Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular mechanisms of spatial protein quality control

Evidence is now accumulating that damaged proteins are not randomly distributed but often concentrated in microscopically visible and functionally distinct inclusion bodies. How misfolded proteins are organized into these compartments, however, is still unknown. We have recently begun to investigate stress-inducible protein quality control (PQC) bodies in yeast cells. Surprisingly, we found that protein misfolding and aggregation were not sufficient to trigger body formation under mild heat stress conditions. Rather, compartment assembly also required the concerted action of molecular chaperones, protein-sorting factors and protein-sequestration factors, thus defining a minimal machinery for spatial PQC. Expression of this machinery was limited to times of acute stress through rapid changes in mRNA abundance and a proteasomal feedback mechanism. These findings demonstrate that yeast cells can control the amount of soluble misfolded proteins through regulated phase transitions in the cytoplasm, thus allowing them to rapidly adapt to changing environmental conditions.
Emotions and user interactions with keyboard and mouse

Knowing user emotional state is crucial for building more adaptive and responsible systems. This study combines data collected in two different experiments. Emotions were inducted by situations or by movie clips, and data about user emotions were collected using Think-Aloud protocol, and two-dimensional feedback, and. In the first experiment, only mouse data were collected, at last study also keyboard data were collected. Supervised machine learning models were generated using features extracted from keyboard and mouse data. Best models predicted user emotion dimensions over 90% of accuracy. Data from the first experiment was tested on second experiment models.
Genome‐wide association study of generalized anxiety symptoms in the Hispanic Community Health Study/Study of Latinos

Although generalized anxiety disorder (GAD) is heritable and aggregates in families, no genomic loci associated with GAD have been reported. We aimed to discover potential loci by conducting a genome‐wide analysis of GAD symptoms in a large, population‐based sample of Hispanic/Latino adults. Data came from 12,282 participants (aged 18–74) in the Hispanic Community Health Study/Study of Latinos. Using a shortened Spielberger Trait Anxiety measure, we analyzed the following: (i) a GAD symptoms score restricted to the three items tapping diagnostic features of GAD as defined by DSM‐V; and (ii) a total trait anxiety score based on summing responses to all ten items. We first calculated the heritability due to common variants (h2SNP) and then conducted a genome‐wide association study (GWAS) of GAD symptoms. Replication was attempted in three independent Hispanic cohorts (Multi‐Ethnic Study of Atherosclerosis, Women's Health Initiative, Army STARRS). The GAD symptoms score showed evidence of modest heritability (7.2%; P = 0.03), while the total trait anxiety score did not (4.97%; P = 0.20). One genotyped SNP (rs78602344) intronic to thrombospondin 2 (THBS2) was nominally associated (P = 5.28 × 10−8) in the primary analysis adjusting for psychiatric medication use and significantly associated with the GAD symptoms score in the analysis excluding medication users (P = 4.18 × 10−8). However, meta‐analysis of the replication samples did not support this association. Although we identified a genome‐wide significant locus in this sample, we were unable to replicate this finding. Evidence for heritability was also only detected for GAD symptoms, and not the trait anxiety measure, suggesting differential genetic influences within the domain of trait anxiety. © 2016 Wiley Periodicals, Inc.
THUSAM at NTCIR-11 IMine Task

This paper describes our approaches and results in NTCIR11 IMine task. In 2014, we participate in subtasks for Chinese/English Subtopic Mining and Chinese Document Ranking. In Subtopic Mining subtask, we mine subtopic candidates from various resources and construct the subtopic hierarchy with several dierent strategies. In Document Ranking subtask, we rerank the result lists with HITS algorithm and then adopt a pruning exhaustive search algorithm to generate diversied result lists.
Efficient Query Specific DTW Distance for Document Retrieval with Unlimited Vocabulary

In this paper, we improve the performance of the recently proposed Direct Query Classifier (dqc). The (dqc) is a classifier based retrieval method and in general, such methods have been shown to be superior to the OCR-based solutions for performing retrieval in many practical document image datasets. In (dqc), the classifiers are trained for a set of frequent queries and seamlessly extended for the rare and arbitrary queries. This extends the classifier based retrieval paradigm to an unlimited number of classes (words) present in a language. The (dqc) requires indexing cut-portions (n-grams) of the word image and dtw distance has been used for indexing. However, dtw is computationally slow and therefore limits the performance of the (dqc). We introduce query specific dtw distance, which enables effective computation of global principal alignments for novel queries. Since the proposed query specific dtw distance is a linear approximation of the dtw distance, it enhances the performance of the (dqc). Unlike previous approaches, the proposed query specific dtw distance uses both the class mean vectors and the query information for computing the global principal alignments for the query. Since the proposed method computes the global principal alignments using n-grams, it works well for both frequent and rare queries. We also use query expansion (qe) to further improve the performance of our query specific dtw. This also allows us to seamlessly adapt our solution to new fonts, styles and collections. We have demonstrated the utility of the proposed technique over 3 different datasets. The proposed query specific dtw performs well compared to the previous dtw approximations.
Cutaneous exposure to hypoxia does not affect skin perfusion in humans

Experiments have indicated that skin perfusion in mice is sensitive to reductions in environmental O2 availability. Specifically, a reduction in skin‐surface PO2 attenuates transcutaneous O2 diffusion, and hence epidermal O2 supply. In response, epidermal HIF‐1α expression increases and facilitates initial cutaneous vasoconstriction and subsequent nitric oxide‐dependent vasodilation. Here, we investigated whether the same mechanism exists in humans.
On the closed form computation of the dynamic matrices and their differentiations

In this paper we review and extend some classic results on rigid body dynamics, in order to give a symbolic expression of the different derivatives of the matrices of the dynamic model of a general tree-structured robot. In what follows the matrices are differentiated with respect to time, state and dynamic parameters. Obviously from the derivatives of the single matrices it is possible to recover the derivatives of the direct and inverse dynamic functions and classic results like the regressor matrix. Moreover an iterative algorithm is sketched which allows to compute all these derivatives as well as the kinematics and dynamics of the robot.
Economic Gains from Educational Reform by US States

There is limited evidence justifying the economic case for state education policy. Using new measures of workers’ cognitive skills that allow for selective internal migration and foreign immigration, we provide preliminary estimates of growth regressions that incorporate worker skills. Our descriptive models show that educational achievement predicts economic growth across US states over the past four decades. Projections from our growth models show the substantial potential scope for state economic development through improving school quality. While we consider the impact of a range of educational reforms, an improvement that moves each state to the best-state level would in the aggregate yield an estimated present value of long-run gains of 8 percent of discounted future GDP.
A transmission electron microscope and X-ray diffraction study of muscovite and chlorite

Summary Single-crystal diffraction patterns produced by transmitted radiation, both X-rays and electrons, reveal varying degrees of disorder and long-range order in common phyllosilicates from several different rock types. The transmission electron micrographs and their selected-area diffraction patterns demonstrate the presence of numerous stacking faults parallel to (001) of muscovite and chlorite. Individual stacking faults can be recognized by the diffraction-contrast fringe patterns they cause, and partial dislocations can be seen where such faults terminate inside a crystal. Long-range order of muscovite explains what seemed to be spurious, high ‘background’ levels that are sometimes encountered in the analysis of rock fabrics by transmitted X-rays.
Determinants of Users’ Intention to Purchase Probability-Based Items in Mobile Social Network Games: A Case of South Korea

The goal of this paper was to identify factors that influence the purchase of probability-based items (PBIs) in mobile social network games (MSNGs). This paper introduces an extended research model based on the technology acceptance model. Statistical results from a survey of MSNG users find that factors that influence the purchase of PBIs include perceived enjoyment, perceived usefulness, perceived number of users, and perceived number of friends which are factors attributed to mobile game and social network characteristics, and also perceived desire for jackpot that is one of the major features of PBIs. We also analyzed the research model by gender to provide MSNG companies with a reference that may guide the development of PBI strategies that are targeted at genders. Males responded differently than females to some factors.
Growth of GaAs nanowires on Si (111) for photovoltaic applications

The goal of this thesis is to master the synthesis of GaAs nanowires ensembles on Si for their application in solar cells. Semiconductor nanowires present promising characteristics for photovoltaic applications: they benefit from their longitudinal high aspect ratio geometry to enhance light absorption, minimize material consumption and efficiently collect the carriers. To fully unleash their potential, the following properties have to be controlled: number density, diameter and orientation. The latter is of utmost importance to have uniform junctions and to avoid leakages/shortcuts, whereas number density and diameter allow to tune light absorption and minimize material utilization. Our nanowires have been grown by molecular beam epitaxy (MBE), a well-known technique for the high crystalline quality and atomically sharp interfaces in thin film applications. Moreover, to develop a scalable technique and to avoid any possible contamination we used a self-assembly and self-catalyzed approach, which involves only Ga and As, without any patterning of the surface. In a first place we studied the occurrence of GaAs nanowires growth for different types of silicon oxides, such as thermal oxide, native oxide and hydrogen silsesquioxane (HSQ). We determined the critical thicknesses to achieve nanowire growth and investigated the influence of surface roughness. This comparison study lead us to choose native oxide as oxide of choice for GaAs nanowires growth on Si. With this type of oxide, reproducibility and uniformity of results outpaced the others. Successively we developed a simple technique to control native oxide thickness and characterized the chemical composition and wetting. Once the behavior of the oxide properties as a function of oxide thickness was clarified we studied their influence over nanowire growth. We found that impacted the overall possibility of nanowires growth and to control their orientation with respect to the substrate. The root cause of the change in growth morphology was identified to be in the different thermal stability of the oxides with different compositions, and the wetting properties. The understanding of the influence of the surface properties over nanowires nucleation was of paramount importance to achieve reproducible, uniform and scalable growth of vertical nanowires. Once full control over the substrate was achieved, we investigated the tailoring of diameter and density by growth conditions using the self-assembly of Ga droplets. We demonstrated an approach to tailor diameter-density distribution that minimize nanowires-array reflectivity. These results give a clear pathway on how to obtain fully controlled nanowires growth in terms of diameter, density and orientation, paving the way to the development of GaAs nanowires based solar cells on Si.
The Stability of The Longley-Rice Irregular Terrain Model for Typical Problems

In this paper, we analyze the numerical stability of the popular Longley-Rice Irregular Terrain Model (ITM). This model is widely used to plan wireless networks and in simulation-validated research and hence its stability is of fundamental importance to the correctness of a large amount of work. We take a systematic approach by first porting the reference ITM implementation to a multiprecision framework and then generating loss predictions along many random paths using real terrain data. We find that the ITM is not unstable for common numerical precisions and practical prediction scenarios.
Freestanding Nanostructures via Layer‐by‐Layer Assembly

Freestanding flexible nanocomposite structures fabricated by layer‐by‐layer (LbL) assembly are promising candidates for many potential applications, such as in the fields of thermomechanical sensing, controlled release, optical detection, and drug delivery. In this article, we review recent advances in the fabrication and characterization of different types of freestanding LbL structures in air and at air/liquid and liquid/liquid interfaces, including micro‐ and nanocapsules, microcantilevers, freely suspended membranes, encapsulated nanoparticle arrays, and sealed‐cavity arrays. Several recently developed fabrication techniques, such as spin‐assisted coating, dipping, and micropatterning, make the assembly process more efficient and impart novel physical properties to the freestanding films.
Electrochemically addressable trisradical rotaxanes organized within a metal–organic framework

Significance This research paper presents a strategy for the organization of artificial molecular switches based on mechanically interlocked molecules within a porous crystalline framework. Once arranged within the pores of the framework, the electronic state of the switches can be altered by the application of an electrochemical potential. This strategy is particularly useful when it comes to integrating dynamic, stimulus-responsive, mechanically interlocked molecules with the robustness and periodicity of porous solids. The findings of the research establish proof-of-concept for the application of postsynthetic transformations of porous crystalline frameworks in the creation of solid-state molecular switches and machines. The organization of trisradical rotaxanes within the channels of a Zr6-based metal–organic framework (NU-1000) has been achieved postsynthetically by solvent-assisted ligand incorporation. Robust ZrIV–carboxylate bonds are forged between the Zr clusters of NU-1000 and carboxylic acid groups of rotaxane precursors (semirotaxanes) as part of this building block replacement strategy. Ultraviolet–visible–near-infrared (UV-Vis-NIR), electron paramagnetic resonance (EPR), and 1H nuclear magnetic resonance (NMR) spectroscopies all confirm the capture of redox-active rotaxanes within the mesoscale hexagonal channels of NU-1000. Cyclic voltammetry measurements performed on electroactive thin films of the resulting material indicate that redox-active viologen subunits located on the rotaxane components can be accessed electrochemically in the solid state. In contradistinction to previous methods, this strategy for the incorporation of mechanically interlocked molecules within porous materials circumvents the need for de novo synthesis of a metal–organic framework, making it a particularly convenient approach for the design and creation of solid-state molecular switches and machines. The results presented here provide proof-of-concept for the application of postsynthetic transformations in the integration of dynamic molecular machines with robust porous frameworks.
Two distinct phases of calcium signalling under flow.

AIMS High shear stress (HSS) can have significant impact on angiogenesis and atherosclerosis in collateral arteries near the bifurcation and curvature regions. Here, we investigate the spatiotemporal pattern of HSS-induced intracellular calcium alteration. METHODS AND RESULTS Genetically encoded biosensors based on fluorescence resonance energy transfer were targeted in the cytoplasm and the endoplasmic reticulum (ER) to visualize the subcellular calcium dynamics in bovine aortic endothelial cells under HSS (65 dyn/cm(2)). Upon HSS application, the intracellular Ca(2+) concentration ([Ca(2+)](i)) increased immediately and maintained a sustained high level, while the ER-stored calcium had a significant decrease only after 300 s. The perturbation of calcium influx across the plasma membrane (PM) by the removal of extracellular calcium or the blockage of membrane channels inhibited the early phase of [Ca(2+)](i) increase upon HSS application, which was further shown to be sensitive to the magnitudes of shear stress and the integrity of cytoskeletal support. In contrast, Src, phospholipase C(PLC), and the inositol 1,4,5-trisphosphate receptor (IP(3)R) can regulate the late phase of HSS-induced [Ca(2+)](i) increase via the promotion of the ER calcium efflux. CONCLUSION The HSS-induced [Ca(2+)](i) increase consists of two well-co-ordinated phases with different sources and mechanisms: (i) an early phase due to the calcium influx across the PM which is dependent on the mechanical impact and cytoskeletal support and (ii) a late phase originated from the ER-calcium efflux which is regulated by the Src, PLC, and IP(3)R signalling pathway. Therefore, our work presented new molecular-level insights into systematic understanding of mechanotransduction in cardiovascular systems.
Enhancement of microplasma-based water-solubilization of single-walled carbon nanotubes using gas bubbling in water

The authors have previously proposed a novel technique for the preparation of water-soluble carbon nanotubes (CNTs) using microplasma generated by a pulsed streamer discharge in water. This paper describes an improvement in the method of the microplasma-based CNT solubilization process by the use of gas bubbling in water. Oxygen, argon and nitrogen were used as bubbling gas in order to clarify the effects of the gas species on the single-walled CNT (SWCNT) solubilization efficiency. Ultraviolet–visible absorption spectra of the SWCNT suspensions revealed that the SWCNT solubility was increased by more than two times by using gas bubbling together with microplasma treatment. No significant difference was observed among the three gas species tested. Fourier transform infrared (FTIR)spectroscopy and x-ray photoelectron spectroscopy (XPS) analysis showed that the number of –OH groups, introduced on the SWCNT surface by the microplasma treatment, was increased by gas bubbling. Optical emission measurements also showed that the number of highly oxidative oxygen and hydrogen radicals, which were generated by the microplasma, was also increased by gas bubbling. These results indicate that gas bubbling has positive effects on microplasma-based SWCNT solubilization as a result of enhanced radical formation and functionalization of the SWCNT surface.
Visualizing collaboration networks implicit in digital libraries using OntoStarFish

This paper presents the design rationale and initial findings derived from preliminary usage of OntoStarFish, a visualization technique aimed at taking advantage of implicit relationships that can be inferred from large collections of documents in digital libraries. OntoStarFish makes such relationships explicit so users may visualize them and detect potential collaboration networks. Users that may be interested in exploring collaboration networks include researchers looking for partners for specific projects as well as funding agencies concerned with the strength of associations among participants of competing proposals. OntoStarFish is based upon the use of multiple fisheye views that can be placed on top of starfields, dynamic scatter plots for which each axis is determined by a lightweight ontology of attributes associated to potential collaborators.
Social Media and Patient Health Outcomes

Summary Objectives: To provide a review of the current excellent research published in the field of Consumer Health Informatics. Method: We searched MEDLINE® and WEB OF SCIENCE® databases for papers published in 2013 in relation with Consumer Health Informatics. The authors identified 16 candidate best papers, which were then reviewed by four reviewers. Results: Five out of the 16 candidate papers were selected as best papers. One paper presents the key features of a system to automate the collection of web-based social media content for subsequent semantic annotation. This paper emphasizes the importance of mining social media to collect novel data from which new findings in drug abuse research were uncovered. The second paper presents a practical method to predict how a community structure would impact the spreading of information within the community. The third paper presents a method for improving the quality of online health communities. The fourth presents a new social network to allow the monitoring of the evolution of individuals’ health status and diagnostic deficiencies, difficulties or barriers in rehabilitation. The last paper reports on teenage patients’ perception on privacy and social media. Conclusion: Selected papers not only show the value of using social media in the medical field but how to use these media to detect emergent diseases or risks, inform patients, promote disease prevention, and follow patients’ opinion on healthcare resources.
Observer Effect and Measurement Bias in Performance Analysis ; CU-CS-1042-08

To evaluate an innovation in computer systems, performance analysts measure execution time or other metrics using one or more standard workloads. The performance analyst may carefully minimize the amount of measurement instrumentation, control the environment in which measurement takes place, and repeat each measurement multiple times. Finally, the performance analyst may use statistical techniques to characterize the data. Unfortunately, even with such a responsible approach, the collected data may be misleading. This paper shows how easy it is to produce poor (and thus misleading) data for computer systems due to observer effect and measurement bias. Observer effect occurs if data collection perturbs the behavior of the system. Measurement bias occurs when a particular environment in which the measurement takes place favors some configurations over others. This paper demonstrates that observer effect and measurement bias have significant impact on performance and can lead to incorrect conclusions. These effects are large enough to easily mislead a performance analyst. Nevertheless, in our literature survey of recent PACT, CGO, and PLDI papers we found that papers rarely acknowledged or used reliable techniques to avoid observer effect or measurement bias. We describe and demonstrate techniques that help a performance analyst identify situations when they have poor quality data. These techniques are based on causality analysis and statistics which natural and social sciences routinely use to avoid the observer effect and measurement bias.