Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Efficacy and Limits of Unmanned Aerial Vehicle (UAV) Technology for Weed Seedling Detection as Affected by Sensor Resolution

In order to optimize the application of herbicides in weed-crop systems, accurate and timely weed maps of the crop-field are required. In this context, this investigation quantified the efficacy and limitations of remote images collected with an unmanned aerial vehicle (UAV) for early detection of weed seedlings. The ability to discriminate weeds was significantly affected by the imagery spectral (type of camera), spatial (flight altitude) and temporal (the date of the study) resolutions. The colour-infrared images captured at 40 m and 50 days after sowing (date 2), when plants had 5–6 true leaves, had the highest weed detection accuracy (up to 91%). At this flight altitude, the images captured before date 2 had slightly better results than the images captured later. However, this trend changed in the visible-light images captured at 60 m and higher, which had notably better results on date 3 (57 days after sowing) because of the larger size of the weed plants. Our results showed the requirements on spectral and spatial resolutions needed to generate a suitable weed map early in the growing season, as well as the best moment for the UAV image acquisition, with the ultimate objective of applying site-specific weed management operations.
The visibility of maintenance in object models: an empirical study

This empirical study analyzes changes in C++ source code which occurred between two releases of an industrial software product and compares them with entities and relations available in object-oriented modeling techniques. The comparison offers increased understanding of what changes can and cannot be described using such object models. The goals were to investigate if the object model in this particular project is either abstract and stable or detailed and sensitive to change, and whether or not changes made to the C++ source code are visible in the object model. Four metrics for characterization of change are formally defined and used, namely correctness, completeness, compliance, and visibility factor. The major finding is that even though many of the classes are changed, the majority of these changes turn out to be invisible in the object model. That is, changes made on the source code level are of a finer granularity than available in common object modeling concepts. This may explain why object models seem to be of little use in release-oriented development.
On Four-Valued Niho-Type Cross-Correlation Functions of $m$-Sequences

Consider the cross-correlation function C<sub>d</sub>(tau) between two m-sequences of period p<sup>2k</sup>-1 that differ by a decimation d. Assume that d is of Niho type and C<sub>d</sub>(tau) is four-valued. In this correspondence, the values of C<sub>d</sub>(tau) are described. If p=2 then the values of C<sub>d</sub>(tau) are -1-2 <sup>k</sup>,-1,-1+2<sup>k</sup>, and -1+2<sup>k+j</sup> for some integer j>0 for which 2j divides k. If p>2 then the values are -1-p<sup>k</sup>,-1,-1+p<sup>k</sup>, and -1+2middotp<sup>k</sup>
Nonrectangular shaping and sizing of soft modules for floorplan-design improvement

Many previous works on floorplanning with nonrectangular modules assume that the modules are predesignated to have particular nonrectangular shapes, e.g., L-shaped, T-shaped, etc. However, this is not common in practice because rectangular shapes are more preferable in many designing steps. Those nonrectangular shapes are actually generated during floorplanning in order to further optimize the solution. In this paper, we study this problem of changing the shapes and dimensions of the flexible modules to fill up the unused area of a preliminary floorplan, while keeping the relative positions between the modules unchanged. This feature will also be useful in fixing small incremental changes during engineering change order modifications. We formulate the problem as a mathematical program. The formulation is such that the dimensions of all of the rectangular and nonrectangular modules can be computed by closed-form equations in O(m) time in each corresponding Lagrangian relaxation subproblem (LRS) where m is the total number of edges in the constraint graphs. As a result, the total time for the whole shaping and sizing process is O(k/spl times/m), where k is the number of iterations on the LRS. Experimental results show that the amount of area reused is 3.7% on average, while the total wirelength can be reduced by 0.43% on average because of the more compacted result packing.
A collaborative workflow for building ontologies: A case study in the biomedical field

Much medical knowledge is contained within available literature, such as clinical guidelines and protocols. Recently, an interest has been developed in automatic content extraction to construct ontologies of this knowledge to make it more widely available. With groups of domain experts distributed geographically, and the growing amount of medical literature, an important challenge is to develop collaborative workflows to support ways for domain experts to contribute in the ontology learning process. This paper presents a collaborative workflow for ontology learning based on coupling an Ontology Learning Tool (OntoLancs) with and Ontology engineer (Protégé) to provide semi-automatic support for text mining and a collaborative tool to model formal ontologies. The work presented in this paper was evaluated with a case study on a Clinical Practice Guideline of Diabetic Retinopathy. The major benefits of coupling OntoLancs with Protégé are: a) a higher level of automation in the creation of domain ontologies and models, and b) strengthened communication and information exchange among domain experts that are physically distributed. Validations of user experiences indicate the applicability of our approach.
Inferring interaction partners from protein sequences

Significance Specific protein−protein interactions play crucial roles in the stability of multiprotein complexes and in signal transduction. Thus, mapping these interactions is key to a systems-level understanding of cells. Systematic experimental identification of protein interaction partners is still challenging. However, a large and rapidly growing amount of sequence data is now available. Is it possible to identify which proteins interact just from their sequences? We propose an approach based on sequence covariation, building on methods used with success to predict the three-dimensional structures of proteins from sequences alone. Our method identifies specific interaction partners with high accuracy among the members of several ubiquitous prokaryotic protein families, and provides a way to predict protein−protein interactions directly from sequence data. Specific protein−protein interactions are crucial in the cell, both to ensure the formation and stability of multiprotein complexes and to enable signal transduction in various pathways. Functional interactions between proteins result in coevolution between the interaction partners, causing their sequences to be correlated. Here we exploit these correlations to accurately identify, from sequence data alone, which proteins are specific interaction partners. Our general approach, which employs a pairwise maximum entropy model to infer couplings between residues, has been successfully used to predict the 3D structures of proteins from sequences. Thus inspired, we introduce an iterative algorithm to predict specific interaction partners from two protein families whose members are known to interact. We first assess the algorithm’s performance on histidine kinases and response regulators from bacterial two-component signaling systems. We obtain a striking 0.93 true positive fraction on our complete dataset without any a priori knowledge of interaction partners, and we uncover the origin of this success. We then apply the algorithm to proteins from ATP-binding cassette (ABC) transporter complexes, and obtain accurate predictions in these systems as well. Finally, we present two metrics that accurately distinguish interacting protein families from noninteracting ones, using only sequence data.
In situ measurements of HCN and CH3CN over the Pacific Ocean: Sources, sinks, and budgets

[1] We report the first in situ measurements of hydrogen cyanide (HCN) and methyl cyanide (CH3CN, acetonitrile) from the Pacific troposphere (0–12 km) obtained during the NASA Transport and Chemical Evolution over the Pacific (TRACE-P) airborne mission (February–April 2001). Mean HCN and CH3CN mixing ratios of 243 ± 118 (median 218) ppt and 149 ± 56 (median 138) ppt, respectively, were measured. These in situ observations correspond to a mean tropospheric HCN column of 4.2 × 1015 molecules cm−2 and a CH3CN column of 2.5 × 1015 molecules cm−2. This is in good agreement with the 0–12 km HCN column of 4.4 (±0.6) × 1015 molecules cm−2 derived from infrared solar spectroscopic observations over Japan. Mixing ratios of HCN and CH3CN were greatly enhanced in pollution outflow from Asia and were well correlated with each other as well as with known tracers of biomass combustion (e.g., CH3Cl, CO). Volumetric enhancement (or emission) ratios (ERs) relative to CO in free tropospheric plumes, likely originating from fires, were 0.34% for HCN and 0.17% for CH3CN. ERs with respect to CH3Cl and CO in selected biomass burning (BB) plumes in the free troposphere and in boundary layer pollution episodes are used to estimate a global BB source of 0.8 ± 0.4 Tg (N) yr−1 for HCN and 0.4 ± 0.1 Tg (N) yr−1 for CH3CN. In comparison, emissions from industry and fossil fuel combustion are quite small (<0.05 Tg (N) yr−1). The vertical structure of HCN and CH3CN indicated reduced mixing ratios in the marine boundary layer (MBL). Using a simple box model, the observed gradients across the top of the MBL are used to derive an oceanic loss rate of 8.8 × 10−15 g (N) cm−2 s−1 for HCN and 3.4 × 10−15 g (N) cm−2 s−1 for CH3CN. An air-sea exchange model is used to conclude that this flux can be maintained if the oceans are undersaturated in HCN and CH3CN by 27% and 6%, respectively. These observations also correspond to an open ocean mean deposition velocity (vd) of 0.12 cm s−1 for HCN and 0.06 cm s−1 for CH3CN. It is inferred that oceanic loss is a dominant sink for these cyanides and that they deposit some 1.4 Tg (N) of nitrogen annually to the oceans. Assuming loss to the oceans and reaction with OH radicals as the major removal processes, a mean atmospheric residence time of 5.0 months for HCN and 6.6 months for CH3CN is calculated. A global budget analysis shows that the sources and sinks of HCN and CH3CN are roughly in balance but large uncertainties remain in part due to a lack of observational data from the atmosphere and the oceans. Pathways leading to the oceanic (and soil) degradation of these cyanides are poorly known but are expected to be biological in nature.
Serum level of eight cytokines in Han Chinese patients with systemic lupus erythematosus using multiplex fluorescent microsphere method

Aim of the study To investigate the role of 8 cytokines and their correlation with clinical characteristics in systemic lupus erythematosus (SLE) in Han Chinese population by detecting their serum levels using the multiplex fluorescent microsphere method. Material and methods Serum was separated from 79 patients with SLE and 40 healthy controls. The serum cytokine detection was conducted according to the instruction of MILLIPLEX MAP human cytokine detection kit on the Luminex liquid phase array platform with 0.01 pg/ml detectable level. The 8 cytokines were interferon α2 (IFN-α2), IFN-γ, interleukin 6 (IL-6), IL-8, IL-10, IFN-γ-inducible protein 10 (IP-10), tumor necrosis factor α (TNF-α) and IL-17. Variable data were in skewed distribution and were expressed with median (P25, P75). Mann-Whitney analysis was used in statistical analysis. Results At the baseline level without any stimulus, the level of IP-10 expression was the highest among the 8 cytokines and the second highest was IL-8. The level of IL-17 was too low to be detected. The level of 7 cytokines was higher in SLE patients than in healthy controls (p < 0.01). The level of dsDNA antibody, C3, CRP, ESR and anti-nucleosome antibody was correlated with IL-10. Proteinuria was not correlated with any cytokine. Conclusions Eight cytokines were measured in our study, while not all of them were detected. The most important finding was the usefulness of IL-10 as a disease activity biomarker for Han Chinese patient with SLE. None of cytokines reflected kidney injury.
Symptomatic Acute Hepatitis C Infection Following a Single Episode of Unprotected Sexual Intercourse

A previously healthy 23-year-old MSM presented with jaundice, systemic upset, and rash 2 months after a single episode of unprotected sexual intercourse. Liver biochemistry was grossly deranged, with markedly elevated transaminases and hyperbilirubinaemia. Serology was positive for genotype 1a hepatitis C virus (HCV) and in the absence of other causes, acute HCV infection was suspected. He was subsequently successfully treated with pegylated interferon and ribavirin for 24 weeks and made a full clinical and biochemical recovery.
Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

Spatial organization of different epigenomic marks was used to infer functions of the epigenome. It remains unclear what can be learned from the temporal changes of the epigenome. Here, we developed a probabilistic model to cluster genomic sequences based on the similarity of temporal changes of multiple epigenomic marks during a cellular differentiation process. We differentiated mouse embryonic stem (ES) cells into mesendoderm cells. At three time points during this differentiation process, we used high-throughput sequencing to measure seven histone modifications and variants—H3K4me1/2/3, H3K27ac, H3K27me3, H3K36me3, and H2A.Z; two DNA modifications—5-mC and 5-hmC; and transcribed mRNAs and noncoding RNAs (ncRNAs). Genomic sequences were clustered based on the spatiotemporal epigenomic information. These clusters not only clearly distinguished gene bodies, promoters, and enhancers, but also were predictive of bidirectional promoters, miRNA promoters, and piRNAs. This suggests specific epigenomic patterns exist on piRNA genes much earlier than germ cell development. Temporal changes of H3K4me2, unmethylated CpG, and H2A.Z were predictive of 5-hmC changes, suggesting unmethylated CpG and H3K4me2 as potential upstream signals guiding TETs to specific sequences. Several rules on combinatorial epigenomic changes and their effects on mRNA expression and ncRNA expression were derived, including a simple rule governing the relationship between 5-hmC and gene expression levels. A Sox17 enhancer containing a FOXA2 binding site and a Foxa2 enhancer containing a SOX17 binding site were identified, suggesting a positive feedback loop between the two mesendoderm transcription factors. These data illustrate the power of using epigenome dynamics to investigate regulatory functions.
Primary School Students' Attitudes towards Computer Based Testing and Assessment in Turkey.

This study investigated the attitudes of primary school students towards computer based testing and assessment in terms of different variables. The sample for this research is primary school students attending a computer based testing and assessment application via CITO-OIS. The “Scale on Attitudes towards Computer Based Testing and Assessment” to collect data and the results obtained were compared in terms of school type, gender, and grade level. The results of this study revealed that significant differences exist between attitudes of students from different schools. Such a difference does not exist between attitudes of students when their genders, grade levels, and participation periods to computer based assessment are taken into account.
Evaluation of Safety and Protective Effect of Combined Extract of Cissampelos pareira and Anethum graveolens (PM52) against Age-Related Cognitive Impairment

The present study aimed to determine acute toxicity, the protective effect, and underlying mechanism of PM52, a combined extract of Cissampelos pareira and Anethum graveolens, against age-related cognitive impairment in animal model of age-related cognitive impairment. PM52 was determined as acute toxicity according to OECD guideline. Male Wistar rats, weighing 180–220 g, were orally given PM52 at doses of 2, 10, and 50 mg/kg at a period of 14 days before and 7 days after the bilateral administration of AF64A via intracerebroventricular route. All animals were assessed according to spatial memory, neuron density, MDA level, the activities of SOD, CAT, GSH-Px, and AChEI effect in hippocampus. It was found that all doses of PM52 could attenuate memory impairment and neurodegeneration in hippocampus. The possible mechanisms might occur via the suppression of AChE and the decreased oxidative stress in hippocampus. Therefore, our data suggest that PM52 may serve as food supplement to protect against age-related cognitive impairment such as mild cognitive impairment (MCI) and early phase of Alzheimer's disease. However, further researches are still essential.
Identification of a Transcription Factor Controlling pH-Dependent Organic Acid Response in Aspergillus niger

Acid formation in Aspergillus niger is known to be subjected to tight regulation, and the acid production profiles are fine-tuned to respond to the ambient pH. Based on transcriptome data, putative trans-acting pH responding transcription factors were listed and through knock out studies, mutants exhibiting an oxalate overproducing phenotype were identified. The yield of oxalate was increased up to 158% compared to the wild type and the corresponding transcription factor was therefore entitled Oxalic Acid repression Factor, OafA. Detailed physiological characterization of one of the ΔoafA mutants, compared to the wild type, showed that both strains produced substantial amounts of gluconic acid, but the mutant strain was more efficient in re-uptake of gluconic acid and converting it to oxalic acid, particularly at high pH (pH 5.0). Transcriptional profiles showed that 241 genes were differentially expressed due to the deletion of oafA and this supported the argument of OafA being a trans-acting transcription factor. Furthermore, expression of two phosphoketolases was down-regulated in the ΔoafA mutant, one of which has not previously been described in fungi. It was argued that the observed oxalate overproducing phenotype was a consequence of the efficient re-uptake of gluconic acid and thereby a higher flux through glycolysis. This results in a lower flux through the pentose phosphate pathway, demonstrated by the down-regulation of the phosphoketolases. Finally, the physiological data, in terms of the specific oxygen consumption, indicated a connection between the oxidative phosphorylation and oxalate production and this was further substantiated through transcription analysis.
The neural basis of mood-congruent processing biases in depression.

BACKGROUND Mood-congruent processing biases are among the most robust research findings in neuropsychological studies of depression. Depressed patients show preferential processing of negatively toned stimuli across a range of cognitive tasks. The present study aimed to determine whether these behavioral abnormalities are associated with specific neural substrates. METHODS Ten depressed patients and 11 healthy control subjects underwent scanning during performance of an emotional go/no-go task using functional magnetic resonance imaging. The task allowed comparison among neural response to happy, sad, and neutral words, in the context of these words as targets (ie, stimuli to which subjects were required to make a motor response) or distractors (ie, stimuli to which the motor response was withheld). RESULTS Depressed patients showed attenuated neural responses to emotional relative to neutral targets in ventral cingulate and posterior orbitofrontal cortices. However, patients showed elevated responses specific to sad targets in rostral anterior cingulate extending to anterior medial prefrontal cortex. Unlike controls, patients showed differential neural response to emotional, particularly sad, distractors in the lateral orbitofrontal cortex. CONCLUSIONS These findings suggest a distinct neural substrate for mood-congruent processing biases in performance. The medial and orbital prefrontal regions may play a key role in mediating the interaction between mood and cognition in affective disorder.
Eliciting preferences over observed behaviours based on relative evaluations

Reinforcement learning addresses the question of programming an autonomous agent to execute tasks that are described as reinforcement functions. Then, the agent is responsible for discovering the best actions to fulfil such task. Most of the work on reinforcement learning considers that reinforcements are given by the environment, not addressing the problem of how to describe tasks as reinforcement functions. Preference elicitation addresses the problem of describing a human preference through utility functions, from which reinforcement functions are special cases. This paper proposes an approach where preference elicitation and reinforcement learning are handled in an integrated manner, providing an autonomous method of programming an agent. The agent is programmed through pairwise evaluations over observed behaviours of the agent, where the evaluations are summarised in the reinforcement function. In this paper we present an approach to solve such a problem based on evaluations over observed behaviours. We propose a new algorithm, PEOB-RS, that can be shown to converge towards an optimal policy, providing the number of trials for each behaviour tends to infinity. Experimental results from learning in a grid stochastic environment are used to obtain a reinforcement function, illustrating the effectiveness of PEOB-RS, even if requiring too many evaluations. Such reinforcement function is then transferred to a more real-like environment simulating a pioneer robot, showing the abstraction property of utility functions.
A Unified Method for Multiple Home Appliances Control through Static Finger Gestures

Various electrical appliances have penetrated into people's daily life including televisions, video and audio equipment, and other household appliances. Many of them provide an infrared Remote Controller (RC) for appliance control. But as the number of controllers increased, it becomes not so convenient to access different controllers to control different devices, especially for the senior citizens with diminished physical and mental ability. In this paper, a one-for-all gesture-based remote control system is proposed by which consumers can control different appliances in a nature and unified way. Firstly, two kinds of fundamental devices for the physical layer of the novel control method is presented, which including a compact wearable sensing mote called Magic Ring (MR) and its command receiver and executer called Electrical Appliance Node (EA-Node). Moreover, a unified control protocol for application layer is defined to solve the problems of effective target selection and function navigation. A comparative study is performed between the proposed MR-based method and traditional RC-based method on three aspects: operation effectiveness, learning curve, and fatigue degree. The results of experiment show that MR-based method can achieve a competitive performance by as much as 88% of RC-based method ( in general for a beginner, the completed tasks using MR is about 40% as many as using RC. And after several minutes of practice, that ratio can raise to about 60%).