Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of Tangible User Interfaces on Designers' Spatial Cognition

ABSTRACT Most studies on tangible user interfaces for the tabletop design systems are being undertaken from a technology viewpoint. Although there have been studies that focus on the development of new interactive environments employing tangible user interfaces for designers, there is a lack of evaluation with respect to designers' spatial cognition. In this research we study the effects of tangible user interfaces on designers' spatial cognition to provide empirical evidence for the anecdotal views of the effect of tangible user interfaces. To highlight the expected changes in spatial cognition while using tangible user interfaces, we compared designers using a tangible user interface on a tabletop system with 3D blocks to designers using a graphical user interface on a desktop computer with a mouse and keyboard. The ways in which designers use the two different interfaces for 3D design were examined using a protocol analysis method. The result reveals that designers using 3D blocks perceived more spatial relationships among multiple objects and spaces and discovered new visuo-spatial features when revisiting their design configurations. The designers using the tangible interfaces spent more time in relocating objects to different locations to test the moves, and interacted with the external representation through large body movements implying an immersion in the design model. These two physical actions assist in designers' spatial cognition by reducing cognitive load in mental visual reasoning. Further, designers using the tangible interfaces spent more time in restructuring the design problem by introducing new functional issues as design requirements and produced more discontinuities to the design processes, which provides opportunity for reflection and modification of the design. Therefore this research shows that tangible user interfaces changes designers' spatial cognition, and the changes of the spatial cognition are associated with creative design processes.
Intraseasonal variability in sea surface height over the South China Sea

Intraseasonal sea surface height (SSH) variability and associated eddy energy in the South China Sea is studied using satellite observations and an eddy-resolving, global ocean general circulation model. In both the model hindcast and satellite observations, a conspicuous minimum of intraseasonal SSH variance is found along the continental break between the shallow shelf and deep basin. Specifically strong intraseasonal variability (ISV) exists in the following regions: on the northern continental shelf, in the Gulf of Thailand, and along two bands in the deep basin with the northern band located west of Luzon Strait and the southern one southeast of Vietnam. SSH ISV exhibits clear seasonality. During active seasons, ISV in the deep water, high-variance bands displays robust propagations in the direction of mean flow. Low correlation between observations and model hindcast suggests the importance dynamical instabilities for ISV in the deep basin, in agreement with an energetics analysis. An exception is along the Vietnam offshore jet during summer, where ISV is forced by wind curls created by Annam Cordillera. In shallow waters, especially in the Gulf of Thailand, SSH ISV is dominated by barotropic response to intraseasonal wind stress forcing. The agreement between altimetry and the model simulation in the Gulf of Thailand demonstrates the ability of satellite altimeters to observe SSH variability in shallow shelves of weak tides.
Fast and high-performance template matching method

This paper proposes a new template matching method that is robust to outliers and fast enough for real-time operation. The template and image are densely transformed in binary code form by projecting and quantizing histograms of oriented gradients. The binary codes are matched by a generic method of robust similarity applicable to additive match measures, such as Lp- and Hamming distances. The robust similarity map is computed efficiently via a proposed Inverted Location Index structure that stores pixel locations indexed by their values. The method is experimentally justified in large image patch datasets. Challenging applications, such as intra-category object detection, object tracking, and multimodal image matching are demonstrated.
“Smooth” Semiparametric Regression Analysis for Arbitrarily Censored Time‐to‐Event Data

Summary A general framework for regression analysis of time‐to‐event data subject to arbitrary patterns of censoring is proposed. The approach is relevant when the analyst is willing to assume that distributions governing model components that are ordinarily left unspecified in popular semiparametric regression models, such as the baseline hazard function in the proportional hazards model, have densities satisfying mild “smoothness” conditions. Densities are approximated by a truncated series expansion that, for fixed degree of truncation, results in a “parametric” representation, which makes likelihood‐based inference coupled with adaptive choice of the degree of truncation, and hence flexibility of the model, computationally and conceptually straightforward with data subject to any pattern of censoring. The formulation allows popular models, such as the proportional hazards, proportional odds, and accelerated failure time models, to be placed in a common framework; provides a principled basis for choosing among them; and renders useful extensions of the models straightforward. The utility and performance of the methods are demonstrated via simulations and by application to data from time‐to‐event studies.
The Effectiveness of Rambutan (Nephelium lappaceum L.) Extract in Stabilization of Sunflower Oil under Accelerated Conditions

The oxidative properties of sunflower oil supplemented with rambutan extract, (crude extract and its fractionated fraction, SF II) in comparison with synthetic antioxidant were investigated. The supplemented sunflower oils were stored under accelerated conditions for 24 days at 60 °C. For every 6-day interval, the oxidative properties of the supplemented sunflower oil were evaluated based on the following tests, namely peroxide value, p-anisidine value, Thiobarbituric Acid Reactive Substances (TBARS) assay, iodine value and free fatty acids. The total oxidation (TOTOX) values were also calculated based on the peroxide values and p-anisidine values. Rambutan extract is a potential source of antioxidant. The oxidative activities of the extracts at all concentrations were significantly (p < 0.05) higher than the control. Generally, the partially fractionated fraction was more effective than the crude extract. With a 2-year storage period at ambient temperature, the fractionated fraction of the extract, SF II at 300 ppm, was observed to work more effectively than the synthetic antioxidant, t-Tocopherol, and it possessed a protective effect comparable with butylatedhydrioxynanisole (BHA). Therefore, rambutan extract could be used as a potential alternative source of antioxidant in the oil industry or other fat-based products to delay lipid oxidation.
Fast Computation of Kernel Estimators

The computational complexity of evaluating the kernel density estimate (or its derivatives) at m evaluation points given n sample points scales quadratically as O(nm)—making it prohibitively expensive for large datasets. While approximate methods like binning could speed up the computation, they lack a precise control over the accuracy of the approximation. There is no straightforward way of choosing the binning parameters a priori in order to achieve a desired approximation error. We propose a novel computationally efficient ε-exact approximation algorithm for the univariate Gaussian kernel-based density derivative estimation that reduces the computational complexity from O(nm) to linear O(n+m). The user can specify a desired accuracy ε. The algorithm guarantees that the actual error between the approximation and the original kernel estimate will always be less than ε. We also apply our proposed fast algorithm to speed up automatic bandwidth selection procedures. We compare our method to the best available binning methods in terms of the speed and the accuracy. Our experimental results show that the proposed method is almost twice as fast as the best binning methods and is around five orders of magnitude more accurate. The software for the proposed method is available online.
Influence of Sae‐regulated and Agr‐regulated factors on the escape of Staphylococcus aureus from human macrophages

Although Staphylococcus aureus is not a classical intracellular pathogen, it can survive within phagocytes and many other cell types. However, the pathogen is also able to escape from cells by mechanisms that are only partially understood. We analysed a series of isogenic S. aureus mutants of the USA300 derivative JE2 for their capacity to destroy human macrophages from within. Intracellular S. aureus JE2 caused severe cell damage in human macrophages and could efficiently escape from within the cells. To obtain this full escape phenotype including an intermittent residency in the cytoplasm, the combined action of the regulatory systems Sae and Agr is required. Mutants in Sae or mutants deficient in the Sae target genes lukAB and pvl remained in high numbers within the macrophages causing reduced cell damage. Mutants in the regulatory system Agr or in the Agr target gene psmα were largely similar to wild‐type bacteria concerning cell damage and escape efficiency. However, these strains were rarely detectable in the cytoplasm, emphasizing the role of phenol‐soluble modulins (PSMs) for phagosomal escape. Thus, Sae‐regulated toxins largely determine damage and escape from within macrophages, whereas PSMs are mainly responsible for the escape from the phagosome into the cytoplasm. Damage of macrophages induced by intracellular bacteria was linked neither to activation of apoptosis‐related caspase 3, 7 or 8 nor to NLRP3‐dependent inflammasome activation.
Borel completeness of some ℵ₀-stable theories

We study @0-stable theories, and prove that if T either has eniDOP or is eni-deep, then its class of countable models is Borel complete. We introduce the notion of �-Borel completeness and prove that such theories are �-Borel complete. Using this, we conclude that
Regulation of isocitrate dehydrogenase by phosphorylation in Escherichia coli K-12 and a simple method for determining the amount of inactive phosphoenzyme

In several Escherichia coli K-12 strains grown on a limiting concentration of glucose, isocitrate dehydrogenase (IDH) was inactivated about 90% after cessation of growth upon exhaustion of the glucose. Such inactivation has been previously observed in several E. coli strains but not in E. coli K-12 (unless acetate was added to the bacterial culture when growth ceased). IDH was inactivated 75 to 80% in all E. coli K-12 strains we examined during growth on acetate. The inactivation involved phosphorylation of the enzyme and is considered to be a regulatory mechanism facilitating metabolite flow along the glyoxylate shunt. Phospho-IDH interacted with antibodies to enzymatically active IDH. We have devised a method, based on this immunological cross-reaction, for determining the proportions of active and inactive (phospho-) IDH in cell extracts.
A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images

Motivation: High-throughput image-based assay technologies can rapidly produce a large number of cell images for drug screening, but data analysis is still a major bottleneck that limits their utility. Quantifying a wide variety of morphological differences observed in cell images under different drug influences is still a challenging task because the result can be highly sensitive to sampling and noise. Results: We propose a graph-based approach to cell image analysis. We define graph transition energy to quantify morphological differences between image sets. A spectral graph theoretic regularization is applied to transform the feature space based on training examples of extremely different images to calibrate the quantification. Calibration is essential for a practical quantification method because we need to measure the confidence of the quantification. We applied our method to quantify the degree of partial fragmentation of mitochondria in collections of fluorescent cell images. We show that with transformation, the quantification can be more accurate and sensitive than that without transformation. We also show that our method outperforms competing methods, including neighbourhood component analysis and the multi-variate drug profiling method by Loo et al. We illustrate its utility with a study of Annonaceous acetogenins, a family of compounds with drug potential. Our result reveals that squamocin induces more fragmented mitochondria than muricin A. Availability: Mitochondrial cell images, their corresponding feature sets (SSLF and WSLF) and the source code of our proposed method are available at http://aiia.iis.sinica.edu.tw/. Contact: chunnan@iis.sinica.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online.
Managing tile drainage, subirrigation, and nitrogen fertilization to enhance crop yields and reduce nitrate loss.

Improving field-crop use of fertilizer nitrogen is essential for protecting water quality and increasing crop yields. The objective of this study was to determine the effectiveness of controlled tile drainage (CD) and controlled tile drainage with subsurface irrigation (CDS) for mitigating off-field nitrate losses and enhancing crop yields. The CD and CDS systems were compared on a clay loam soil to traditional unrestricted tile drainage (UTD) under a corn (Zea Mays L.)-soybean (Glycine Max. (L.) Merr. ) rotation at two nitrogen (N) fertilization rates (N1: 150 kg N ha(-1) applied to corn, no N applied to soybean; N2: 200 kg N ha(-1) applied to corn, 50 kg N ha(-1) applied to soybean). The N concentrations in tile flow events with the UTD treatment exceeded the provisional long-term aquatic life limit (LT-ALL) for freshwater (4.7 mg N L(-1)) 72% of the time at the N1 rate and 78% at the N2 rate, whereas only 24% of tile flow events at N1 and 40% at N2 exceeded the LT-ALL for the CDS treatment. Exceedances in N concentration for surface runoff and tile drainage were greater during the growing season than the non-growing season. At the N1 rate, CD and CDS reduced average annual N losses via tile drainage by 44 and 66%, respectively, relative to UTD. At the N2 rate, the average annual decreases in N loss were 31 and 68%, respectively. Crop yields from CDS were increased by an average of 2.8% relative to UTD at the N2 rate but were reduced by an average of 6.5% at the N1 rate. Hence, CD and CDS were effective for reducing average nitrate losses in tile drainage, but CDS increased average crop yields only when additional N fertilizer was applied.
Lack of Phospholipase A2 Receptor Increases Susceptibility to Cardiac Rupture After Myocardial Infarction

Rationale: Recent evidence indicates that the biological effects of secretory phospholipase A2 (sPLA2) cannot be fully explained by its catalytic activity. A cell surface receptor for sPLA2 (PLA2 receptor 1 [PLA2R]) and its high-affinity ligands (including sPLA2-IB, sPLA2-IIE, and sPLA2-X) are expressed in the infarcted myocardium. Objective: This study asked whether PLA2R might play a pathogenic role in myocardial infarction (MI) using mice lacking PLA2R (PLA2R–/–). Methods and Results: MI was induced by permanent ligation of the left coronary artery. PLA2R–/– mice exhibited higher rates of cardiac rupture after MI compared with PLA2R wild-type (PLA2R+/+) mice (46% versus 21%, respectively; P=0.015). PLA2R–/– mice had a 31% decrease in collagen content and a 45% decrease in the number of &agr;-smooth muscle actin–positive fibroblasts in the infarcted region compared with PLA2R+/+ mice. PLA2R was primarily found in myofibroblasts in the infarcted region. PLA2R–/– myofibroblasts were impaired in collagen-dependent migration, proliferation, and activation of focal adhesion kinase in response to sPLA2-IB. Binding of sPLA2-IB to PLA2R promoted migration and proliferation of myofibroblasts through functional interaction with integrin &bgr;1, independent of the catalytic activity of sPLA2-IB. In rescue experiments, the injection of PLA2R+/+ myofibroblasts into the infarcted myocardium prevented post-MI cardiac rupture and reversed the decrease in collagen content in the infarcted region in PLA2R–/– mice. Conclusions: PLA2R deficiency increased the susceptibility to post-MI cardiac rupture through impaired healing of the infarcted region. This might be partly explained by a reduction in integrin &bgr;1–mediated migratory and proliferative responses of PLA2R–/– myofibroblasts.
Role of rpoS in the Development of Cell Envelope Resilience and Pressure Resistance in Stationary-Phase Escherichia coli

ABSTRACT This work investigated the role of rpoS in the development of increased cell envelope resilience and enhanced pressure resistance in stationary-phase cells of Escherichia coli. Loss of both colony-forming ability and membrane integrity, measured as uptake of propidium iodide (PI), occurred at lower pressures in E. coli BW3709 (rpoS) than in the parental strain (BW2952). The rpoS mutant also released much higher concentrations of protein under pressure than the parent. We propose that RpoS-regulated functions are responsible for the increase in membrane resilience as cells enter stationary phase and that this plays a major role in the development of pressure resistance. Strains from the Keio collection with mutations in two RpoS-regulated genes, cfa (cyclopropane fatty acyl phospholipid synthase) and osmB (outer membrane lipoprotein), were significantly more pressure sensitive and took up more PI than the parent strain, with cfa having the greatest effect. Mutations in the bolA morphogene and other RpoS-regulated lipoprotein genes (osmC, osmE, osmY, and ybaY) had no effect on pressure resistance. The cytoplasmic membranes of the rpoS mutant failed to reseal after pressure treatment, and strains with mutations in o smB and nlpI (new lipoprotein) were also somewhat impaired in the ability to reseal their membranes. The cfa mutant, though pressure sensitive, was unaffected in membrane resealing, implying that the initial transient permeabilization event is critical for loss of viability rather than the failure to reseal. The enhanced pressure sensitivity of polA, recA, and xthA mutants suggested that DNA may be a target of oxidative stress in pressure-treated cells.
Power and delay optimisation in multi-hop wireless networks

In this paper, we study the optimisation problem of transmission power and delay in a multi-hop wireless network consisting of multiple nodes. The goal is to determine the optimal policy of transmission rates at various buffer and channel states in order to minimise the power consumption and the queueing delay of the whole network. With the assumptions of interference-free links and independently and identically distributed (i.i.d.) channel states, we formulate this problem using a semi-open Jackson network model for data transmission and a Markov model for channel states transition. We derive a difference equation of the system performance under any two different policies. The necessary and sufficient condition of optimal policy is obtained. We also prove that the system performance is monotonic with respect to (w.r.t.) the transmission rate and the optimal transmission rate can be either maximal or minimal. That is, the ‘bang-bang’ control is an optimal control. This optimality structure greatly reduces the problem complexity. Furthermore, we develop an iterative algorithm to find the optimal solution. Finally, we conduct the simulation experiments to demonstrate the effectiveness of our approach. We hope our work can shed some insights on solving this complicated optimisation problem.
The Hα Galaxy Survey ⋆ I. The galaxy sample, Hα narrow-band observations and star formation parameters for 334 galaxies

We discuss the selection and observations of a large sample of nearby galaxies, which we are using to quantify the star formation activity in the local Universe. The sample consists of 334 galaxies across all Hubble types from S0/a to Im and with recession velocities of between 0 and 3000 km s 1 . The basic data for each galaxy are narrow band H�+(Nii) and R-band imaging, from which we derive star formation rates, H�+(Nii) equivalent widths and surface brightnesses, and R-band total magnitudes. A strong correlation is found between total star formation rate and Hubble type, with the strongest star formation in isolated galaxies occurring in Sc and Sbc types. More surprisingly, no significant trend is found between H�+(Nii) equivalent width and galaxy R-band luminosity. More detailed analyses of the data set presented here will be described in subsequent papers.
Loss of PTEN Is Not Associated with Poor Survival in Newly Diagnosed Glioblastoma Patients of the Temozolomide Era

Introduction Pre-temozolomide studies demonstrated that loss of the tumor suppressor gene PTEN held independent prognostic significance in GBM patients. We investigated whether loss of PTEN predicted shorter survival in the temozolomide era. The role of PTEN in the PI3K/Akt pathway is also reviewed. Methods Patients with histologically proven newly diagnosed GBM were identified from a retrospective database between 2007 and 2010. Cox proportional hazards analysis was used to calculate the independent effects of PTEN expression, age, extent of resection, Karnofsky performance scale (KPS), and treatment on overall survival. Results Sixty-five percent of patients were men with median age of 63 years, and 70% had KPS≥80. Most patients (81%) received standard treatment (temozolomide with concurrent radiation). A total of 72 (47%) patients had retained PTEN expression. Median overall survival (OS) was 19.1 months (95% CI: 15.0–22.5). Median survival of 20.0 months (95% CI: 15.0–25.5) and 18.2 months (95% CI: 13.0–25.7) was observed in PTEN retained and PTEN loss patients, respectively (p = .71). PTEN loss patients were also found to have amplifications of EGFR gene more frequently than patients with retained PTEN (70.8% vs. 47.8%, p = .01). Multivariate analysis showed that older age (HR 1.64, CI: 1.02–2.63, p = .04), low KPS (HR 3.57, CI: 2.20–5.79, p<.0001), and lack of standard treatment (HR 3.98, CI: 2.38–6.65, p<.0001) yielded worse survival. PTEN loss was not prognostic of overall survival (HR 1.31, CI: 0.85–2.03, p = .22). Conclusions Loss of expression of PTEN does not confer poor overall survival in the temozolomide era. These findings imply a complex and non-linear molecular relationship between PTEN, its regulators and effectors in the tumorigenesis of glioblastoma. Additionally, there is evidence that temozolomide may be more effective in eradicating GBM cancer cells with PTEN loss and hence, level the outcomes between the PTEN retained and loss groups.