Miracle-dz/UniFAR-FTUs huggingface dataset:
Ontology-based web forms — Acquisition and modification of structured data

Semantic Web technologies and its best practice known as Linked Data are on the rise, but their incorporation into information systems still poses challenges. An issue of acquisition, processing or usage of such data is well-known and discussed. On the contrary, modification of semantic web data is not given such attention. The creation of structured semantic data that could be checked or even validated before submission is an important element for their subsequent use, including the possibility of sharing them. Existing data may need to be edited and the ability to efficiently change data is an absolute necessity, when using Semantic Web technologies in the information system. This paper describes a prototype web application for collecting and editing RDF data via web forms generated from ontology.
Adverse reactions to antidepressants.

BACKGROUND Adverse drug reactions are important determinants of non-adherence to antidepressant treatment, but their assessment is complicated by overlap with depressive symptoms and lack of reliable self-report measures. AIMS To evaluate a simple self-report measure and describe adverse reactions to antidepressants in a large sample. METHOD The newly developed self-report Antidepressant Side-Effect Checklist and the psychiatrist-rated UKU Side Effect Rating Scale were repeatedly administered to 811 adult participants with depression in a part-randomised multicentre open-label study comparing escitalopram and nortriptyline. RESULTS There was good agreement between self-report and psychiatrists' ratings. Most complaints listed as adverse reactions in people with depression were more common when they were medication-free rather than during their treatment with antidepressants. Dry mouth (74%), constipation (33%) and weight gain (15%) were associated with nortriptyline treatment. Diarrhoea (9%), insomnia (36%) and yawning (16%) were more common during treatment with escitalopram. Problems with urination and drowsiness predicted discontinuation of nortriptyline. Diarrhoea and decreased appetite predicted discontinuation of escitalopram. CONCLUSIONS Adverse reactions to antidepressants can be reliably assessed by self-report. Attention to specific adverse reactions may improve adherence to antidepressant treatment.
Orientation regression in hand radiographs: a transfer learning approach

Most radiologists prefer an upright orientation of the anatomy in a digital X-ray image for consistency and quality reasons. In almost half of the clinical cases, the anatomy is not upright orientated, which is why the images must be digitally rotated by radiographers. Earlier work has shown that automated orientation detection results in small error rates, but requires specially designed algorithms for individual anatomies. In this work, we propose a novel approach to overcome time-consuming feature engineering by means of Residual Neural Networks (ResNet), which extract generic low-level and high-level features, and provide promising solutions for medical imaging. Our method uses the learned representations to estimate the orientation via linear regression, and can be further improved by fine-tuning selected ResNet layers. The method was evaluated on 926 hand X-ray images and achieves a state-of-the-art mean absolute error of 2.79°.
Conformational diversity analysis reveals three functional mechanisms in proteins

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions.
Optimal Algorithms for Hitting (Topological) Minors on Graphs of Bounded Treewidth

For a fixed collection of graphs ${\cal F}$, the ${\cal F}$-M-DELETION problem consists in, given a graph $G$ and an integer $k$, decide whether there exists $S \subseteq V(G)$ with $|S| \leq k$ such that $G \setminus S$ does not contain any of the graphs in ${\cal F}$ as a minor. We are interested in the parameterized complexity of ${\cal F}$-M-DELETION when the parameter is the treewidth of $G$, denoted by $tw$. Our objective is to determine, for a fixed ${\cal F}$, the smallest function $f_{{\cal F}}$ such that ${\cal F}$-M-DELETION can be solved in time $f_{{\cal F}}(tw) \cdot n^{O(1)}$ on $n$-vertex graphs. Using and enhancing the machinery of boundaried graphs and small sets of representatives introduced by Bodlaender et al. [J ACM, 2016], we prove that when all the graphs in ${\cal F}$ are connected and at least one of them is planar, then $f_{{\cal F}}(w) = 2^{O (w \cdot\log w)}$. When ${\cal F}$ is a singleton containing a clique, a cycle, or a path on $i$ vertices, we prove the following asymptotically tight bounds: $\bullet$ $f_{\{K_4\}}(w) = 2^{\Theta (w \cdot \log w)}$. $\bullet$ $f_{\{C_i\}}(w) = 2^{\Theta (w)}$ for every $i \leq 4$, and $f_{\{C_i\}}(w) = 2^{\Theta (w \cdot\log w)}$ for every $i \geq 5$. $\bullet$ $f_{\{P_i\}}(w) = 2^{\Theta (w)}$ for every $i \leq 4$, and $f_{\{P_i\}}(w) = 2^{\Theta (w \cdot \log w)}$ for every $i \geq 6$. The lower bounds hold unless the Exponential Time Hypothesis fails, and the superexponential ones are inspired by a reduction of Marcin Pilipczuk [Discrete Appl Math, 2016]. The single-exponential algorithms use, in particular, the rank-based approach introduced by Bodlaender et al. [Inform Comput, 2015]. We also consider the version of the problem where the graphs in ${\cal F}$ are forbidden as topological minors, and prove that essentially the same set of results holds.
Trackside Loss Analysis: An Application in a Radio-Frequency Chain of a Communication-Based Train Control System

A key assumption in the process of optimized design of radio-frequency (RF) networks is the efficient transfer of power from the transmitter source to the load (i.e., the end antenna). Unless the transmitter is located directly next to the load, a transmission circuit composed of multiple cascaded or forked segments connects one to the other. An example of such a transmission network is the RF transmission chain of the communication-based train control (CBTC) trackside antenna system. The data communication subsystem (DCS) design requirements and validation processes necessitate development of means for realistic evaluation and analysis of the reflection/return loss (RL) and insertion loss (IL) values offered by the trackside RF chains of a radio-based CBTC system. The aim of this research is to present a comparative study of three different models developed to quantitatively assess RL and IL values in a general multistage RF transmission network. To provide a more realistic and credible assessment, the comparison has been further substantiated with measurement data.
Internet of things: A comparative study

Internet of Things (IoT) is the field that connects things together and to the Internet, letting them exchange data, communicate with each other and interact with the human. Recently, it has been widely used to go beyond the machine to machine (M2M) communication and covers variety of protocols and applications that facilitates people's way of living. However, many challenges still hinder its advances, especially security and power issues. In this paper, a comparative study for IoT architectures, platforms and applications is presented with a case study to illustrate the main IoT concepts and levels of abstraction. Then, a Strengths – Weaknesses – Opportunities – Threats (SWOT) analysis is presented to assess the present and the future of IoT.
Quantitative analysis of charge trapping and classification of sub-gap states in MoS2 TFT by pulse I–V method

The threshold voltage instabilities and huge hysteresis of MoS2 thin film transistors (TFTs) have raised concerns about their practical applicability in next-generation switching devices. These behaviors are associated with charge trapping, which stems from tunneling to the adjacent trap site, interfacial redox reaction and interface and/or bulk trap states. In this report, we present quantitative analysis on the electron charge trapping mechanism of MoS2 TFT by fast pulse I–V method and the space charge limited current (SCLC) measurement. By adopting the fast pulse I–V method, we were able to obtain effective mobility. In addition, the origin of the trap states was identified by disassembling the sub-gap states into interface trap and bulk trap states by simple extraction analysis. These measurement methods and analyses enable not only quantitative extraction of various traps but also an understanding of the charge transport mechanism in MoS2 TFTs. The fast I–V data and SCLC data obtained under various measurement temperatures and ambient show that electron transport to neighboring trap sites by tunneling is the main charge trapping mechanism in thin-MoS2 TFTs. This implies that interfacial traps account for most of the total sub-gap states while the bulk trap contribution is negligible, at approximately 0.40% and 0.26% in air and vacuum ambient, respectively. Thus, control of the interface trap states is crucial to further improve the performance of devices with thin channels.
Modeling Spiking Neural Networks on SpiNNaker

SpiNNaker is a massively parallel architecture with more than a million processing cores that can model up to 1 billion spiking neurons in biological real time. Here, we offer an overview of our research project and describe the first experiments with these test chips running spiking neurons based on Eugene Izhikevich's model. Note that we're not targeting artificial neural networks (such as perceptrons or multilayer networks) that were inspired by, but don't model, biologically plausible neural systems.
Experimental Study on the Road Properties of High Liquid Limit Soil Improved by Lime

Several laboratory experiments were completed by adding different ratios of lime to modify the high liquid limit soil of LiuLi Expressway,and the physico-mechanical properties and the strength change laws of the lime improved high liquid limit soil were studied.Through synthetically considering testing result and economic benefit,the best lime quantity of the high liquid limit soil of Liu-Li Expressway.The results show that the high liquid limit soil can be well used as subgrade filling of expressway after being treated with 4% lime.
Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis

ABSTRACT Soil bacteria engage each other in competitive and cooperative ways to determine their microenvironments. In this study, we report the identification of a large number of genes required for Myxococcus xanthus to engage Bacillus subtilis in a predator-prey relationship. We generated and tested over 6,000 individual transposon insertion mutants of M. xanthus and found many new factors required to promote efficient predation, including the specialized metabolite myxoprincomide, an ATP-binding cassette (ABC) transporter permease, and a clustered regularly interspaced short palindromic repeat (CRISPR) locus encoding bacterial immunity. We also identified genes known to be involved in predation, including those required for the production of exopolysaccharides and type IV pilus (T4P)-dependent motility, as well as chemosensory and two-component systems. Furthermore, deletion of these genes confirmed their role during predation. Overall, M. xanthus predation appears to be a multifactorial process, with multiple determinants enhancing predation capacity. IMPORTANCE Soil bacteria engage each other in complex environments and utilize multiple traits to ensure survival. Here, we report the identification of multiple traits that enable a common soil organism, Myxococcus xanthus, to prey upon and utilize nutrients from another common soil organism, Bacillus subtilis. We mutagenized the predator and carried out a screen to identify genes that were required to either enhance or diminish capacity to consume prey. We identified dozens of genes encoding factors that contribute to the overall repertoire for the predator to successfully engage its prey in the natural environment.
HER-2 (c-erbB-2) test update: Present status and problems

HER-2 tests are routinely used for the identification of patients with metastatic breast cancer that is potentially responsive to trastuzumab (herceptin) therapy. Recently, convincing data have been published with regard to the efficacy of trastuzumab as a drug for neoadjuvant therapy or adjuvant therapy for operable primary breast cancer that overexpresses HER-2. It is also noteworthy that at the St. Gallen International Consensus Conference 2005, HER-2 protein overexpression or HER-2 gene amplification has been included as an indicator for higher risk of recurrence for both node-negative and node-positive breast cancers. To measure the HER-2 level, the worldwide consensus appears to be that immunohistochemistry (IHC) should be performed first and, if the results of IHC are uncertain, fluorescencein situ hybridization (FISH) should be performed later, although some investigators argue that FISH should be performed first. These tests should be performed in strict adherence to existing instructions. Quality control is of utmost importance when performing HER-2 tests, both internal and external, for routine diagnosis and in clinical protocol studies.
A novel two-tier paradigm for labeling water bodies in supervised satellite image classification

The satellite images are the high dimensional data with huge spatial details which needs intelligent interpretation methods. The use of satellite images is more prevalent nowadays in many real time surveillance applications and it leads to the need of simple and accurate processing. The advent of machine learning classifiers improved the efficiency of satellite image applications. However, the ground truth data availability and spatial data labeling are certain serious limitations for supervised satellite image classification. Thus change monitoring models are highly dependent on unsupervised clustering methods with the compromised level of accuracy. This paper is focused on addressing the steps to overcome the above said ground truth validation, labeling and other feature discrimination issues in a supervised soft classifier model for simple change recognition of seasonal water bodies in satellite images.
CD2+ Tetraploid Acute Promyelocytic Leukemia Variant with Double (15;17) Translocations

We report a patient with a variant form of CD2+ acute promyelocytic leukemia (APL) who had double translocations (15;17) in a single leukemic cell. The patient presented with severe neutropenia, thrombocytopenia, and disseminated intravascular coagulation. The bone marrow showed marked hyperplasia with large leukemic cells that had bizarre nuclear configuration and basophilic, hypogranular cytoplasm. Leukemic cells were positive for CD2, 13, 33, 34, and 56 and negative for HLA-DR.The karyotype of the abnormal clone was characterized as 92,XXYY, t(15;17)(q22;q21)x2. No other additional abnormal clone was found, and the patient’s condition was diagnosed as tetraploid APL variant. Fluorescence in situ hybridization assay revealed 2 promyelocytic leukemia and retinoic acid receptor α (PML/RARA) fusion signals, and reverse transcription-polymerase chain reaction assay revealed short-form PML/RARA fusion transcript. Tetraploidy in APL is a very rare abnormality. Double translocations were an additional abnormality in this case, and this patient’s karyotype might have had some influence on morphological characteristics, expression of CD2, and poor clinical outcome.
Monte Carlo and experimental determination of correction factors for gamma knife perfexion small field dosimetry measurements

Detector-, field size- and machine-specific correction factors are required for precise dosimetry measurements in small and non-standard photon fields. In this work, Monte Carlo (MC) simulation techniques were used to calculate the kQmsr,Q0fmsr,fref and kQclin,Qmsrfclin,fmsr correction factors for a series of ionization chambers, a synthetic microDiamond and diode dosimeters, used for reference and/or output factor (OF) measurements in the Gamma Knife Perfexion photon fields. Calculations were performed for the solid water (SW) and ABS plastic phantoms, as well as for a water phantom of the same geometry. MC calculations for the kQclin,Qmsrfclin,fmsr correction factors in SW were compared against corresponding experimental results for a subset of ionization chambers and diode detectors. Reference experimental OF data were obtained through the weighted average of corresponding measurements using TLDs, EBT-2 films and alanine pellets. kQmsr,Q0fmsr,fref values close to unity (within 1%) were calculated for most of ionization chambers in water. Greater corrections of up to 6.0% were observed for chambers with relatively large air-cavity dimensions and steel central electrode. A phantom correction of 1.006 and 1.024 (breaking down to 1.014 from the ABS sphere and 1.010 from the accompanying ABS phantom adapter) were calculated for the SW and ABS phantoms, respectively, adding up to kQmsr,Q0fmsr,fref corrections in water. Both measurements and MC calculations for the diode and microDiamond detectors resulted in lower than unit kQclin,Qmsrfclin,fmsr correction factors, due to their denser sensitive volume and encapsulation materials. In comparison, higher than unit kQclin,Qmsrfclin,fmsr results for the ionization chambers suggested field size depended dose underestimations (being significant for the 4 mm field), with magnitude depending on the combination of contradicting phenomena associated with volume averaging and electron fluence perturbations. Finally, the presence of 0.5 mm air-gap between the diodes’ frontal surface and their phantom-inserts may considerably influence OF measurements, reaching 4.6% for the Razor diode.
How does dietary particle size affect carnivore gastrointestinal transit: A dog model

The effect of dietary particle size on gastrointestinal transit in carnivores has not been studied and might offer more insight into their digestive physiology. This study evaluated the effect of two dietary particle sizes (fine = 7.8 mm vs. coarse = 13 mm) of chunked day-old chicks on transit parameters in dogs. Six beagle dogs were fed both dietary treatments in a crossover design of 7 days with transit testing on the fifth day. Transit parameters were assessed using two markers, that is a wireless motility capsule (IntelliCap® ) and titanium oxide (TiO2 ). Dietary particle size did not affect gastric emptying time (GRT), small bowel transit time (SBTT), colonic transit time (CTT) and total transit time (aTTT) of the capsule (p > .05). There was no effect of dietary particle size on TiO2 mean retention time (MRT) (p > .05). The time of last TiO2 excretion (MaxRT) differed (p = .013) between diets, being later for the coarse diet. Both MRT (R = 0.617, p = .032) and MaxRT (R = 0.814; p = .001) were positively correlated to aTTT. The ratio MRT/aTTT tended towards a difference between diets (p = .059) with the coarse diet exceeding fine diet values. Results show that the difference between capsule measurements and TiO2 is larger for the fine than the coarse diet suggesting that the capsule becomes more accurate when dietary particle size approaches marker size. Dietary particle size might have affected transit parameters but differences are too small to claim major physiological consequences.
Ether-Toolbars: Evaluating Off-Screen Toolbars for Mobile Interaction

In mobile touchscreebn interaction, an important challenge is to find solutions to balance the size of individual widgets against the number of widgets needed during interaction. In this work, to address display space limitations, we explore the design of invisible off-screen toolbars (ether-toolbars) that leverage computer vision to expand application features by placing widgets adjacent to the display screen. We show how simple computer vision algorithms can be combined with a natural human ability to estimate physical placing to support highly accurate targeting. Our ether-toolbar design promises targeting accuracy approximating on-screen widget accuracy while significantly expanding the interaction space of mobile devices. Through two experiments, we examine off-screen content placement metaphors and off-screen precision of participants accessing these toolbars. From the data of the second experiment, we provide a basic model that reflects how users perceive mobile surroundings for ether-widgets and validate it. We also demonstrate a prototype system consisting of an inexpensive 3D printed mount for a mirror that supports ether-toolbar implementations. Finally, we discuss the implications of our work and potential design extensions that can increase the usability and the utility of ether-toolbars.
Enhanced rate of wlan using different protocols in infrastructure and ad-hoc mode

In this paper, we have discussed the experiments performed by us on Wireless local area network technology. These experiments are divided into two sections that describes it using infrastructure-based and infrastructure-less network. Section A: Infrastructure-based mode and Section B: Infrastructure-less mode consists of both static and mobile modes with constant bit rate application along with Voice over internet protocol based on H.323 respectively. We have also shown the difference in the two modes using different protocols like adhoc on-demand distance vector and dynamic mobile adhoc network on-demand for both the sections. We have calculated the throughput for each section and the simulation of each configuration has been done using QualNet software of version 6.1. From the experiments we have shown the comparison between the two functional modes of Wireless local area network i.e. infrastructure and ad-hoc. We have also discussed different applications where either ad-hoc and infrastructure modes or either of them can be used, with enhanced rate using suitable protocols.