was compared with that of the three conventional radio map models, respectively. The evaluation revealed that the performance of the radio maps was very sensitive to the design of radio map models and the number of fingerprints collected at each location. The performance achieved by SFM-based positioning was comparable with that of the other models despite using a small number of fingerprints.
Knowledge and Skills Associated with Information Technology: Levels and Influences

In recent years, research on IT usage has increasingly focused on post-adoption usage, rather than initial acceptance of a technology regarded as new. Consistent with this recent trend, we seek to understand what factors influence employees’ ongoing IT use and processes they rely on for expanding their knowledge and skills within organizational workgroups. Based on recommendations by Jasperson, Carter and Zmud (2005), we seek to understand feature-level IT use of office software applications that are most frequently used within four workgroups. We first document the knowledge and skills of each employee at the feature level. Second, we analyze detailed, featurelevel knowledge with a novel method based on Venn diagrams that reflects the degree to which coworkers have fully-, partially-, or non-overlapping knowledge and skills. Finally, we employ open-coding methods to identify enabling and inhibiting factors that shape the amount and effectiveness of IT-related knowledge transfer among coworkers. Our study yields surprising findings – including the fact that some employees have unique IT skills that do not overlap with their coworkers. Moreover, employees seek help from other workers who are at similar levels in the organizational hierarchy, and usually avoid seeking help from colleagues whose knowledge level is considerably higher, or whose knowledge base is radically different. Our results show that employees prefer to seek help from coworkers whose knowledge is similar to their own. We conclude by discussing the implication of our findings for managers and researchers.
Fischer-Tropsch Synthesis on Multicomponent Catalysts: What Can We Learn from Computer Simulations?

In this concise review paper, we will address recent studies based on the generalized-gradient approximation (GGA) of the density functional theory (DFT) and on the periodic slab approach devoted to the understanding of the Fischer-Tropsch synthesis process on transition metal catalysts. As it will be seen, this computational combination arises as a very adequate strategy for the study of the reaction mechanisms on transition metal surfaces under well-controlled conditions and allows separating the influence of different parameters, e.g., catalyst surface morphology and coverage, influence of co-adsorbates, among others, in the global catalytic processes. In fact, the computational studies can now compete with research employing modern experimental techniques since very efficient parallel computer codes and powerful computers enable the investigation of more realistic molecular systems in terms of size and composition and to explore the complexity of the potential energy surfaces connecting reactants, to intermediates, to products of reaction. In the case of the Fischer-Tropsch process, the calculations were used to complement experimental work and to clarify the reaction mechanisms on different catalyst models, as well as the influence of additional components and co-adsorbate species in catalyst activity and selectivity.
Experimental tests of hidden variable theories from dBB to stochastic electrodynamics

The studies concerning the possible existence of a deterministic theory, of which quantum mechanics would be an approximation, date to the celebrated 1935 Einstein-Podolsky-Rosen paper. Since Bell's proposal of 1964 various experiments were addressed to a general experimental test of local hidden variable theories, leading to strong indications favourable to Standard Quantum Mechanics. Nevertheless, detection loophole still persists. After a short presentation of recent PDC photon experiments, we will present our recent works in this field and, in particular, a conclusive negative test of stochastic electrodynamics. Finally, we will also mention possible tests of non-local deterministic models and give some detail on our test of the dBB model.
Formation of Nanowrinkles on Varied Polymers Using Reactive Ion Etching

The optical and mechanical properties of many materials can be altered by forming nanoscale structures on their surfaces, such as wrinkles, without altering the bulk properties of the materials. Such nanowrinkled materials have important applications in many fields, including the production of photodetectors and solar cells. Wrinkles are formed when compressive strain is applied to a stiff skin bonded to a softer, elastomeric main material, or substrate, causing the skin to buckle in a periodic fashion. The most commonly used method involves bonding a thin layer of metal to the substrate to create the skin. This method has trouble forming wrinkles with large amplitudes relative to their wavelengths, a trait that is desirable for many applications. A recently discovered method, however, forms nanowrinkles through altering the surface of the substrate, and has shown increased control over the average wavelength, amplitude, and orientation of the wrinkles. This is accomplished through reactive ion etching (RIE), in which the substrate is treated with plasma formed from various gases, such as argon (Ar), carbon tetrafluoride (CF4), and trifluoromethane (CHF3), creating a stiff skin . Applying this method to various polymers with different properties would be highly beneficial, with applications ranging from biomechanical work such as brain and cardiac monitors to flexible electronics for deformable transparent displays and microlens arrays.
Optimizing Job Scheduling on Multicore Computers

It is common nowadays that multiple cores reside on the same chip and share the on-chip cache. Resource sharing may cause performance degradation of the co-running jobs. Job co-scheduling is a technique that can effectively alleviate the contention. Many co-schedulers have been developed in the literature, but most of them do not aim to find the optimal co-scheduling solution. Being able to determine the optimal solution is critical for evaluating co-scheduling systems. Moreover, most co-schedulers only consider serial jobs. However, there often exist both parallel and serial jobs in some situations. This paper aims to tackle these issues. In this paper, a graph-based method is developed to find the optimal co-scheduling solution for serial jobs, and then the method is extended to incorporate parallel jobs. The extensive experiments have been conducted to evaluate the effectiveness and efficiency of the proposed co-scheduling algorithms. The results show that the proposed algorithms can find the optimal co-scheduling solution for both serial and parallel jobs.
Emolah: A Malay Language Spontaneous Speech Emotion Recognition on iOS Platform

This paper presented the implementation of spontaneous speech emotion recognition (SER) using smartphone on iOS platform. The novelty of this work is at the time of writing, no similar work has been done using Malay language spontaneous speech. The development of SER using a mobile device is important for ease of use anytime and anywhere. The main factors to be considered is the computational complexity of classifying the emotions in real-time. Therefore, we introduced EmoLah, a Malay language spontaneous SER that is able to recognize emotions on the go with satisfactory accuracy rate. Pitch and energy prosody features are used to represent the emotions in the spontaneous speech and Naïve Bayes learning model is selected as the classifier. EmoLah is trained and tested using Malay language spontaneous speech acquired from television talk shows, live interviews from news broadcast and mini-parliament sessions conducted by children. Four types of speech emotions are collected that are happy, sad, angry and neutral. The total duration of all the speech emotion is four hours. The speech emotion training is using MATLAB scripts and the weights are implemented in XCODE as the iOS software for application development. Emolah accuracy is evaluated using cross-validation test and the result showed that it can discriminate angry, sad and happy. However, most emotions are misclassified as neutral emotion.
Rational Prepayment and the Valuation of Mortgage-Backed Securities

This article presents a new model of mortgage prepayments, based on rational decisions by mortgage holders. These mortgage holders face heterogeneous transaction costs, which are explicitly modeled. The model is estimated using a version of Hansen's (1982) generalized method of moments, and is shown to capture many of the empirical features of mortgage prepayment. Estimation results indicate that mortgage holders act as though they face transaction costs that far exceed the explicit costs usually incurred on refinancing. They also wait an average of more than a year before refinancing, even when it is optimal to do so. The model fits observed prepayment behavior as well as the recent empirical model of Schwartz and Torous (1989). Implications for pricing mortgage-backed securities are discussed. Article published by Oxford University Press on behalf of the Society for Financial Studies in its journal, The Review of Financial Studies.
Stock assessment and end-to-end ecosystem models alter dynamics of fisheries data

Although all models are simplified approximations of reality, they remain useful tools for understanding, predicting, and managing populations and ecosystems. However, a model’s utility is contingent on its suitability for a given task. Here, we examine two model types: single-species fishery stock assessment and multispecies marine ecosystem models. Both are efforts to predict trajectories of populations and ecosystems to inform fisheries management and conceptual understanding. However, many of these ecosystems exhibit nonlinear dynamics, which may not be represented in the models. As a result, model outputs may underestimate variability and overestimate stability. Using nonlinear forecasting methods, we compare predictability and nonlinearity of model outputs against model inputs using data and models for the California Current System. Compared with model inputs, time series of model-processed outputs show more predictability but a higher prevalence of linearity, suggesting that the models misrepresent the actual predictability of the modeled systems. Thus, caution is warranted: using such models for management or scenario exploration may produce unforeseen consequences, especially in the context of unknown future impacts.
A Local Source of FGF Initiates Development of the Unmyelinated Lineage of Sensory Neurons

The principle by which unmyelinated primary sensory neurons transducing thermal, itch and pain perception are specified in early development is unknown. These classes of sensory neurons diversify from a common population of late-born neurons, which initiate expression of Runt homology domain transcription factor RUNX1 and the nerve growth factor receptor TrkA. Here, we report that signals emanating from within the mouse dorsal root ganglion mediated partly by early-born neurons destined to a myelinated phenotype participate in fating late-born RUNX1+/TrkA+ neurons. Inductive factors include FGFs via activation of FGF receptor 1 (FGFR1). Consistently, FGF2 is sufficient to induce expression of RUNX1, and Fgfr1 conditional mutant mice display deficits in fating of the common population of late-born RUNX1+/TrkA+ neurons that develop into unmyelinated neurons. Thus, the distinct lineages of sensory neurons are acquired in response to increasing FGF levels provided by a rising number of born neurons.
Social Media and its implications for Viral Marketing

Social media presents potentially seductive opportunities for new forms of communication and commerce between marketers and consumers. As advertisers typically want to find some way to follow their target audiences, many new media opportunities are presented to advertisers. However, we are still social media pioneers. While the boom in social marketing appears persuasive with an estimated 70% of consumers visiting a social website for information, other research points out that 90% of WOM conversations still occur face to face or by phone, and only 7 percent occurs online. In contrast to traditional advertising media such as television, there are measurement and consumer behaviour modelling issues that will need to be addressed before marketers that measure and manage their media investments will be able to fully embrace the opportunities and navigate the risks presented by social media. Ultimately, advertisers will be forced beyond the “oldschool” approaches to adopt many of the principles and techniques of relationship marketing in order to effectively use social media and likely the multiple niche co-creation of products and services.
The Derivation of a Grammatically Indexed Lexicon from the Longman Dictionary of Contemporary English

We describe a methodology and associated software system for the construction of a large lexicon from an existing machine-readable (published) dictionary. The lexicon serves as a component of an English morphological and syntactic analyser and contains entries with grammatical definitions compatible with the word and sentence grammar employed by the analyser. We describe a software system with two integrated components. One of these is capable of extracting syntactically rich, theory-neutral lexical templates from a suitable machine-readable source. The second supports interactive and semi-automatic generation and testing of target lexical entries in order to derive a sizeable, accurate and consistent lexicon from the source dictionary which contains partial (and occasionally in-accurate) information. Finally, we evaluate the utility of the Longman Dictionary of Contemporary English as a suitable source dictionary for the target lexicon.
Escholarship@umms Program in Gene Function and Expression Publications and Presentations Program in Gene Function and Expression a Separable Domain of the P150 Subunit of Human Chromatin Assembly Factor-1 Promotes Protein and Chromosome Associations with Nucleoli Repository Citation a Separable Doma

A separable domain of the p150 subunit of human Chromatin Assembly Factor-1 promotes protein and chromosome associations with nucleoli" (2014). Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. separable domain of the p150 subunit of human Chromatin Assembly Factor-1 promotes protein and chromosome associations with nucleoli. ABSTRACT Chromatin assembly factor-1 (CAF-1) is a three-subunit protein complex conserved throughout eukaryotes that deposits histones during DNA synthesis. Here we present a novel role for the human p150 subunit in regulating nucleolar macromolecular interactions. Acute depletion of p150 causes redistribution of multiple nucleolar proteins and reduces nucleolar association with several repetitive element–containing loci. Of note, a point mutation in a SUMO-interacting motif (SIM) within p150 abolishes nucleolar associations, whereas PCNA or HP1 interaction sites within p150 are not required for these interactions. In addition, acute depletion of SUMO-2 or the SUMO E2 ligase Ubc9 reduces α-satellite DNA association with nucleoli. The nucleolar functions of p150 are separable from its interactions with the other subunits of the CAF-1 complex because an N-terminal fragment of p150 (p150N) that cannot interact with other CAF-1 subunits is sufficient for maintaining nucleolar chromosome and protein associations. Therefore these data define novel functions for a separable domain of the p150 protein, regulating protein and DNA interactions at the nucleolus.
High-Selectivity Tunable Bandpass Filters With Harmonic Suppression

This paper presents harmonic-suppressed tunable bandpass filters with two movable transmission zeros. For tunable bandpass filters, tuning the passband frequency will cause the harmonic to shift, complicating the harmonic suppression. To overcome this problem, lumped elements are utilized to realize harmonic suppression without degrading passband performance. It is found from theoretical analysis that at even-order harmonic frequencies, the lumped elements could not only decrease the resonator Q and dissipate RF power, but also control even-order impedance and cause mismatching at filter input/output ports. Both of the factors help reject even-order harmonics. Meanwhile, the features at fundamental resonant frequencies are nearly not affected by these elements, indicating harmonic suppression could be achieved without affecting passband performance. This property is experimentally verified by comparing the responses of tunable bandpass filters with and without harmonic suppression. Finally, a harmonic-suppressed tunable bandpass filter with constant bandwidth and passband shape is designed. A novel input and output coupling structure with a bandpass response is employed to maintain constant bandwidth and help reject both even- and odd-order harmonics. For each tuning state, two transmission zeros are created near the passband, ensuring high selectivity.