Miracle-dz/UniFAR-FTUs huggingface dataset:
Weak alignment offers new NMR opportunities to study protein structure and dynamics

Protein solution nuclear magnetic resonance (NMR) can be conducted in a slightly anisotropic environment, where the orientational distribution of the proteins is no longer random. In such an environment, the large one‐bond internuclear dipolar interactions no longer average to zero and report on the average orientation of the corresponding vectors relative to the magnetic field. The desired very weak ordering, on the order of 10−3, can be induced conveniently by the use of aqueous nematic liquid crystalline suspensions or by anisotropically compressed hydrogels. The resulting residual dipolar interactions are scaled down by three orders of magnitude relative to their static values, but nevertheless can be measured at high accuracy. They are very precise reporters on the average orientation of bonds relative to the molecular alignment frame, and they can be used in a variety of ways to enrich our understanding of protein structure and function. Applications to date have focused primarily on validation of structures, determined by NMR, X‐ray crystallography, or homology modeling, and on refinement of structures determined by conventional NMR approaches. Although de novo structure determination on the basis of dipolar couplings suffers from a severe multiple minimum problem, related to the degeneracy of dipolar coupling relative to inversion of the internuclear vector, a number of approaches can address this problem and potentially can accelerate the NMR structure determination process considerably. In favorable cases, where large numbers of dipolar couplings can be measured, inconsistency between measured values can report on internal motions.
Equal reverberance matching of running musical stimuli having various reverberation times and SPLs

This paper examines effects of listening level and reverberation time on the reverberance of running musical stimuli. A listening test was conducted which tested an anechoic music stimulus convolved with synthetic RIRs having a range of listening levels and reverberation times: in the test, subjects adjusted the reverberance of a musical stimulus (by adjusting the decay rate of an impulse response convolved with dry music) to match that of reference stimuli. In this way, we constructed equal reverberance contours as a function of sound pressure level and reverberation time. The experiment results confirm that the listening level and reverberation time both have a significant effect on reverberance: increased listening level or reverberation time leads to greater reverberance. Loudness-based predictors of reverberance outperform the conventional reverberance predictors.
Serious games: Quality characteristics evaluation framework and case study

The use of serious games in teaching and training is increasing; however, there is a lack of suitable evaluation frameworks to evaluate the different quality characteristics in the serious games. This study highlights previous evaluation frameworks and then emphasizes different quality characteristics that have been used in evaluating serious games. The study divided the discussed quality characteristics into primary and secondary characteristics based on their use in the literature. The study proposes a framework to evaluate several dimensions of serious games by choosing and combining appropriate quality characteristics. Robocode a programming serious game was used as a case study in which the framework has been applied to it where fifteen students in Queen's University Belfast played the game and evaluated different quality characteristics based on the proposed framework. The results showed that Robocode overall evaluation is good; however, the framework recommends changes to be applied to the game to increase the game understandability to be played by the users without the need for supervision or tutors.
Purdue e-Pubs Purdue e-Pubs

We present an n-processor and O(lo~ n)-time parallel RAM algorithm for find ing a depth-first-search tree in an n·vertex planar graph. The algorithm is based on a new n-processor algorithm for finding a cyclic separator in a pla nar graph and Smith's original parallel depth-first-search algorithm for planar graphs [Smi86].
The Possibility of mW/cm2-Class On-Chip Power Generation Using Ultrasmall Si Nanowire-Based Thermoelectric Generators

A simple structure of planar silicon nanowire (SiNW)-based thermoelectric (TE) generators (TEGs) is presented in this paper, which has the ability to sustain temperature difference along SiNW under ultrashort channel length for achieving mW/cm<sup>2</sup>-class power output from environmental heat energy. The TE performance of the proposed SiNW-based TEGs was evaluated by finite-element simulation and analytic modeling. The channel length, pad length, and the thickness of the SiO<sub>2</sub> layer were varied in the model while keeping a series of constant proportions toward finding the optimal SiNW-based TEG structure for high power generation. Based on the analysis, we demonstrated that decreasing the dimension of SiNW-based TEG is beneficial to improving the total TE power density. A very high power density of 4.2 mW/cm<sup>2</sup> is possible to be achieved at SiNW length of <inline-formula> <tex-math notation="LaTeX">$0.1~\mu \text{m}$ </tex-math></inline-formula> and pad length of <inline-formula> <tex-math notation="LaTeX">$0.1~\mu \text{m}$ </tex-math></inline-formula> under a temperature difference of 5 K across the hot and cold regions. The miniaturized SiNW-based TEG has a great potential to obtain the output power density which is 100–1000 times higher than conventional planar TEGs with air cavity but has a simple structure and can easily be fabricated.
Transient analysis of a modular multilevel converter with coupled arm inductors

The influence of the coupling of the arm inductors of a modular multilevel converter has been investigated through transient simulations. In particular, positive, negative and zero coupling coefficient were considered for both steady-state and transient operating conditions. The effect of the coupling on the transient response, the capacitor voltage ripple, the circulating current, the DC short-circuit current and the switch power losses has been closely examined. The possibility to reduce either the circulating current or the DC short-circuit current has been demonstrated, opening the door to improved performances of modular multilevel converter with only minor modifications.
Clinical Information Systems as the Backbone of a Complex Information Logistics Process: Findings from the Clinical Information Systems Perspective for 2016

Summary Objective: To summarize recent research and to propose a selection of best papers published in 2016 in the field of Clinical Information Systems (CIS). Method: The query used to retrieve the articles for the CIS section of the 2016 edition of the IMIA Yearbook of Medical Informatics was reused. It again aimed at identifying relevant publications in the field of CIS from PubMed and Web of Science and comprised search terms from the Medical Subject Headings (MeSH) catalog as well as additional free text search terms. The retrieved articles were categorized in a multi-pass review carried out by the two section editors. The final selection of candidate papers was then peer-reviewed by Yearbook editors and external reviewers. Based on the review results, the best papers were then chosen at the selection meeting with the IMIA Yearbook editorial board. Text mining, term co-occurrence mapping, and topic modelling techniques were used to get an overview on the content of the retrieved articles. Results: The query was carried out in mid-January 2017, yielding a consolidated result set of 2,190 articles published in 921 different journals. Out of them, 14 papers were nominated as candidate best papers and three of them were finally selected as the best papers of the CIS field. The content analysis of the articles revealed the broad spectrum of topics covered by CIS research. Conclusions: The CIS field is multi-dimensional and complex. It is hard to draw a well-defined outline between CIS and other domains or other sections of the IMIA Yearbook. The trends observed in the previous years are progressing. Clinical information systems are more than just sociotechnical systems for data collection, processing, exchange, presentation, and archiving. They are the backbone of a complex, trans-institutional information logistics process.
17 Virtual Colonoscopy-Technical Aspects

Virtual colonoscopy (VC) is a diagnostic method enabling the generation of twodimensional and three-dimensional images of the colon and rectum from the data obtained with relevant imaging modality, usually spiral computed tomography (CT). If CT is used, the method is also called CT colonoscopy, CT colonography, or CT pneumocolon. The main advantages of the VC which support its broader application in medical practice include: limited invasiveness, improved compliance of patients and value for screening for colorectal cancer. The introduction of virtual endoscopy technique originates from the extended processing options of the data sets obtained with available imaging modalities. The Visible Human Project and related activities (Hong et al., 1996; Hong, 1997) were of key importance for development of the VC. The quality of first VC images limited the potential of the clinical use of this technique. But with next generations of the imaging equipment and advanced processing algorithms, their applicability in medical practice was established. VC may be performed with all imaging techniques which result in cross-sections of the abdominal cavity. It can be generated both from CT and magnetic resonance imaging (MRI) cross-sections. However, the CT remains the first choice imaging modality for the VC. It is required that spiral acquisition mode with overlapping reconstructions is applied. The quality of the images generated within VC techniques depends strongly on the spatial resolution obtained with imaging modality. Nowadays, multidetector computed tomography (MDCT) is commonly available and this adds to overall quality of assessment of the colon and rectum resulting from VC. The patient undergoing helical computed tomography with the intent of obtaining VC should undergo complete bowel preparation as for other procedures within abdomen, e.g. endoscopic colonoscopy. The priority is assigned to evacuation of the contents of the colon before CT. For this purpose, many agents are used including ethylene glycol electrolyte solution, magnesium citrate or oral sodium phospate. Netherless, the quality of bowel preparation for VC varies considerably between different centres (Van Uitert et al., 2008). The trend for the optimisation of the diagnostic procedures and limitation of the burden to the patient resulted also in a strategy focusing on the performing of the optical colonoscopy just after VC, if it is positive for pathological lesions in the colon, in order to avoid repetition
3D-SWIFT: a high-performance 3D-stacked wide IO DRAM

Wide IO has been standardized as a low-power, high-bandwidth DRAM for embedded system. The performance of Wide IO, however, is limited by the power constraint and unexploited fine-grained memory parallelism. In this work, we propose a novel architecture, 3D-SWIFT, that achieves high access parallelism by partitioning a memory bank into sub-banks with a fine access granularity, which takes advantage of 3D die-stacking. The power constraint is naturally eliminated by the fine-grained structure due to the reduced activation power. Moreover, we propose sub-bank autonomy and introduce corresponding management policies to enable an intelligent interface protocol. Thanks to sub-rank autonomy, the overhead of tracking huge concurrent accesses in the memory controller is significantly reduced, making our 3D-SWIFT architecture scalable for future memory systems. We evaluate our 3D-SWIFT and the results show that 3D-SWIFT can achieve 87.6% performance improvement compared to the state-of-the-art Wide IO.
Target Wake Time: Scheduled Access in IEEE 802.11ax WLANs

The increasing interest in ubiquitous networking, and the tremendous popularity gained by IEEE 802.11 WLANs in recent years, is leading to very dense deployments where high levels of channel contention may prevent meeting the increasing user demands. To mitigate the negative effects of channel contention, the TWT mechanism included in the IEEE 802.11ax amendment can have a significant role, as it provides an extremely simple but effective mechanism to schedule transmissions in time. Moreover, in addition to reducing the contention between stations, the use of TWT may also contribute to taking full advantage of other novel mechanisms in the IEEE 802.11 universe, such as multiuser transmissions, multi-AP cooperation, spatial reuse and coexistence in high-density WLAN scenarios. Overall, we believe TWT may be a first step toward a practical collision-free and deterministic access in future WLANs.
Super-Sampling with a Reservoir

We introduce an alternative to reservoir sampling, a classic and popular algorithm for drawing a fixed-size subsample from streaming data in a single pass. Rather than draw a random sample, our approach performs an online optimization which aims to select the subset that provides the best overall approximation to the full data set, as judged using a kernel two-sample test. This produces subsets which minimize the worst-case relative error when computing expectations of functions in a specified function class, using just the samples from the subset. Kernel functions are approximated using random Fourier features, and the subset of samples itself is stored in a random projection tree. The resulting algorithm runs in a single pass through the whole data set, and has a per-iteration computational complexity logarithmic in the size of the subset. These "super-samples" subsampled from the full data provide a concise summary, as demonstrated empirically on mixture models and the MNIST dataset.
Integrating Non-Linguistic Events into Discourse Structure

Interpreting an utterance sometimes depends on the presence and nature of non-linguistic actions. In this paper, we motivate and develop a semantic model of embodied interaction in which the contribution that non-linguistic events make to the content of the interaction is dependent on their rhetorical connections to other actions, both linguistic and non-linguistic. We support our claims with concrete examples from a corpus of online chats, comparing annotations of the linguistic-only content against annotations in which non-linguistic events in the context are taken into account.
Melatonin partially protects 661W cells from H2O2-induced death by inhibiting Fas/FasL-caspase-3

Purpose Previous studies have shown that melatonin (MEL) signaling is involved in the modulation of photoreceptor viability during aging. Recent work by our laboratory suggested that MEL may protect cones by modulating the Fas/FasL-caspase-3 pathway. In this study, we first investigated the presence of MEL receptors (MT1 and MT2) in 661W cells, then whether MEL can prevent H2O2-induced cell death, and last, through which pathway MEL confers protection. Methods The mRNA and proteins of the MEL receptors were detected with quantitative PCR (q-PCR) and immunocytochemistry, respectively. To test the protective effect of MEL, 661W cells were treated with H2O2 for 2 h in the presence or absence of MEL, a MEL agonist, and an antagonist. To study the pathways involved in H2O2–mediated cell death, a Fas/FasL antagonist was used before the exposure to H2O2. Finally, Fas/FasL and caspase-3 mRNA was analyzed with q–PCR and immunocytochemistry in cells treated with H2O2 and/or MEL. Cell viability was analyzed by using Trypan Blue. Results Both MEL receptors (MT1 and MT2) were detected at the mRNA and protein levels in 661W cells. MEL partially prevented H2O2-mediated cell death (20–25%). This effect was replicated with IIK7 (a melatonin receptor agonist) when used at a concentration of 1 µM. Preincubation with luzindole (a melatonin receptor antagonist) blocked MEL protection. Kp7–6, an antagonist of Fas/FasL, blocked cell death caused by H2O2 similarly to what was observed for MEL. Fas, FasL, and caspase-3 expression was increased in cells treated with H2O2, and this effect was prevented by MEL. Finally, MEL treatment partially prevented the activation of caspase-3 caused by H2O2. Conclusions The results demonstrate that MEL receptors are present and functional in 661W cells. MEL can prevent photoreceptor cell death induced by H2O2 via the inhibition of the proapoptotic pathway Fas/FasL-caspase-3.
Boceprevir in the treatment of chronic hepatitis C virus infection

1Hepatology-Liver Transplantation Unit, Digestive Medicine Service, Hospital Universitari La Fe, and National Network Center for Hepatology and Gastroenterology Research, instituto de Salud Carlos iii, CiBeReHD Spain; 2CSiSP, Center for Public Health Research, Public Health Department, Generalitat Valenciana and Microbioloy Department/ institut Cavanilles, University of Valencia, Valencia, Spain; 3National Network Center for Biomedical Research in epidemiology and Public Health, instituto de Salud Carlos iii, CiBeReSP Spain
From east to west across the Palearctic: Phylogeography of the invasive lime leaf miner Phyllonorycter issikii (Lepidoptera: Gracillariidae) and discovery of a putative new cryptic species in East Asia

Knowing the phylogeographic structure of invasive species is important for understanding the underlying processes of invasion. The micromoth Phyllonorycter issikii, whose larvae damage leaves of lime trees Tilia spp. , was only known from East Asia. In the last three decades, it has been recorded in most of Europe, Western Russia and Siberia. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene region to compare the genetic variability of P. issikii populations between these different regions. Additionally, we sequenced two nuclear genes (28S rRNA and Histone 3) and run morphometric analysis of male genitalia to probe for the existence of cryptic species. The analysis of COI data of 377 insect specimens collected in 16 countries across the Palearctic revealed the presence of two different lineages: P. issikii and a putative new cryptic Phyllonorycter species distributed in the Russian Far East and Japan. In P. issikii, we identified 31 haplotypes among which 23 were detected in the invaded area (Europe) and 10 were found in its putative native range in East Asia (Russian Far East, Japan, South Korea and China), with only two common haplotypes. The high number of haplotypes found in the invaded area suggest a possible scenario of multiple introductions. One haplotype H1 was dominant (119 individuals, 67.2%), not only throughout its expanding range in Europe and Siberia but, intriguingly, also in 96% of individuals originating from Japan. We detected eight unique haplotypes of P. issikii in East Asia. Five of them were exclusively found in the Russian Far East representing 95% of individuals from that area. The putative new cryptic Phyllonorycter species showed differences from P. issikii for the three studied genes. However, both species are morphologically undistinguishable. They occur in sympatry on the same host plants in Japan (Sendai) and the Russian Far East (Primorsky krai) without evidence of admixture.
Estimating Riparian and Agricultural Actual Evapotranspiration by Reference Evapotranspiration and MODIS Enhanced Vegetation Index

Abstract: Dryland river basins frequently support both irrigated agriculture and riparian vegetation and remote sensing methods are needed to monitor water use by both crops and natural vegetation in irrigation districts. We developed an algorithm for estimating actual evapotranspiration (ET a ) based on the Enhanced Vegetation Index (EVI) from the Moderate Resolution Imaging Spectrometer (MODIS) sensor on the EOS-1 Terra satellite and locally-derived measurements of reference crop ET (ET o ). The algorithm was calibrated with five years of ET a data from three eddy covariance flux towers set in riparian plant associations on the upper San Pedro River, Arizona, supplemented with ET a data for alfalfa and cotton from the literature. The algorithm was based on an equation of the form ET a = ET o [a(1 − e −bEVI ) − c], where the term (1 − e −bEVI ) is derived from the Beer-Lambert Law to express light absorption by a canopy, with EVI replacing leaf area index as an estimate of the density of light-absorbing units. The resulting algorithm capably predicted ET
Dynamic language modeling using Bayesian networks for spoken dialog systems

We introduce a new framework employing statistical language models (SLMs) for spoken dialog systems that facilitates the dynamic update of word probabilities based on dialog history. In combination with traditional state-dependent SLMs, we use a Bayesian Network to capture dependencies between user goal concepts and compute accurate distributions over words that express these concepts. This allows the framework to exploit information provided by the user in previous turns to predict the value of the unobserved concepts. We evaluate this approach on a large corpus of publicly available dialogs from the CMU Let’s Go bus information system, and show that our approach significantly improves concept understanding precision over purely state-dependent SLMs.
A full power emulation platform for evaluating power semiconductors

The operation principles of the full-bridge energy recirculation and storage circuit are explored and extended to evaluate power semiconductors under both soft-switching and hard-switching conditions. Combining frequency varying and phase shifting control, the energy is able to be recirculated inside the circuit emulating the high-power conditions for device under test. With a low-power supply only compensating for system losses, the use of costly high-power supply and load is successfully avoided. As an example, an IMS-based half-bridge power module with four 30 A/650 V GaN HEMTs in parallel is evaluated by the proposed full power emulation platform. The results show a good correlation between theoretical projections, simulation and experiments.