Miracle-dz/UniFAR-FTUs huggingface dataset:
OsASR2 regulates the expression of a defence‐related gene, Os2H16, by targeting the GT‐1 cis‐element

Summary The GT‐1 cis‐element widely exists in many plant gene promoters. However, the molecular mechanism that underlies the response of the GT‐1 cis‐element to abiotic and biotic stresses remains elusive in rice. We previously isolated a rice short‐chain peptide‐encoding gene, Os2H16, and demonstrated that it plays important roles in both disease resistance and drought tolerance. Here, we conducted a promoter assay of Os2H16 and identified GT‐1 as an important cis‐element that mediates Os2H16 expression in response to pathogen attack and osmotic stress. Using the repeated GT‐1 as bait, we characterized an abscisic acid, stress and ripening 2 (ASR2) protein from yeast‐one hybridization screening. Sequence alignments showed that the carboxy‐terminal domain of OsASR2 containing residues 80–138 was the DNA‐binding domain. Furthermore, we identified that OsASR2 was specifically bound to GT‐1 and activated the expression of the target gene Os2H16, as well as GFP driven by the chimeric promoter of 2 × GT‐1‐35S mini construct. Additionally, the expression of OsASR2 was elevated by pathogens and osmotic stress challenges. Overexpression of OsASR2 enhanced the resistance against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani, and tolerance to drought in rice. These results suggest that the interaction between OsASR2 and GT‐1 plays an important role in the crosstalk of the response of rice to biotic and abiotic stresses.
Documentation of Flexible Business Processes - A Healthcare Case Study

In many industries, such as manufacturing and logistics, semi-formal process models have become a common means to reason and communicate about business processes. However, in a dynamic and flexible environment the suitability of semiformal process models as an instrument of process documentation may be challenged. Hospital processes are typical examples of business processes that are characterized by both the existence of well-defined procedures and the need for operational flexibility. This research investigates the current practice of process documentation in healthcare by means of a case study in a German hospital. We aim at getting an understanding of how flexible processes may be documented to give medical staff effective guidance and how this documentation has to be managed in order to provide value in everyday routine. On the basis of our findings we give suggestions on how to effectively implement process documentations in similar settings.
Trust Needs Touch: Understanding the Building of Trust through Social Presence

Trust is gaining in importance in today’s digital world where interactions become more and more impersonal. In this context, many studies show that social presence, i.e. the feeling of human contact, has a positive effect on the formation of trust. However, the theoretical explanation of the relationship is still somewhat unexplored in the IS domain. In this study, we draw on psychology literature and derive a comprehensive framework to conceptualize and explain the relationship in detail. Particularly, we identify four mechanisms that were not yet explicated by IS research. Using the developed framework as a structuring device, we then carry out a structured literature review in the IS domain to identify existing studies and their theoretical focus as well as to point out research gaps. We are able to show that there is much more to the relationship between social presence and trust than the IS domain has yet recognized.
Adjuvant use of melatonin for treatment of fibromyalgia

Abstract: Fibromyalgia syndrome (FMS) is a chronic musculoskeletal disorder characterized by generalized muscular pain accompanied by fatigue and tenderness at specific anatomic sites called tender points. Although preliminary evidence indicates that melatonin may be effective in treating the pain associated with FMS, no definitive evidence supports this claim. This study was designed to evaluate the significance of using different doses of melatonin, alone or in combination with fluoxetine for the management of FMS. A double‐blind, placebo‐controlled clinical study was performed on 101 patients (95 women and 6 men) who fulfilled the criteria of the American College of Rheumatology (ACR) of FMS. The patients were randomized into four groups: group A (24 patients) treated with 20 mg/day fluoxetine alone; group B (27 patients) treated with melatonin 5 mg alone; group C (27 patients) treated with 20 mg fluoxetine plus 3 mg melatonin; group D (23 patients) treated with 20 mg fluoxetine plus 5 mg melatonin. Both drugs were given once daily in the morning and night time, respectively, for 8 wk. Each patient was clinically evaluated through direct interview with the patients using the Fibromyalgia Impact Questionnaire (FIQ) at zero time and after 8 wk. Using melatonin (3 mg or 5 mg/day) in combination with 20 mg/day fluoxetine resulted in significant reduction in both total and different components of FIQ score compared to the pretreatment values. In conclusion, administration of melatonin, alone or in a combination with fluoxetine, was effective in the treatment of patients with FMS.
Variations in mid-latitude North Atlantic surface water properties during the mid-Brunhes (MIS 9–14) and their implications for the thermohaline circulation

Abstract. Stable isotope and ice-rafted debris records from three core sites in the mid-latitude North Atlantic (IODP Site U1313, MD01-2446, MD03-2699) are combined with records of ODP Sites 1056/1058 and 980 to reconstruct hydrographic conditions during the middle Pleistocene spanning Marine Isotope Stages (MIS) 9–14 (300–540 ka). Core MD03-2699 is the first high-resolution mid-Brunhes record from the North Atlantic's eastern boundary upwelling system covering the complete MIS 11c interval and MIS 13. The array of sites reflect western and eastern basin boundary current as well as north to south transect sampling of subpolar and transitional water masses and allow the reconstruction of transport pathways in the upper limb of the North Atlantic's circulation. Hydrographic conditions in the surface and deep ocean during peak interglacial MIS 9 and 11 were similar among all the sites with relative stable conditions and confirm prolonged warmth during MIS 11c also for the mid-latitudes. Sea surface temperature (SST) reconstructions further reveal that in the mid-latitude North Atlantic MIS 11c is associated with two plateaus, the younger one of which is slightly warmer. Enhanced subsurface northward heat transport in the eastern boundary current system, especially during early MIS 11c, is denoted by the presence of tropical planktic foraminifer species and raises the question how strongly it impacted the Portuguese upwelling system. Deep water ventilation at the onset of MIS 11c significantly preceded surface water ventilation. Although MIS 13 was generally colder and more variable than the younger interglacials the surface water circulation scheme was the same. The greatest differences between the sites existed during the glacial inceptions and glacials. Then a north – south trending hydrographic front separated the nearshore and offshore waters off Portugal. While offshore waters originated from the North Atlantic Current as indicated by the similarities between the records of IODP Site U1313, ODP Site 980 and MD01-2446, nearshore waters as recorded in core MD03-2699 derived from the Azores Current and thus the subtropical gyre. Except for MIS 12, Azores Current influence seems to be related to eastern boundary system dynamics and not to changes in the Atlantic overturning circulation.
Design and implementation of smart solar LED street light

This paper proposes energy efficient of smart street lighting system using low cost microcontroller based Arduino. The main objective is to design energy efficient smart streetlight for energy conservation in existing streetlights of rural area, urban area and exclusively for smart cities. The system consists of LED luminaire, LED driver, PV panel, charge controller light sensor, motion sensor, Arduino. The smart streetlight is controlled on the basis of traffic on road and day/night time [8]. The system is programmed to automatically turn off during the hours of daylight and only operate during the night and heavy raining or bad weather. Many times we see that street lights are remain switched ON even during day time, this is total of wastes of electricity while India is facing lack of electricity. Another problem is the traditional street lamp e.g. Sodium vapour, Metal halide, Incandescent, Fluorescent lamps consumes more power as compared to new advanced Led Lights. Streetlights can be operated free of cost by using automatic controlled, self-powered, efficient solar LED street light.
Obstacle Detection System Based on Stereo Vision and a Structured Light

Obstacle detection is a crucial issue for pilotless device guidance function and it has to be performed with high reliability to avoid any potential collision with the front object. The vision-based obstacle detection systems are regarded perfect for this purpose because they require little on all kind of condition. In this paper, an obstacle detection system using stereo vision sensors and structured light is developed. This system realizes rapid feature matching and high precision measurement distance with the help of structured light, avoiding the time-consuming of the initial corresponding pairs. After the initial detection, the system executes the tracking light strip algorithm for the obstacles. The proposed system can detect a front obstacle in vision field and obtain the size of obstacle. The proposed obstacle detection system is set up and its performance is verified experimentally
Globally Variance-Constrained Sparse Representation and Its Application in Image Set Coding

Sparse representation leads to an efficient way to approximately recover a signal by the linear composition of a few bases from a learnt dictionary based on which various successful applications have been achieved. However, in the scenario of data compression, its efficiency and popularity are hindered. It is because of the fact that encoding sparsely distributed coefficients may consume more bits for representing the index of nonzero coefficients. Therefore, introducing an accurate rate constraint in sparse coding and dictionary learning becomes meaningful, which has not been fully exploited in the context of sparse representation. According to the Shannon entropy inequality, the variance of Gaussian distributed data bound its entropy, indicating the actual bitrate can be well estimated by its variance. Hence, a globally variance-constrained sparse representation (GVCSR) model is proposed in this paper, where a variance-constrained rate term is introduced to the optimization process. Specifically, we employ the alternating direction method of multipliers (ADMMs) to solve the non-convex optimization problem for sparse coding and dictionary learning, both of them have shown the state-of-the-art rate-distortion performance for image representation. Furthermore, we investigate the potential of applying the GVCSR algorithm in the practical image set compression, where the optimized dictionary is trained to efficiently represent the images captured in similar scenarios by implicitly utilizing inter-image correlations. Experimental results have demonstrated superior rate-distortion performance against the state-of-the-art methods.
Viewport-aware adaptive 360° video streaming using tiles for virtual reality

360° video is attracting an increasing amount of attention in the context of Virtual Reality (VR). Owing to its very high-resolution requirements, existing professional streaming services for 360° video suffer from severe drawbacks. This paper introduces a novel end-to-end streaming system from encoding to displaying, to transmit 8K resolution 360° video and to provide an enhanced VR experience using Head Mounted Displays (HMDs). The main contributions of the proposed system are about tiling, integration of the MPEG-Dynamic Adaptive Streaming over HTTP (DASH) standard, and viewport-aware bitrate level selection. Tiling and adaptive streaming enable the proposed system to deliver very high-resolution 360° video at good visual quality. Further, the proposed viewport-aware bitrate assignment selects an optimum DASH representation for each tile in a viewport-aware manner. The quality performance of the proposed system is verified in simulations with varying network bandwidth using realistic view trajectories recorded from user experiments. Our results show that the proposed streaming system compares favorably compared to existing methods in terms of PSNR and SSIM inside the viewport.
Limits on information transduction through amplitude and frequency regulation of transcription factor activity

Signaling pathways often transmit multiple signals through a single shared transcription factor (TF) and encode signal information by differentially regulating TF dynamics. However, signal information will be lost unless it can be reliably decoded by downstream genes. To understand the limits on dynamic information transduction, we apply information theory to quantify how much gene expression information the yeast TF Msn2 can transduce to target genes in the amplitude or frequency of its activation dynamics. We find that although the amount of information transmitted by Msn2 to single target genes is limited, information transduction can be increased by modulating promoter cis-elements or by integrating information from multiple genes. By correcting for extrinsic noise, we estimate an upper bound on information transduction. Overall, we find that information transduction through amplitude and frequency regulation of Msn2 is limited to error-free transduction of signal identity, but not signal intensity information. DOI: http://dx.doi. org/10.7554/eLife.06559. 001
$k$-Distinct In- and Out-Branchings in Digraphs

An out-branching and an in-branching of a digraph $D$ are called $k$-distinct if each of them has $k$ arcs absent in the other. Bang-Jensen, Saurabh and Simonsen (2016) proved that the problem of deciding whether a strongly connected digraph $D$ has $k$-distinct out-branching and in-branching is fixed-parameter tractable (FPT) when parameterized by $k$. They asked whether the problem remains FPT when extended to arbitrary digraphs. Bang-Jensen and Yeo (2008) asked whether the same problem is FPT when the out-branching and in-branching have the same root. By linking the two problems with the problem of whether a digraph has an out-branching with at least $k$ leaves (a leaf is a vertex of out-degree zero), we first solve the problem of Bang-Jensen and Yeo (2008). We then develop a new digraph decomposition called the rooted cut decomposition and using it we prove that the problem of Bang-Jensen et al. (2016) is FPT for all digraphs. We believe that the \emph{rooted cut decomposition} will be useful for obtaining other results on digraphs.
Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

Objective To evaluate the potential for diagnosing colorectal cancer (CRC) from faecal metagenomes. Design We performed metagenome-wide association studies on faecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls. Results Besides confirming known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with CRC, we found significant associations with several species, including Parvimonas micra and Solobacterium moorei. We identified 20 microbial gene markers that differentiated CRC and control microbiomes, and validated 4 markers in the Danish cohort. In the French and Austrian cohorts, these four genes distinguished CRC metagenomes from controls with areas under the receiver-operating curve (AUC) of 0.72 and 0.77, respectively. qPCR measurements of two of these genes accurately classified patients with CRC in the independent Chinese cohort with AUC=0.84 and OR of 23. These genes were enriched in early-stage (I–II) patient microbiomes, highlighting the potential for using faecal metagenomic biomarkers for early diagnosis of CRC. Conclusions We present the first metagenomic profiling study of CRC faecal microbiomes to discover and validate microbial biomarkers in ethnically different cohorts, and to independently validate selected biomarkers using an affordable clinically relevant technology. Our study thus takes a step further towards affordable non-invasive early diagnostic biomarkers for CRC from faecal samples.
Maximum a posteriori estimation for radar angular super-resolution

Angular super-resolution performance is the key problem in the field of radar imaging. In this paper, we propose an approach to radar angular super-resolution through deconvolution, which is able to increase the resolution of radar image beyond the limitation of system parameters. It relies on the Bayesian formulation approach that enables to incorporate the prior information about the system and the statistical characteristics of scene. We first formulate the radar angular superresolution problem as an linear inverse problem and then convert it to a maximum a posterior (MAP) task using Bayesian theory. We then solve the MAP problem in a convex optimization framework using a shrinkage based iterative procedure, leading to algorithm that guarantees the solution to converge the global maximizer of an associated MAP criterion. Numerical experiments with synthetic data demonstrate the performance of proposed angular super-resolution algorithm.
Interior Penalty Discontinuous Galerkin Method for Magnetostatic Field Problems in Two Dimensions

An interior penalty discontinuous Galerkin method for solving 2-D magnetostatic field problems using the magnetic vector potential <inline-formula> <tex-math notation="LaTeX">${A}$ </tex-math></inline-formula> is presented. The use of the <inline-formula> <tex-math notation="LaTeX">${A}$ </tex-math></inline-formula>-formulation in two dimensions results in a second-order elliptic boundary value problem. Due to the proposed method, the scheme is symmetric and the resulting mass matrix is block diagonal, whereas each block belongs to one element of the triangulation. The applicability of the method is demonstrated by solving a simple 2-D C-shaped ferromagnetic material with a coil surrounding one part of the magnetic yoke. Thereby, the permeability of the material is supposed to be homogeneous and isotropic. The solution <inline-formula> <tex-math notation="LaTeX">${A}$ </tex-math></inline-formula> and the resulting field quantities are compared with the standard finite element analysis.
Young Women in the UAE Have Higher Incidence of HER2 Positive Breast Cancer

To the Editor: Breast cancer is a heterogeneous disease with variable biological behaviors, characterized by a wide spectrum of clinical, pathological, and molecular characteristics that comprise a number of recognized biological subtypes (1). The expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) is affected by multiple factors. Numerous studies, mostly from the west, have demonstrated variable marker expressions and different breast cancer characteristics among different racial groups (2–4). Studies have shown that black women are more likely to have ER/PR negative and triple negative (TN) tumors than white women, although white women are more likely to have ER+/ PR+/HER2 tumors compared to black women (2,3,5). This hormone receptor status has an important therapeutic and prognostic value in breast cancer. The United Arab Emirates (UAE) is a young multiethnic population consisting of 20% nationals and 80% non nationals (6). UAE women come from diverse ethnic backgrounds such as the Arabian gulf region, mediterranean region, Middle East, Iran, Indian subcontinent, and far east Asia (7). We reviewed the electronic medical records of 192 breast cancer patients who were diagnosed, treated or referred to our breast care center in the UAE, Tawam Hospital, from April 2008 to May 2009. Our analysis (Table 1) indicated that 24.0% of our cancer patients were diagnosed at age <40. It is not clear whether our finding was due to the fact that UAE’s population has high percentage of young women or whether it was due to ethnic predisposition. However, we believe that this was a reflection of the younger demographic profile in the Arab population as demonstrated by Freedman et al. (8). The overall incidence of ER positive, PR positive, HER2 positive, and TN tumors was 59.3%, 51.0%, 39.1%, and 20.8%, respectively. Patients younger than 40 years were less likely to have ER and PR positive tumors (45.7% and 34.8%, respectively) than older women. However, this difference was not statistically significant. The incidence of HER2 positive tumors was highest in patients younger than 40 years (54.3%) with a p-value of . 007. However, the incidence of TN tumors did not differ significantly among different age groups (Table 1). Young women in the UAE are more likely to have HER2 positive and ER/ PR negative tumors, which are known to be associated with worse disease outcome (1,9–11). Although the sample size of our study was only 192 patients, it was large enough to show a statistical difference in the incidence of HER2 positive tumors in young patients. However, a larger sample may be needed to show a statistical difference in the incidence of ER and PR positive tumors. Future studies including a larger sample size of patients with exact ethnicity and stage of disease will be helpful to shed more light on the characteristics of breast cancer in the UAE.
The quality of reporting of diagnostic accuracy studies in glaucoma using the Heidelberg retina tomograph.

PURPOSE Scanning laser tomography with the Heidelberg retina tomograph (HRT; Heidelberg Engineering, Heidelberg, Germany) has been proposed as a useful diagnostic test for glaucoma. This study was conducted to evaluate the quality of reporting of published studies using the HRT for diagnosing glaucoma. METHODS A validated Medline and hand search of English-language articles reporting on measures of diagnostic accuracy of the HRT for glaucoma was performed. Two reviewers selected and appraised the papers independently. The Standards for Reporting of Diagnostic Accuracy (STARD) checklist was used to evaluate the quality of each publication. RESULTS A total of 29 articles were included. Interobserver rating agreement was observed in 83% of items (kappa=0.76). The number of STARD items properly reported ranged from 5 to 18. Less than a third of studies (7/29) explicitly reported more than half of the STARD items. Descriptions of key aspects of the methodology were frequently missing. For example, the design of the study (prospective or retrospective) was reported in 6 of 29 studies, and details of participant sampling (e.g., consecutive or random selection) were described in 5 of 29 publications. The commonest description of diagnostic accuracy was sensitivity and specificity (25/29) followed by area under the ROC curve (13/29), with 9 of 29 publications reporting both. CONCLUSIONS The quality of reporting of diagnostic accuracy tests for glaucoma with HRT is suboptimal. The STARD initiative may be a useful tool for appraising the strengths and weaknesses of diagnostic accuracy studies.