Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study transcriptional regulation by TFs. Our results reveal a notable difference in the prediction accuracy of expression levels of transcription start sites (TSSs) captured by different technologies and RNA extraction protocols. In general, the expression levels of TSSs with high CpG content are more predictable than those with low CpG content. For genes with alternative TSSs, the expression levels of downstream TSSs are more predictable than those of the upstream ones. Different TF categories and specific TFs vary substantially in their contributions to predicting expression. Between two cell lines, the differential expression of TSS can be precisely reflected by the difference of TF-binding signals in a quantitative manner, arguing against the conventional on-and-off model of TF binding. Finally, we explore the relationships between TF-binding signals and other chromatin features such as histone modifications and DNase hypersensitivity for determining expression. The models imply that these features regulate transcription in a highly coordinated manner.
Comparison of physical body growth and metabolic and reproductive endocrine functions between north and south climates of Japan in trained Thoroughbred yearling horses

ABSTRACT This study aimed to compare body growth, metabolic, and reproductive hormonal changes in trained Thoroughbred yearling horses under different climate conditions with and without light supplementation (LS). Thoroughbred yearlings raised at research centers of the Japan Racing Association in Hokkaido (north) or Miyazaki (south) were divided into control and LS groups. In the LS groups, 44 colts and 47 fillies from Hokkaido and 11 colts and 11 fillies from Miyazaki were exposed to LS with an extended photoperiod of 14.5 hr of daylight and 9.5 hr of darkness. One week before and once a month after LS, circulating total thyroxine (T4), insulin-like growth factor-I (IGF-1), prolactin (PRL), cortisol, and progesterone (P4) concentrations were measured by radioimmunoassay and fluoroimmunoassay, respectively. Growth parameters, including body weight, height, girth, and cannon bone circumferences, were measured monthly. Hair coat (HC) condition was scored. Under natural conditions, the T4 concentrations of Hokkaido yearlings tended to be higher, whereas the IGF-1 (colt) and PRL levels were significantly lower than those of yearlings in Miyazaki. Growth parameters and HC scores were lower in Hokkaido yearlings. With LS, the PRL and P4 concentrations in Hokkaido and Miyazaki were higher, and the first ovarian activity tended to be earlier than in the controls. Only LS Hokkaido yearlings showed significantly higher HC scores than the controls. Comparing the different climates among the LS yearlings, the levels of PRL and P4 and the HC scores in Hokkaido yearlings increased and reached levels similar to those in Miyazaki yearlings. The body weight and girth increment percentages of Hokkaido yearlings in January dramatically decreased and then eventually increased to levels similar to those of Miyazaki yearlings. This suggested that yearlings in naturally colder Hokkaido exhibit higher basal metabolism to maintain homeostasis. However, providing LS may help to improve growth and early development of reproductive function in Hokkaido yearlings to levels equal to those of Miyazaki horses.
A holistic mathematical modelling and simulation for cathodic delamination mechanism – a novel and an efficient approach

This paper addresses a holistic mathematical design using a novel approach for understanding the mechanism of cathodic delamination. The approach employed a set of interdependent parallel processes with each process representing: cation formation, oxygen reduction and cation transport mechanism, respectively. Novel mathematical equations have been developed for each of the processes based on the observations recorded from experimentation. These equations are then solved using efficient time-iterated algorithms. Each process consists of distinct algorithms which communicate with each other using duplex channels carrying signals. Each signal represents a distinct delamination parameter. As a result of interdependency of various processes and their parallel behaviour, it is much easier to analyse the quantitative agreement between various delamination parameters. The developed modelling approach provides an efficient and reliable prediction method for the delamination failure. The results obtained are in good agreement with the previously reported experimental interpretations and numerical results. This model provides a foundation for the future research within the area of coating failure analysis and prediction.
A Novel Pulse Measurement System by Using Laser Triangulation and a CMOS Image Sensor

This paper presents a novel, non-invasive, non-contact system to measure pulse waveforms of artery via applying laser triangulation method to detect skin surface vibration. The proposed arterial pulsation measurement (APM) system chiefly consists of a laser diode and a low cost complementary metal-oxide semiconductor (CMOS) image sensor. Laser triangulation and centroid method are combined with the Fast Fourier Transform (FFT) in this study. The shape and frequency of the arterial pulsation can be detected rapidly by using our APM system. The relative variation of the pulse at different measurement points near wrist joint is used as a prognostic guide in traditional Chinese medicine (TCM). An extensive series of experiments was conducted to evaluate the performance of the designed APM system. From experimental results, the pulse amplitude and frequency at the Chun point (related to the small intestine) of left hand showed an obvious increase after having food. In these cases, the peak to peak amplitudes and the frequencies of arterial pulsations range from 38 to 48 μm and from 1.27 to 1.35 Hz, respectively. The height of arterial pulsations on the area near wrist joint can be estimated with a resolution of better than 4 μm. This research demonstrates that applying a CMOS image sensor in designing a non-contact, portable, easy-to-use, low cost pulse measurement system is feasible. Also, the designed APM system is well suited for evaluating and pre-diagnosing the health of a human being in TCM clinical practice.
Thermophilic Coenzyme B12-Dependent Acyl Coenzyme A (CoA) Mutase from Kyrpidia tusciae DSM 2912 Preferentially Catalyzes Isomerization of (R)-3-Hydroxybutyryl-CoA and 2-Hydroxyisobutyryl-CoA

ABSTRACT The recent discovery of a coenzyme B12-dependent acyl-coenzyme A (acyl-CoA) mutase isomerizing 3-hydroxybutyryl- and 2-hydroxyisobutyryl-CoA in the mesophilic bacterium Aquincola tertiaricarbonis L108 (N. Yaneva, J. Schuster, F. Schäfer, V. Lede, D. Przybylski, T. Paproth, H. Harms, R. H. Müller, and T. Rohwerder, J Biol Chem 287:15502–15511, 2012, http://dx.doi.org/10.1074/jbc.M111.314690) could pave the way for a complete biosynthesis route to the building block chemical 2-hydroxyisobutyric acid from renewable carbon. However, the enzyme catalyzes only the conversion of the stereoisomer (S)-3-hydroxybutyryl-CoA at reasonable rates, which seriously hampers an efficient combination of mutase and well-established bacterial poly-(R)-3-hydroxybutyrate (PHB) overflow metabolism. Here, we characterize a new 2-hydroxyisobutyryl-CoA mutase found in the thermophilic knallgas bacterium Kyrpidia tusciae DSM 2912. Reconstituted mutase subunits revealed highest activity at 55°C. Surprisingly, already at 30°C, isomerization of (R)-3-hydroxybutyryl-CoA was about 7,000 times more efficient than with the mutase from strain L108. The most striking structural difference between the two mutases, likely determining stereospecificity, is a replacement of active-site residue Asp found in strain L108 at position 117 with Val in the enzyme from strain DSM 2912, resulting in a reversed polarity at this binding site. Overall sequence comparison indicates that both enzymes descended from different prokaryotic thermophilic methylmalonyl-CoA mutases. Concomitant expression of PHB enzymes delivering (R)-3-hydroxybutyryl-CoA (beta-ketothiolase PhaA and acetoacetyl-CoA reductase PhaB from Cupriavidus necator) with the new mutase in Escherichia coli JM109 and BL21 strains incubated on gluconic acid at 37°C led to the production of 2-hydroxyisobutyric acid at maximal titers of 0.7 mM. Measures to improve production in E. coli, such as coexpression of the chaperone MeaH and repression of thioesterase II, are discussed.
Repeatability of retinal thickness and volume metrics in neovascular age-related macular degeneration using the topcon 3doct-1000

Introduction: Optical coherence tomography (OCT) is a commonly used imaging modality that provides detailed cross-sectional retinal images. This has revolutionised management of neovascular age-related macular degeneration. The need for repeated anti-vascular endothelial growth factor injections has led to therapy being delivered using OCT-guided retreatment strategies with both qualitative OCT features of disease activity (e.g. macular fluid) and changes in retinal thickness as triggers for retreatment The purpose of this study is to determine the intra-session repeatability of retinal thickness and volume measurements using the Topcon 3DOCT-1000 spectral-domain optical coherence tomography (SDOCT) device in patients with neovascular age-related macular degeneration (nAMD). This is the largest study to date looking specifically at the Topcon 3DOCT-1000. Materials and Methods: Two SDOCT raster scans were performed by the same blinded observer in the same sitting in consecutive patients attending for nAMD treatment as part of standard validation of a new device. Retrospective analysis was undertaken, with retinal thickness and volume measurements automatically calculated by the onboard software for each Early Treatment of Diabetic Retinopathy Study subfield for each scan. Bland-Altman methods of analysis were used to assess repeatability. Results: Data from the 73 patients were analyzed with a mean age of 78 years (standard deviation 8). The 95% coefficient of repeatability (CR) was 64 μm and 0.050 mm3 for retinal thickness and volume respectively in the central 1 mm macular subfield. The CR did not exceed 85 μm (0.30 mm3) in any subfield. The revised CR for retinal thickness and volume for the subgroup of 37 patients with no segmentation error in the central 1 mm subfield was 53 μm and 0.050 mm3 respectively. Discussion: We report relatively modest intra-sessional repeatability of SDOCT retinal thickness and volume metrics in patients with nAMD in a clinical setting. Though useful in detecting clinical change from measurement variability in clinical practice, these results suggest the precision of macular thickness measurement does not approach the theoretical resolution of SDOCT.
The importance of aboveground–belowground interactions on the evolution and maintenance of variation in plant defense traits

Over the past two decades a growing body of empirical research has shown that many ecological processes are mediated by a complex array of indirect interactions occurring between rhizosphere-inhabiting organisms and those found on aboveground plant parts. Aboveground–belowground studies have thus far focused on elucidating processes and underlying mechanisms that mediate the behavior and performance of invertebrates in opposite ecosystem compartments. Less is known about genetic variation in plant traits such as defense as that may be driven by above- and belowground trophic interactions. For instance, although our understanding of genetic variation in aboveground plant traits and its effects on community-level interactions is well developed, little is known about the importance of aboveground–belowground interactions in driving this variation. Plant traits may have evolved in response to selection pressures from above- and below-ground interactions from antagonists and mutualists. Here, we discuss gaps in our understanding of genetic variation in plant-related traits as they relate to aboveground and belowground multitrophic interactions. When metabolic resources are limiting, multiple attacks by antagonists in both domains may lead to trade-offs. In nature, these trade-offs may critically depend upon their effects on plant fitness. Natural enemies of herbivores may also influence selection for different traits via top–down control. At larger scales these interactions may generate evolutionary “hotspots” where the expression of various plant traits is the result of strong reciprocal selection via direct and indirect interactions. The role of abiotic factors in driving genetic variation in plant traits is also discussed.
New Zealand Sauvignon blanc Distinct Flavor Characteristics: Sensory, Chemical, and Consumer Aspects

A trained sensory panel (n = 14) identified key flavors in Sauvignon blanc wines from Australia, France, New Zealand, Spain, South Africa, and the United States. Sixteen characteristics were identified and measured: sweet sweaty passion fruit, capsicum, passion fruit skin/stalk, boxwood/cat urine, grassy, mineral/flinty, citrus, bourbon, apple lolly/candy, tropical, mint, fresh asparagus, canned asparagus, stone fruit, apple and snow pea. Principal component analysis was used to describe differences among regions and countries. Sauvignon blanc wines from Marlborough, New Zealand, were described by tropical and sweet sweaty passion fruit characteristics, while French and South African Sauvignon blanc wines were described as having flinty/mineral and bourbon-like flavors. Chemical analyses of these wines also showed that wines from Marlborough had more methoxypyrazine and thiol compounds. A consumer study (n = 105) showed that New Zealanders significantly prefer New Zealand-style Sauvignon blanc.
The reproducibility of a food frequency questionnaire among controls participating in a case-control study on cancer.

This study was designed to test the reproducibility of a food frequency questionnaire used in a population-based case-control study on diet and pancreatic cancer. Repeat questionnaires covering the same time period were obtained using 63 male and female population controls, 35-79 years of age. For selected food items included in the case-control study, the attenuation of the odds ratios due to random error was estimated. Using 54 male and female population controls, 35-79 years of age, we conducted a second study to examine the agreement between original and repeat interviews when the time interval between interview and the period of interest was constant. In the first study, the median correlation coefficient was 0.72 for foods (ranging from 0.36 and 0.59 for subgroups of vegetables to 0.96 for alcoholic beverages) and 0.77 for nutrients (ranging from 0.62 for beta-carotene to 0.85 for energy and 0.91 for ethanol). In the second study, the median correlation coefficient was 0.68 for foods (ranging from 0.28 for eggs to 0.87 for alcoholic beverages) and 0.75 for nutrients (ranging from 0.48 for beta-carotene to 0.76 for energy). We conclude that for most items the agreement between original and repeat estimates was moderate (r > 0.50) to high (r > 0.70). Moderate agreement was found for 28 of 33 food items (85%) and for all 21 nutrient items (100%) and high agreement for 19 of 33 of food items (56%) and 15 of 21 nutrient items (71%). In the second study, agreement was somewhat lower but closely paralleled the results of the first study. On average, random error presumably attenuated most of the observed diet-cancer relationships only moderately; i.e., an observed odds ratio of 1.5 and a correlation coefficient of 0.70 yield an unattenuated odds ratio of 2.1.
Evaluation of performance and design of GFRP dowels in jointed plain concrete pavement – part 2: numerical simulation and design considerations

The article presents a numerical investigation using three-dimensional finite element analysis (FEA) to compare the performance of glass fibre reinforced polymer (GFRP) and steel dowel bars as load transfer devices across the transverse joints of jointed plain concrete pavements (JPCP). The FEA model used concrete damaged plasticity formulation to characterise the concrete pavement; elastic, transversely isotropic material characteristics were assumed for the GFRP dowels and classical metal plasticity formulation was used for the steel dowels. The numerical results were validated with the experimental results, and a good agreement was achieved. The results showed less stress concentration in the concrete underneath the GFRP dowels (38 mm diameter) compared with the steel dowels (25 mm diameter) of similar flexural rigidity. Finally, on the basis of a detailed parametric study, design considerations for the GFRP dowels in JPCP are suggested.
Infection in the pathogenesis and course of chronic obstructive pulmonary disease.

New molecular, cellular, and immunologic techniques used to study host–pathogen interactions have led to a reexamination of the role of infection in chronic obstructive pulmonary disease (COPD). There is now considerable evidence that infection plays a major role in the pathogenesis and clinical course of COPD. A vicious circle of infection and inflammation is thought to lead to exacerbations of the disease.
Recent Deceleration of the Ice Elevation Change of Ecology Glacier (King George Island, Antarctica)

Glacier change studies in the Antarctic Peninsula region, despite their importance for global sea level rise, are commonly restricted to the investigation of frontal position changes. Here we present a long term (37 years; 1979–2016) study of ice elevation changes of the Ecology Glacier, King George Island ( 62 ∘ 11 ′ S, 58 ∘ 29 ′ W). The glacier covers an area of 5.21 km 2 and is located close to the H. Arctowski Polish Antarctic Station, and therefore has been an object of various multidisciplinary studies with subject ranging from glaciology, meteorology to glacial microbiology. Hence, it is of great interest to assess its current state and put it in a broader context of recent glacial change. In order to achieve that goal, we conducted an analysis of archival cartographic material and combined it with field measurements of proglacial lagoon hydrography and state-of-art geodetic surveying of the glacier surface with terrestrial laser scanning and satellite imagery. Overall mass loss was largest in the beginning of 2000s, and the rate of elevation change substantially decreased between 2012–2016, with little ice front retreat and no significant surface lowering. Ice elevation change rate for the common ablation area over all analyzed periods (1979–2001–2012–2016) has decreased from −1.7 ± 0.4 m/year in 1979–2001 and −1.5 ± 0.5 m/year in 2001–2012 to −0.5 ± 0.6 m/year in 2012–2016. This reduction of ice mass loss is likely related to decreasing summer temperatures in this region of the Antarctic Peninsula.
Biodegradable microspheres as carriers for native superoxide dismutase and catalase delivery

The purpose of this research was to encapsulate superoxide dismutase (SOD) and catalase (CAT) in biodegradable microspheres (MS) to obtain suitable sustained protein delivery. A modified water/oil/water double emulsion method was used for poly(D,L-lactide-co-glycolide) (PLGA) and poly(D,L-lactide) PLA MS preparation co-encapsulating mannitol, trehalose, and PEG400 for protein stabilization. Size, morphology, porosity, mass loss, mass balance, in vitro release and in vitro activity were assessed by using BCA protein assay, scanning electron microscopy, BET surface area, and particle-sizing techniques. In vitro activity retention within MS was evaluated by nicotinammide adenine dinucleotide oxidation and H2O2 consumption assays. SOD encapsulation efficiency resulted in 30% to 34% for PLAMS and up to 51% for PLGA MS, whereas CAT encapsulation was 34% and 45% for PLGA and PLAMS, respectively. All MS were spherical with a smooth surface and low porosity. Particle mean diameters ranged from 10 to 17 μm. CAT release was prolonged, but the results were incomplete for both PLA and PLGA MS, whereas SOD was completely released from PLGA MS in a sustained manner after 2 months. CAT results were less stable and showed a stronger interaction than SOD with the polymers. Mass loss and mass balance correlated well with the release profiles. SOD and CAT in vitro activity was preserved in all the preparations, and SOD was better stabilized in PLGA MS. PLGA MS can be useful for SOD delivery in its native form and is promising as a new depot system.
Collision Detection and Analysis in a Physically Based Simulation

We consider the geometric support in detecting and analyzing collisions and contact between arbitrarily shaped polyhedral objects for a physically based simulation. The contact detection is formulated as a static collisiondetection problem in three-dimensional space. We address both robustness and efficiency of the problem, and show how both can be achieved by using the brep-index data structure.
Semantic systematicity and context in connectionist networks

A bstract . Fodor and Pylyshyn argued that connectionist models could not be used to exhibit and explain a phenomenon that they termed systematicity, and which they explained by possession of composition syntax and semantics for mental representations and structure sensitivity of mental processes. This inability of connectionist models, they argued, was particularly serious since it meant that these models could not be used as alternative models to classical symbolic models to explain cognition. In this paper, a connectionist model is used to identify some properties which collectively show that connectionist networks supply means for accomplishing a stronger version ofsystematicity than Fodor and Pylyshyn opted for. It is argued that 'context-dependent systematicity' is achievable within a connectionist framework. The arguments put forward rest on a particular formulation of content and context of connectionist representation, firmly and technically based on connectionist primitives in a learning environment. The perspective is motivated by the fundamental differences between the connectionist and classical architectures, in terms of prerequisites, lower-level functionality and inherent constraints. The claim is supported by a set of experiments using a connectionist architecture that demonstrates both an ability of enforcing, what Fodor and Pylyshyn term systematic and nonsystematic processing using a single mechanism, and how novel items can be handled without prior classification. The claim relies on extended learning feedback which enforces representational context dependence.
On a parametric family of Thue inequalities over function fields

Abstract In this paper we completely solve a family of Thue inequalities defined over the field of functions $\mathbb{C}(T)$, namely deg (X4−4cX3Y+(6c+2)X2Y2+4cXY3+Y4) ≤ deg c, where the solutions x,y come from the ring $\mathbb{C}\left[ T\right] $ and the parameter $c\in \mathbb{C}\left[ T\right] $ is some non-constant polynomial.
Clustering web video search results with convolutional neural networks

Convolutional Neural Networks (CNNs) have been established as a powerful class of models for image recognition problems giving state-of-the-art results on recognition, detection, segmentation, classification and retrieval. Encouraged by these results, we develop our previous work [14] by implementing deep neural network architecture for extracting and representing visual features to improve the clustering quality of web video search results. Experiments were conducted on a dataset published in [14]. This dataset includes 1580 videos from 18 queries issued to the YouTube search engine. Our method exhibits significant performance improvements over the previously published result evaluated by Entropy measure (23.27% vs. 39.46%) and Purity measure (77.09% vs. 61.50%).