Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian Non-parametric Inference of Multimodal Topic Hierarchies

Research on multimodal data analysis such as annotated image analysis is becoming more important than ever due to the increase in the amount of data. One of the approaches to this problem is multimodal topic models as an extension of Latent Dirichlet allocation (LDA). Symmetric correspondence topic models (SymCorrLDA) are state-of-the-art multimodal topic models that can appropriately model multimodal data considering inter-modal dependencies. Incidentally, hierarchically structured categories can help users find relevant data from a large amount of data collection. Hierarchical topic models such as Hierarchical latent Dirichlet allocation (hLDA) can discover a tree-structured hierarchy of latent topics from a given unimodal data collection; however, no hierarchical topic models can appropriately handle multimodal data considering inter-modal mutual dependencies. In this paper, we propose hSymCorrLDA to discover latent topic hierarchies from multimodal data by combining the ideas of the two previously mentioned models: multimodal topic models and hierarchical topic models. We demonstrate the effectiveness of our model compared with several baseline models through experiments with three datasets of annotated images.
Abundance of narG, nirS, nirK, and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

ABSTRACT Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 × 105 to 8.9 × 105 copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 × 103 to 2.6 × 104, 7.4 × 102 to 1.4 × 103, 2.5 × 102 to 6.4 × 103, and 1.2 × 103 to 5.5 × 103, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.
Variations in tumor size and position due to irregular breathing in 4D-CT: a simulation study.

PURPOSE To estimate the position and volume errors in 4D-CT caused by irregular breathing. METHODS A virtual 4D-CT scanner was designed to reproduce axial mode scans with retrospective resorting. This virtual scanner creates an artificial spherical tumor based on the specifications of the user, and recreates images that might be produced by a 4D-CT scanner using a patient breathing waveform. 155 respiratory waveforms of patients were used to test the variability of 4D-CT scans. Each breathing waveform was normalized and scaled to 1, 2, and 3 cm peak-to-peak motion, and artificial tumors with 2 and 4 cm radius were simulated for each scaled waveform. The center of mass and volume of resorted 4D-CT images were calculated and compared to the expected values of center of mass and volume for the artificial tumor. Intrasubject variability was investigated by running the virtual scanner over different subintervals of each patient's breathing waveform. RESULTS The average error in the center of mass location of an artificial tumor was less than 2 mm standard deviation for 2 cm motion. The corresponding average error in volume was less than 4%. In the worst-case scenarios, a center of mass error of 1.0 cm standard deviation and volume errors of 30%-60% at inhale were found. Systematic errors were observed in a subset of patients due to irregular breathing, and these errors were more pronounced when the tumor volume is smaller. CONCLUSIONS Irregular breathing during 4D-CT simulation causes systematic errors in volume and center of mass measurements. These errors are small but depend on the tumor size, motion amplitude, and degree of breathing irregularity.
The Unified Parkinson's Disease Rating Scale: Validation study of the mentation, behavior, and mood section

The objective of this study was to examine the validity of the mentation, behavior, and mood items included in Part I of the Unified Parkinson's Disease Rating Scale (UPDRS) and to assess its usefulness to screen for dementia, psychosis, depression, and apathy. A consecutive series of 168 patients with PD were assessed by neurologists with the UPDRS, and by psychiatrists using a comprehensive neuropsychiatric evaluation blind to each other's ratings. ROC analysis demonstrated that a score of 2 or greater on the intellectual impairment item of the UPDRS had 60% sensitivity and 92% specificity to detect dementia, as diagnosed with DSM‐IV criteria. When a score of 23 or lower on the MMSE was included as an additional classification variable, the sensitivity increased to 85%. A score of 2 or greater on the thought disorder item had 43% sensitivity and 92% specificity to detect psychotic symptoms (delusions or hallucinations). A score of 2 or greater on the depression item had 77% sensitivity and 82% specificity to detect major depression as diagnosed with DSM‐IV criteria. Finally, a score of 2 or greater on the motivation/initiative item had 73% sensitivity and 65% specificity to detect apathy, as diagnosed with a standardized criteria. When the sample was divided into mild (i.e. Hohen‐Yahr stages I and II) versus moderate‐severe PD (i.e. Hohen‐Yahr stages III–V), findings remained unchanged, except that the UPDRS show unacceptably low accuracy to detect psychosis in mild PD. The mentation, behavior, and mood section of the UPDRS is an adequate screen for depression and apathy, and has adequate sensitivity to detect dementia when combined with the Mini‐Mental State Exam, but has low sensitivity to detect psychosis. © 2007 Movement Disorder Society
Augmented Tabletop Games Workshop

This workshop gathers researchers and practitioners interested in augmented tabletop games: physical games that include digital augmentation. Participants will compile ways of knowing for this unique research space and share their methods of research, demonstrating, where possible, through a research gaming and prototyping session. Post-workshop, we will assemble an online compendium for findings, which will include video sketches recorded during the workshop and an annotated bibliography.
COMP-assisted collagen secretion – a novel intracellular function required for fibrosis

ABSTRACT Cartilage oligomeric matrix protein (COMP) is an abundant component in the extracellular matrix (ECM) of load-bearing tissues such as tendons and cartilage. It provides adaptor functions by bridging different ECM structures. We have previously shown that COMP is also a constitutive component of healthy human skin and is strongly induced in fibrosis. It binds directly and with high affinity to collagen I and to collagen XII that decorates the surface of collagen I fibrils. We demonstrate here that lack of COMP–collagen interaction in the extracellular space leads to changes in collagen fibril morphology and density, resulting in altered skin biomechanical properties. Surprisingly, COMP also fulfills an important intracellular function in assisting efficient secretion of collagens, which were retained in the endoplasmic reticulum of COMP-null fibroblasts. Accordingly, COMP-null mice showed severely attenuated fibrotic responses in skin. Collagen secretion was fully restored by introducing wild-type COMP. Hence, our work unravels a new, non-structural and intracellular function of the ECM protein COMP in controlling collagen secretion. Highlighted Article: In addition to its known function in organizing extracellular collagen fibrils, COMP is identified as assisting in secretion of collagen. COMP-null mice display significantly attenuated skin fibrosis.
Demystifying histograms of multi-quantised DCT coefficients

JPEG compression artefacts are among the most prominent features in the forensic analysis of digital images. Here, we focus on the spectral analysis of histograms of single- and multi-quantised DCT coefficients. We present a model of the frequency response of finite-support histograms, which explains position and magnitude of characteristic quantisation peaks with reasonable precision and gives valuable insights into the formation of quantisation artefacts in general. We derive a set of practical rules for the efficient analysis of single- and multi-compressed images and discuss applications in the estimation of quantisation tables.
Listening to Theatre: The Aural Dimension of Beijing Opera

Behind its elaborate costumes and make-up, its pantomime and acrobatics, Beijing opera is above all a world created in sound - so much so that attending a performance in China is referred to as "listening to theatre," and performing itself is termed "singing theatre", rather than "acting". This study takes the reader to the heart of the Chinese art form by showing how the elements of song, speech and musical composition are used to create a performance, and how that performance is understood by its audience. It begins with a discussion of the aesthetics of traditional Beijing opera, and then explores each facet of aural performance in turn - language, music, voice and orchestra. Numerous charts and musical transcriptions help to draw a vivid picture of the variety of "languages" at play in the opera - those with vocabularies of tones and sound patterns as well as those made up of words. The emphasis throughout is on the supremacy of the performer as both composer and interpreter of the sounds heard in traditional Beijing opera.
Principal stratification: All-or-none versus partial compliance

I would like to add another perspective to that in Shrier et al [1] on the application of principal stratification [2] to all-or-none versus partial compliance. With all-or-none compliance in randomized trials [3] or all-or-none changes in availability in the paired availability design [4, 5], the assumptions needed for identifiability of the principal stratification model are often reasonable. Consider a binary outcome and suppose participants are randomized to either group 0 (assigned T0) or group 1 (assigned T1). The principal strata partition participants into pairs defined by (treatment received if in group 0, treatment received if in group 1), namely (T0,T0), (T0,T1), (T1,T0), and (T1,T1). Assuming rational decision making so no (T1,T0), persons receiving T0 in group 0 are a mixture of (T0,T0) and (T0,T1); persons receiving T1 in group 0 are (T1,T1); persons receiving T0 in group 1 are (T0,T0); and persons receiving T1 in group 1 are a mixture of (T0,T1) and (T1,T1). With the additional assumption that probabilities of outcome not depend on group for (T0, T0) and (T1, T1), one can estimate the effect of receipt of T0 versus T1 (treatment efficacy) in the principal stratum (T0,T1) for compliers, a result which can be elucidated graphically [5, 6]. In essence, this estimation peels away the irrelevant (T0,T0) and (T1,T1) strata [7] to obtain a more informative estimate of treatment efficacy (if the assumptions hold) than an intent-to-treat estimate. This identifiability of treatment efficacy in principal stratification under all-or-none compliance extends to missing binary outcomes [7, 8] and survival outcomes [9].
Robust H∞ filtering for 2D continuous systems with finite frequency specifications

ABSTRACT This paper investigates the design problem of robust H∞ filtering for uncertain two-dimensional (2D) continuous systems described by Roesser model with polytopic uncertainties and frequency domain specifications. Our aim is to design a new filter guaranteeing an H∞ performance level in specific finite frequency (FF) domains. Using the well-known generalised Kalman Yakubovich Popov lemma and homogeneous polynomially parameter-dependent matrices of arbitrary degrees, sufficient conditions for the existence of H∞ filters for different FF ranges are proposed and then unified in terms of solving a set of linear matrix inequalities. Illustrative examples are provided to show the usefulness and potential of the proposed results.
Rappelling by a humanoid robot based on transition motion generation and reliable rope manipulation

For robots to act in outdoor environments, the ability for locomotion is an important factor because it influences the range of activities. Humanoid robots are acquiring the ability for locomotion in horizontal directions so far, and the ability for vertical locomotion is now required in order to extend their range of activities further. Therefore, we propose rappelling as a method for vertical locomotion. Rappelling is a method to descend from a high place using a rope and a belay device. With this method, humanoid robots are expected to get the ability for vertical locomotion without additional actuators. In this paper, we propose a full-body motion for rappelling based on the sequential transition of the centroid position and the contact states. We also propose the reliable manipulation of a rope grasped by both hands. With the proposed methods, we conducted an experiment of rappelling with HRP2, and it could successfully descend from a height of 2m50cm in 277 seconds.
Nanocrystalline Diamond Films: Applications and Advances in Nanomedicine

Ying-Chieh Chen1,2, Don-Ching Lee1 and Ing-Ming Chiu1,3,4* 1Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 2Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, 3Department of Life Sciences, National Chung Hsing University, Taichung 4Department of Internal Medicine, The Ohio State University, Columbus 1,3Taiwan 2,4USA
Intraoperative diffusion tensor imaging predicts the recovery of motor dysfunction after insular lesions

Insular lesions remain surgically challenging because of the need to balance aggressive resection and functional protection. Motor function deficits due to corticospinal tract injury are a common complication of surgery for lesions adjacent to the internal capsule and it is therefore essential to evaluate the corticospinal tract adjacent to the lesion. We used diffusion tensor imaging to evaluate the corticospinal tract in 89 patients with insular lobe lesions who underwent surgery in Chinese PLA General Hospital from February 2009 to May 2011. Postoperative motor function evaluation revealed that 57 patients had no changes in motor function, and 32 patients suffered motor dysfunction or aggravated motor dysfunction. Of the affected patients, 20 recovered motor function during the 6–12-month follow-up, and an additional 12 patients did not recover over more than 12 months of follow-up. Following reconstruction of the corticospinal tract, fractional anisotropy comparison demonstrated that preoperative, intraoperative and follow-up normalized fractional anisotropy in the stable group was higher than in the transient deficits group or the long-term deficits group. Compared with the transient deficits group, intraoperative normalized fractional anisotropy significantly decreased in the long-term deficits group. We conclude that intraoperative fractional anisotropy values of the corticospinal tracts can be used as a prognostic indicator of motor function outcome.
3D MRI image super-resolution for brain combining rigid and large diffeomorphic registration

Most of the recent leading multiple magnetic resonance imaging (MRI) super-resolution techniques for brain are limited to rigid motion. In this study, the authors aim to develop a super-resolution technique with diffeomorphism mainly for longitudinal brain MRI data. For the images from different time slots, unpredicted deformation may occur. In previous studies, sole rigid registration or traditional non-rigid registration has been frequently used to achieve multi-plane super-resolution. However, non-rigid motion of two brains from different time slots is difficult to model, since brain contains a wealth of complex structure such as the cerebral cortex. In order to address such problem, rigid and large diffeomorphic registration has been embedded into their super-resolution framework. In addition, many previous researchers use L 2 norm to achieve super-resolution framework. In this work, L 1 norm minimisation and regularisation based on a bilateral prior are adopted. These operations ensure its robustness to the assumed model of data and noise. Their approach is evaluated using Alzheimer datasets from seven different resolutions. Results show that their reconstructions have advantages over rigid and conventional non-rigid registration-based super-resolution, in terms of the root-mean-square error and structure similarity. Furthermore, their reconstruction results improve the precision of brain automatic segmentation.
Rosiglitazone and cardiotoxicity--weighing the evidence.

The recently published meta-analysis by Nissen and Wolski,1 which suggested a significant increase in the risk of myocardial infarction associated with treatment with rosiglitazone (Avandia) and an increase of similar magnitude, albeit nonsignificant, in the risk of death from cardiovascular causes, has created a furor in the press and a quandary for physicians and their patients. Given the vagaries of meta-analyses in general and of this meta-analysis in particular — owing to the absence of primary or time-to-event data, as acknowledged both in the article and in the accompanying editorial2 — clinicians have been left uncertain as to whether rosiglitazone .
Adenovirus E1B55K Region Is Required To Enhance Cyclin E Expression for Efficient Viral DNA Replication

ABSTRACT Adenoviruses (Ads) with E1B55K mutations can selectively replicate in and destroy cancer cells. However, the mechanism of Ad-selective replication in tumor cells is not well characterized. We have shown previously that expression of several cell cycle-regulating genes is markedly affected by the Ad E1b gene in WI-38 human lung fibroblast cells (X. Rao, et al., Virology 350:418-428, 2006). In the current study, we show that the Ad E1B55K region is required to enhance cyclin E expression and that the failure to induce cyclin E overexpression due to E1B55K mutations prevents viral DNA from undergoing efficient replication in WI-38 cells, especially when the cells are arrested in the G0 phase of the cell cycle by serum starvation. In contrast, cyclin E induction is less dependent on the function encoded in the E1B55K region in A549 and other cancer cells that are permissive for replication of E1B55K-mutated viruses, whether the cells are in the S phase or G0 phase. The small interfering RNA that specifically inhibits cyclin E expression partially decreased viral replication. Our study provides evidence suggesting that E1B55K may be involved in cell cycle regulation that is important for efficient viral DNA replication and that cyclin E overexpression in cancer cells may be associated with the oncolytic replication of E1B55K-mutated viruses.
Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies

ABSTRACT This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 104 L mol−1 at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II).
A Unified Learning Framework for Memristive Neuromorphic Hardware

Realizing adaptive brain functions subserving perception, cognition, and motor behavior on biological temporal and spatial scales remains out of reach for even the fastest computers. Newly introduced memristive hardware approaches open the opportunity to implement dense, low-power synapti c memories of up to10 bits per square centimeter. Memristors have the unique property of “remembering” the past history of their stimulation in their resistive state and do not require power to maintain their memory, making them ideal candidates to implement large arrays of plastic synapses supporting le arning in neural models. Over the past decades, many learning laws have been proposed in the literature to explain how neural activity shapes synaptic connections to support ada ptive behavior. To ensure an optimal implementation of a large variety of learning laws in hardware, some general and easil y parameterized form of learning law must be designed. This general form learning equation would allow instantiation of multiple learning laws through different parameterizations, without rewiring the hardware. This paper characterizes a subset of local learning laws amenable to implementation in memristive hardware. The analyzed laws belong to four broad classes: Hebb rule derivatives with various methods f or gating learning and decay; Threshold rule variations including the covariance and BCM families; Input reconstruction-based learning rules; and Explicit temporal trace-based rules.
Recombinant Avian Infectious Bronchitis Virus Expressing a Heterologous Spike Gene Demonstrates that the Spike Protein Is a Determinant of Cell Tropism

ABSTRACT A recombinant infectious bronchitis virus (IBV), BeauR-M41(S), was generated using our reverse genetics system (R. Casais, V. Thiel, S. G. Siddell, D. Cavanagh, and P. Britton, J. Virol. 75:12359-12369, 2001), in which the ectodomain region of the spike gene from IBV M41-CK replaced the corresponding region of the IBV Beaudette genome. BeauR-M41(S) acquired the same cell tropism phenotype as IBV M41-CK in four different cell types, demonstrating that the IBV spike glycoprotein is a determinant of cell tropism.
Factors determining response to antiepileptic drugs in randomized controlled trials. A systematic review and meta‐analysis

Purpose: Because of the lack of head‐to‐head adjunctive‐therapy trials of antiepileptic drugs (AEDs) in refractory partial epilepsy, meta‐analyses of placebo‐controlled randomized controlled trials (RCTs) represent a potentially important source of evidence to guide treatment decisions. However, such indirect comparisons raise various methodologic issues that may hamper their relevance.