Miracle-dz/UniFAR-FTUs huggingface dataset:
Hydrodynamic fluctuations in quasi-two dimensional diffusion

We study diffusion of colloids on a fluid–fluid interface using particle simulations and fluctuating hydrodynamics. Diffusion on a two-dimensional interface with three-dimensional hydrodynamics is known to be anomalous, with the collective diffusion coefficient diverging like the inverse of the wavenumber. This unusual collective effect arises because of the compressibility of the fluid flow in the plane of the interface, and leads to a nonlinear nonlocal convolution term in the diffusion equation for the ensemble-averaged concentration. We extend the previous hydrodynamic theory to account for a species/color labeling of the particles, as necessary to model experiments based on fluorescent techniques. We study the magnitude and dynamics of density and color density fluctuations using a novel Brownian dynamics algorithm, as well as fluctuating hydrodynamics theory and simulation. We find that hydrodynamic coupling between a single tagged particle and collective density fluctuations leads to a reduction of the long-time self-diffusion coefficient, even for an ideal gas of non-interacting particles. This unexpected finding demonstrates that density functional theories that do not account for thermal fluctuations are incomplete even for ideal systems. Using linearized fluctuating hydrodynamics theory, we show that for diffusion on a fluid–fluid interface, nonequilibrium fluctuations of the total density are small compared to the equilibrium fluctuations, but fluctuations of color density are giant and exhibit a spectrum that decays as the inverse cubed power of the wavenumber. We confirm these predictions through Brownian dynamics simulations of diffusive mixing with two indistinguishable species. We also examine nonequilibrium fluctuations in systems with two-dimensional hydrodynamics, such as thin smectic films in vacuum. We find that nonequilibrium fluctuations are colossal and comparable in magnitude to the mean, and can be accurately modeled using numerical solvers for the nonlinear equations of fluctuating hydrodynamics.
Nutritional Assessment of Snacks and Beverages in Southeastern Virginia Daycare Centers

This study sought to determine the nutritional quality of snacks and beverages provided at licensed daycare centers of variable sizes in Southeastern Virginia. This cross-sectional study employed self-report surveys about snack offerings administered at each daycare site that agreed to participate. In addition, researchers completed an observation survey on the day of visit to observe and document the food and beverages actually served at snack time. Although many daycare directors reported serving fresh fruit and vegetables for snacks, there was a poor correlation on the offering of these healthy snacks between researchers and directors (P < .05). Researchers observed salty, caloric dense foods for snack time more frequently than fresh fruits and vegetables. These findings demonstrate the importance of improving and perhaps regulating the quality and diversity of snacks and beverages offered in childcare, as dietary amendments may prevent the development of childhood obesity.
Impact of Location Popularity on Throughput and Delay in Mobile Ad Hoc Networks

With the advent of smart portable devices and location-based applications, user's mobility pattern is found to be highly dependent on varying locations. In this paper, we analyze asymptotic throughput-delay performance of mobile ad hoc networks (MANETs) under a location popularity based scenario, where users are more likely to visit popular locations. This work provides a complementary perspective compared with previous studies on fundamental scaling laws for MANETs, mostly assuming that nodes move uniformly in the network. Specifically, we consider a cell-partitioned network model with cells of known popularity, which follows a Zipf's law distribution with popularity exponent α. We first conduct the analysis under traditional store-carry-forward paradigm, and find that location heterogeneity affects the network performance negatively, which is due to the waste of potential transmission opportunities in popular cells. Motivated by this observation, we further propose a novel store-carry-accelerate-forward paradigm to enhance the network communication, exploiting these potential transmissions. Theoretical results demonstrate that our proposed scheme outperforms all delay-capacity results obtained in conventional scheme for any α. In particular, when α = 1, it can achieve a constant capacity with an average delay of Θ(√n) (except for a polylogarithmic factor), while the delay is Θ(n) in conventional scheme. And by letting α = 0, our results can cover Neely's scaling laws. Moreover, we show that the delay-capacity tradeoff ratio satisfies ≥Θ(√n), revealing that exploiting location popularity can effectively improve the performance in MANETs.
IRWRLDA: improved random walk with restart for lncRNA-disease association prediction

In recent years, accumulating evidences have shown that the dysregulations of lncRNAs are associated with a wide range of human diseases. It is necessary and feasible to analyze known lncRNA-disease associations, predict potential lncRNA-disease associations, and provide the most possible lncRNA-disease pairs for experimental validation. Considering the limitations of traditional Random Walk with Restart (RWR), the model of Improved Random Walk with Restart for LncRNA-Disease Association prediction (IRWRLDA) was developed to predict novel lncRNA-disease associations by integrating known lncRNA-disease associations, disease semantic similarity, and various lncRNA similarity measures. The novelty of IRWRLDA lies in the incorporation of lncRNA expression similarity and disease semantic similarity to set the initial probability vector of the RWR. Therefore, IRWRLDA could be applied to diseases without any known related lncRNAs. IRWRLDA significantly improved previous classical models with reliable AUCs of 0.7242 and 0.7872 in two known lncRNA-disease association datasets downloaded from the lncRNADisease database, respectively. Further case studies of colon cancer and leukemia were implemented for IRWRLDA and 60% of lncRNAs in the top 10 prediction lists have been confirmed by recent experimental reports.
miRmine: a database of human miRNA expression profiles

Motivation: MicroRNAs (miRNAs) are small non‐coding RNAs that are involved in post‐transcriptional regulation of gene expression. In this high‐throughput sequencing era, a tremendous amount of RNA‐seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly. Results: We used 304 high‐quality microRNA sequencing (miRNA‐seq) datasets from NCBI‐SRA and calculated expression profiles for different tissues and cell‐lines. In each miRNA‐seq dataset, we found an average of more than 500 miRNAs with higher than 5x coverage, and we explored the top five highly expressed miRNAs in each tissue and cell‐line. This user‐friendly miRmine database has options to retrieve expression profiles of single or multiple miRNAs for a specific tissue or cell‐line, either normal or with disease information. Results can be displayed in multiple interactive, graphical and downloadable formats. Availability and Implementation: http://guanlab.ccmb. med.umich.edu/mirmine Contact: bharatpa@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Elasto-Plastic Failure Analysis of Composite Bolted Joints

An elasto-plastic finite element analysis of pin loaded joints in laminated composites has been investigated and comparisons made with both existing 2-D linear elastic plane stress analytical solutions and experimental results for a graphite/epoxy laminate. The finite element analysis included nonlinear material behavior after initial failure by assuming an elastic-perfectly plastic bimodular material model. Laminated plate theory was used to obtain lamina stresses and the Hill yield criterion applied in each layer to create a ply-by-ply failure analysis. The effect of including friction forces along the fastener hole interface on the stress distribution around the hole was also studied. Based upon the results, failure criteria are proposed for each of the basic failure modes, bearing, shearout and net-tension. Failure maps for each ply were developed to characterize the damage progression and identify critical failure strength and mode. For the [0i/±45j/90k] family of laminates the elasto-plastic finite element stress analysis coupled with the developed failure criteria resulted in good agreement with experimental results.
0.2 V 8T SRAM With PVT-Aware Bitline Sensing and Column-Based Data Randomization

In sub/near-threshold operation, SRAMs suffer from considerable bitline swing degradation when the data pattern of a column is skewed to `1' or `0'. The worst scenarios regarding this problem occur when the currently read SRAM cell has different data compared to the rest of the cells in the same column. In this work, we overcome this challenge by using a column-based randomization engine (CBRE). This CBRE circuit randomizes data stored to SRAM. This makes distribution of “1” and “0” in each column close to 50%, significantly increasing bitline swing. To further improve the bitline swing, we employ bitline boost biasing and dynamic bitline keeper schemes. Based on the mentioned techniques, we fabricated a 256 rows × 128 columns (32 Kb) 8T SRAM array in 65 nm CMOS technology. In our silicon measurement, the SRAM array shows successful 200 mV operation at room temperature, where energy consumption and access time are 1 pJ and 2.5 s, respectively.
Deterioration of FRP-to-Concrete Bond under Failure Loading

Characteristics of FRP-to-concrete bond are observed to deteriorate under cyclic loads. Deterioration has been observed under load conditions which result in a stress range in the bonded FRP of only 4% of the material capacity. Current design recommendations and “accepted practice” often neglect this detrimental effect. The clear effects of bond deterioration under fatigue loading are demonstrated for moderate-scale laboratory specimens and in full-scale specimens recovered from a forty-year old interstate highway bridge. The results suggest additional limit states that must be considered when even relatively small fatigue loads are present.
Strategic Teaching and Learning in Games

We show there is no uncoupled learning heuristic leading to Nash equilibrium in all finite games that a player has an incentive to adopt, that would be evolutionary stable, or that could “learn itself. ” Rather, a player has an incentive to strategically teach a learning opponent to secure at least the Stackelberg leader payoff. This observation holds even when we restrict to generic games, two-player games, potential games, games with strategic complements, or 2 × 2 games, in which learning is known to be “nice. ” It also applies to uncoupled learning heuristics leading to correlated equilibria, rationalizability, iterated admissibility, or minimal CURB sets. (JEL C73, D83)
Nutritional ecology of nominally herbivorous fishes on coral reefs

Nominally herbivorous acanthurids (surgeonfishes) and scarids (parrotfishes) have often been considered a ‘homogeneous’ functional group that consumes and digests algae. Recent work demonstrates that many of these fishes consume detritus. The objective of this study was to investigate the composition of dietary nutrients targeted by these and other fishes in terms of feeding behaviour, diet and short chain fatty acids (SCFA). We undertook a nutritional analysis of a range of species including detritivores, algivores, omnivores and planktivores from north eastern Australia. We calculated assimilation efficiencies for total protein amino acids (TAA), carbohydrate and lipid, and measured TAA in gut fluid along the intestine. Nutrients were assimilated similarly to their dietary proportions, with planktivores assimilating a high proportion of TAA, a moderate proportion of lipid and little carbohydrate. Omnivores assimilated moderate proportions of TAA and carbohydrate, and a low proportion of lipid. Algivores assimilated a low proportion of TAA and lipid, but a high proportion of carbohydrate. Detritivorous scarids and acanthurids differed significantly from algivores, assimilating a high proportion of TAA, a low proportion of carbohydrate and a moderate proportion of lipid. TAA levels in gut fluid of all species were highest in the anterior and lowest in the posterior intestine. Gut segments with highest TAA values were compared between dietary groups and followed a similar trend to TAA assimilation. Planktivores had high concentrations of TAA, while omnivores had intermediate, and algivores the lowest, concentrations. The highest gut fluid TAA concentrations were found in detritivorous scarids and acanthurids, and were significantly higher than in algivores. A significant negative correlation was found between anterior intestinal fluid TAA and posterior intestinal SCFA values. Detritivores had the highest levels of TAA but the lowest levels of SCFA. Planktivorous species had high levels of TAA and low to intermediate levels of SCFA. Omnivores had moderate levels of both TAA and SCFA. Algivores had low levels of TAA but high levels of SCFA. This indicates that there are major differences in the food resources targeted by detritivorous and algivorous fish species on coral reefs.
microRNA-199a-3p, DNMT3A, and aberrant DNA methylation in testicular cancer

It was previously demonstrated that miR-199a was downregulated in testicular germ cell tumor (TGCT), probably due to hypermethylation of its promoter. Further study found that re-expression of miR-199a in testicular cancer cells (NT2) led to suppression of cell growth, cancer migration, invasion and metastasis. More detailed analyses showed that these properties of miR-199a could be assigned to miR-199a-5p, one of its two derivatives. The biological role of the other derivative, miR-199a-3p in TGCT, remains largely uncharacterized. In this report, we identified DNA (cytosine-5)-methyltransferase 3A (DNMT3A), the de novo methyltransferase, as a direct target of miR-199a-3p using a 3′-UTR reporter assay. Transient expression of miR-199a-3p in NT2 cells led to decrease, while knocking down of miR-199a-3p in a normal human testicular cell line (HT) led to elevation, of DNMT3A2 (DNMT3A gene isoform 2) mRNA and protein levels. In clinical samples, DNMT3A2 was significantly overexpressed in malignant testicular tumor, and the expression of DNMT3A2 was inversely correlated with the expression of miR-199a-3p. However, DNMT3A did not affect miR-199a expression in NT2 cells. Further characterization of miR-199a-3p revealed that it negatively regulated DNA methylation, partly through targeting DNMT3A. Overexpression of miR-199a-3p restored the expression of APC and MGMT tumor-suppressor genes in NT2 cells by affecting DNA methylation of their promoter regions. Our studies demonstrated the deregulation of miR-199a-3p expression in TGCT may provide novel mechanistic insights into TGCT carcinogenesis and suggested a potentially therapeutic use of synthetic miR-199a-3p oligonucleotides as effective hypomethylating compounds in the treatment of TGCT.
Defense-GAN: Protecting Classifiers Against Adversarial Attacks Using Generative Models

In recent years, deep neural network approaches have been widely adopted for machine learning tasks, including classification. However, they were shown to be vulnerable to adversarial perturbations: carefully crafted small perturbations can cause misclassification of legitimate images. We propose Defense-GAN, a new framework leveraging the expressive capability of generative models to defend deep neural networks against such attacks. Defense-GAN is trained to model the distribution of unperturbed images. At inference time, it finds a close output to a given image which does not contain the adversarial changes. This output is then fed to the classifier. Our proposed method can be used with any classification model and does not modify the classifier structure or training procedure. It can also be used as a defense against any attack as it does not assume knowledge of the process for generating the adversarial examples. We empirically show that Defense-GAN is consistently effective against different attack methods and improves on existing defense strategies. Our code has been made publicly available at this https URL
Temperate forest methane sink diminished by tree emissions.

Global budgets ascribe 4-10% of atmospheric methane (CH4 ) sinks to upland soils and have assumed until recently that soils are the sole surface for CH4 exchange in upland forests. Here we report that CH4 is emitted from the stems of dominant tree species in a temperate upland forest, measured using both the traditional static-chamber method and a new high-frequency, automated system. Tree emissions averaged across 68 observations on 17 trees from May to September were 1.59 ± 0.88 μmol CH4 m-2 stem h-1 (mean ± 95% confidence interval), while soils adjacent to the trees consumed atmospheric CH4 at a rate of -4.52 ± 0.64 μmol CH4 m-2 soil h-1 (P < 0.0001). High-frequency measurements revealed diurnal patterns in the rate of tree-stem CH4 emissions. A simple scaling exercise suggested that tree emissions offset 1-6% of the growing season soil CH4 sink and may have briefly changed the forest to a net CH4 source.
Factors Influencing the Total Inpatient Pharmacy Cost at a Tertiary Hospital in Malaysia: A Retrospective Study

The steady growth of pharmaceutical expenditures is a major concern for health policy makers and health care managers in Malaysia. Our study examined the factors affecting the total inpatient pharmacy cost (TINPC) at the Universiti Kebangsaan Malaysia Medical Centre (UKMMC). In this retrospective study, we used 2011 administration electronic prescriptions records and casemix databases at UKMMC to examine the impact of sociodemographic, diagnostic, and drug variables on the TINPC. Bivariate and multivariate analyses of the factors associated with TINPC were conducted. The mean inpatient pharmacy cost per patient was USD 102.07 (SD = 24.76). In the multivariate analysis, length of stay (LOS; B = 0.349, P < .0005) and severity level III (B = 0.253, P < .0005) were the primary factors affecting the TINPC. For each day increase in the LOS and each increase of a case of severity level III, there was an increase of approximately USD 11.97 and USD 171.53 in the TINPC per year, respectively. Moreover, the number of prescribed items of drugs and supplies was positively associated with the TINPC (B = 0.081, P < .0005). Gender appears to have affected the TINPC; male patients seem to be associated with a higher TINPC than females (mean = 139.55, 95% confidence interval [CI]: 112.97-166.13, P < .001). Surgical procedures were associated with higher cost than medical cases (mean = 87.93, 95% CI: 61.00-114.85, P < .001). Malay (MYR 242.02, SD = 65.37) and Chinese (MYR 214.66, SD = 27.99) ethnicities contributed to a lower TINPC compared with Indian (MYR 613.93, SD = 98.41) and other ethnicities (MYR 578.47, SD = 144.51). A longer hospitalization period accompanied by major complications and comorbidities had the greatest influence on the TINPC.
Simulating coherent flow with cellular automaton model

At present, different viewpoints and theories are put forward on divisions and transitions of traffic states in highway, for which decide the fundamental properties of traffic flow. Coherent-moving state, among these states, was firstly proposed in Helbing's paper [1] to discuss the hypothetical steady states in mixed traffic flow in highway traffic. Since then, possible explanations on existence, stability and transition of coherent-moving state have been proposed in other research. In the paper, fast simulation and scenario reproduction in cellular automaton model are taken to test and verify those assumptions. A two-lane highway scenario with variety of vehicle parameters is built to reproduce the situation where coherent-moving phenomenon is likely to occur. At last, according to the simulation results, we bring forward our explanations on coherent-moving state which may be helpful on further study.
A 2.7-M Pixels 64-mW CMOS Image Sensor With Multicolumn-Parallel Noise-Shaping SAR ADCs

This paper presents a CMOS image sensor (CIS) utilizing a noise-shaping successive-approximation register analog-to-digital converter (SAR ADC) incorporating the delta-readout scheme. While the noise-shaping SAR ADC with a proposed two-tap passive finite-impulse response (FIR) filter improves effective resolution, the delta-readout scheme reduces its power consumption. A prototype <inline-formula> <tex-math notation="LaTeX">$1920\times 1440$ </tex-math></inline-formula> pixel CIS was fabricated in a 90-nm CIS process. A single-channel readout SAR ADC occupying an area of <inline-formula> <tex-math notation="LaTeX">${22.4}\,\,\mu \textsf {m}\times {715}\,\,\mu \text{m}$ </tex-math></inline-formula> was implemented for reading out 16 columns of pixel array, consuming <inline-formula> <tex-math notation="LaTeX">$437~\mu \text{W}$ </tex-math></inline-formula>. Owing to the proposed noise-shaping SAR ADC with oversampling ratio of 16, this paper achieves a noise reduction of 14 dB compared with the noise of a conventional SAR ADC. The delta-readout reduces the power consumption of the SAR ADC by 10% due to the high hit rate of the full high definition image format. The measured differential nonlinearity of the ADC is +0.77/ −0.54 LSB and the integral nonlinearity is +0.81/ −0.5 LSB. The prototype CIS consumes a total power of 64 mW and achieves a dynamic range of 66.5 dB and a figure of merit of <inline-formula> <tex-math notation="LaTeX">$127~\mu \text{V}\cdot $ </tex-math></inline-formula>nJ at a data rate of 138 Mpixels/s.
Mortgage Product Innovation in Advanced Economies: More Choice, More Risk 1

Abstract In many developed countries, house prices have been rising rapidly, mortgage debt has been increasing and affordability has worsened. It is in this context that the standard annuity mortgage is increasingly being supplanted by mortgages with non-standard features, such as longer terms or interest-only payments. Many of these new features aim to reduce the borrower's monthly debt service in the initial period of the loan. While these new mortgage types help households to enter owner-occupation and to vary their expenditure patterns, the long-term cost to the borrower cannot normally be less than for a standard product. Moreover, such mortgages can also be more risky: the interest-only borrower does not accumulate equity as an annuity borrower does, and loans with longer terms expose the borrower to greater risk of interest-rate or other economic shocks. As a result both borrowers pay more and the housing finance system may be more fragile. This paper brings together evidence from 13 developed countries about house prices, debt and affordability, and particularly the availability and market share of mortgages with these new features. It analyses trends over the last ten years and discusses the risks of these mortgages compared to standard annuity products.
Governing Misvalued Firms

Equity overvaluation is thought to create the potential for managerial misbehavior, while monitoring and corporate governance curb misbehavior. We combine these two insights from the literatures on misvaluation and governance to ask 'when does governance matter? ' Examining firms with standard long-run measures of corporate governance as they are shocked by plausible misvaluation, we provide consistent evidence that firm performance is impacted by governance when firms become overvalued - overvaluation causes weaker performance in poorly governed firms. Our findings imply that firm oversight is important during market booms, just when stock prices suggest all is well.