Miracle-dz/UniFAR-FTUs huggingface dataset:
Homograph Disambiguation through Selective Diacritic Restoration

Lexical ambiguity, a challenging phenomenon in all natural languages, is particularly prevalent for languages with diacritics that tend to be omitted in writing, such as Arabic. Omitting diacritics leads to an increase in the number of homographs: different words with the same spelling. Diacritic restoration could theoretically help disambiguate these words, but in practice, the increase in overall sparsity leads to performance degradation in NLP applications. In this paper, we propose approaches for automatically marking a subset of words for diacritic restoration, which leads to selective homograph disambiguation. Compared to full or no diacritic restoration, these approaches yield selectively-diacritized datasets that balance sparsity and lexical disambiguation. We evaluate the various selection strategies extrinsically on several downstream applications: neural machine translation, part-of-speech tagging, and semantic textual similarity. Our experiments on Arabic show promising results, where our devised strategies on selective diacritization lead to a more balanced and consistent performance in downstream applications.
A Paraphrase Generation System for EHR Question Answering

This paper proposes a dataset and method for automatically generating paraphrases for clinical questions relating to patient-specific information in electronic health records (EHRs). Crowdsourcing is used to collect 10,578 unique questions across 946 semantically distinct paraphrase clusters. This corpus is then used with a deep learning-based question paraphrasing method utilizing variational autoencoder and LSTM encoder/decoder. The ultimate use of such a method is to improve the performance of automatic question answering methods for EHRs.
Service-Based, interactive portrayal of 3D geovirtual environments

This report summarizes my work in the HPI Research School on Service Oriented Systems Engineering. It motivates and points out the underlying research questions in the field of service-based 3D portrayal of large and complex 3D geovirtual environments, presents my approach to solving these questions, and demonstrates and highlights results by example. A focus is on my work during the past months.
Arabic Dialect Identification for Travel and Twitter Text

This paper presents the results of the experiments done as a part of MADAR Shared Task in WANLP 2019 on Arabic Fine-Grained Dialect Identification. Dialect Identification is one of the prominent tasks in the field of Natural language processing where the subsequent language modules can be improved based on it. We explored the use of different features like char, word n-gram, language model probabilities, etc on different classifiers. Results show that these features help to improve dialect classification accuracy. Results also show that traditional machine learning classifier tends to perform better when compared to neural network models on this task in a low resource setting.
Insect-scale fast moving and ultrarobust soft robot

An insect-scale soft robot has fast relative speed of motion, high load-carrying capability, and exceptional robustness. Mobility and robustness are two important features for practical applications of robots. Soft robots made of polymeric materials have the potential to achieve both attributes simultaneously. Inspired by nature, this research presents soft robots based on a curved unimorph piezoelectric structure whose relative speed of 20 body lengths per second is the fastest measured among published artificial insect-scale robots. The soft robot uses several principles of animal locomotion, can carry loads, climb slopes, and has the sturdiness of cockroaches. After withstanding the weight of an adult footstep, which is about 1 million times heavier than that of the robot, the system survived and continued to move afterward. The relatively fast locomotion and robustness are attributed to the curved unimorph piezoelectric structure with large amplitude vibration, which advances beyond other methods. The design principle, driving mechanism, and operating characteristics can be further optimized and extended for improved performances, as well as used for other flexible devices.
Dynamics and stability analysis on stairs climbing of wheel–track mobile robot

A transformable wheel–track robot with the tail rod whose winding will coordinate the center of gravity of the robot is researched, and a theoretical basis for the stable climbing of the robot is provided. After a general introduction of the research, firstly the mechanical hardware and control hardware composition of the wheel–track robot is provided and the principles of its mechanical structure are illustrated. Secondly, through studying the fundamental constrains during the process of the robot climbing the obstacles, a mathematical model based on classical mechanics method is built to help analyze the dynamic principles of a wheel–track mobile robot climbing stairs. Thirdly, the dynamic stability analysis is carried out by analyzing not only the interaction among forces of track, track edge, and stair step but also the different stabilities of the robot when the track and the stairs have different touch points. Finally, an experiment of the modeling track robot climbing the stairs has convinced the effectiveness of the dynamic theories researched, which will be a beneficial reference for the future mobile robots obstacle climbing studies.
Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches

The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. Zika virus disease has been linked to several health problems such as microcephaly and the Guillain–Barré syndrome, but to date, there has been no vaccine available for Zika. Problems related to the development of a vaccine include the vaccination target, which covers pregnant women and children, and the antibody dependent enhancement (ADE), which can be caused by non-neutralizing antibodies. The peptide vaccine was chosen as a focus of this study as a safer platform to develop the Zika vaccine. In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine.
A novel curriculum to train physician assistant students how to write effective discharge summaries

ABSTRACT Background: Physician assistants (PAs) are an integral part of inpatient care teams, but many PAs do not receive formal education on authoring discharge summaries. High-quality discharge summaries can mitigate patient risk during transitions of care by improving inter-provider communication. Objective: To understand the current state of discharge summary education at our institution, and describe a novel curriculum to teach PA students to write effective discharge summaries. Design: Students completed a pre-survey to assess both knowledge and comfort levels regarding discharge summaries. They wrote a discharge summary and received feedback from two evaluators, an inpatient provider (IPP) familiar with the described patient and a simulated primary care provider (PCP). Students completed a post-survey reassessing knowledge and comfort. Results: Prior to instituting this curriculum, the majority of students (92.9%) reported rarely or never receiving feedback on discharge summaries. Eighty-four of 88 (95.5%) eligible students participated. There was discordance between IPP and simulated PCP feedback on their assessment of the quality of discharge summaries; simulated PCPs gave significantly lower global quality ratings (7.9 versus 8.5 out of 10, p = 0.006). Key elements were missing from >10% of discharge summaries. Student response was favorable. Conclusion: Clinically relevant deficiencies were common in students’ discharge summaries, highlighting the need for earlier, structured training. IPPs and simulated PCPs gave discordant feedback, emphasizing differing needs of different providers during transitions of care. This novel curriculum improved students’ knowledge and confidence.
Double diabetes: A distinct high‐risk group?

The term double diabetes (DD) has been used to refer to individuals with type 1 diabetes (T1D) who are overweight, have a family history of type 2 diabetes and/or clinical features of insulin resistance. Several pieces of evidence indicate that individuals who display features of DD are at higher risk of developing future diabetes complications, independently of average glucose control, measured as glycated haemoglobin (HbA1c) concentration. Given the increased prevalence of individuals with features of DD, pragmatic criteria are urgently required to identify and stratify this group, which will help with subsequent implementation of more effective personalized interventions. In this review, we discuss the potential criteria for the clinical identification of individuals with DD, highlighting the strengths and weaknesses of each definition. We also cover potential mechanisms of DD and how these contribute to increased risk of diabetes complications. Special emphasis is placed on the role of estimated glucose disposal rate (eGDR) in the diagnosis of DD, which can be easily incorporated into clinical practice and is predictive of adverse clinical outcome. In addition to the identification of individuals with DD, eGDR has potential utility in monitoring response to different interventions. T1D is a more heterogeneous condition than initially envisaged, and those with features of DD represent a subgroup at higher risk of complications. Pragmatic criteria for the diagnosis of individuals with DD will help with risk stratification, allowing a more personalized and targeted management strategy to improve outcome and quality of life in this population.
Femtosecond Laser Micro-/nano-texturing of Stainless Steels for Surface Property Control

Surface geometry has had an influence on the surface property, in addition to the intrinsic surface energy, of materials. Many physical surface modification methods had been proposed to control the solid surface geometry for modification of surface properties. Recently, short-pulse lasers were utilized to perform nano-texturing onto metallic and polymer substrates for the improvement of surface properties. Most of the papers reported that the hydrophilic metallic surface was modified to have a higher contact angle than 120–150°. Little studies explained the relationship between surface geometry and surface properties. In the present study, the laser micro-/nano-texturing was developed to describe this surface-geometric effect on the static contact angles for pure water. Micropatterns with multi spatial frequencies are designed and synthesized into a microtexture. This tailored microtexture was utilized to prepare for computer aided machining (CAM) data to control the femtosecond laser beams. The nano-length ripples by laser induced periodic surface structuring (LIPSS) supposed onto this microtexture to form the micro-/nano-texture on the AISI304 substrate surface. Computational geometry was employed to describe this geometric profile. The fractal dimension became nearly constant by 2.26 and insensitive to increase of static contact angle (θ) for θ > 150°. Under this defined self-similarity, the micro-/nano-textured surface state was controlled to be super-hydrophobic by increasing the ratio of the highest spatial frequency in microtextures to the lowest one. This controllability of surface property on the stainless steels was supported by tailoring the wavelength and pitch of microtextures. Exposure testing was also used to evaluate the engineering durability of this micro-/nano-textured surface. Little change of the measured fractal dimension during the testing proved that this physically modified AISI304 surface had sufficient stability for its long-term usage in air.
Identifying genetic markers for a range of phylogenetic utility–From species to family level

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
Compact Size and Slotted Patch Antenna for WiMAX and WLAN

Objectives: Dual-Band, reduced size, coaxial fed probe, Inverted C-slot patch antenna for wireless communication is designed in this paper. The excellent dual-band performance is attained by using inverted C-slots on the patch. Methods/Statistical Analysis: The slots provide two notched bands covering 2.7 GHz to 4.04 GHz for WiMAX and 5.32 GHz to 6 GHz for WLAN with excellent return loss and satisfactory VSWR. Findings: Two resonant peaks obtained are at 3.2 GHz and at 5.4 GHz. The proposed antenna size is 29 mm × 29 mm. The antenna has been effectively simulated on HFSS and tested on VNA tool. The peak gain of 4.65 dB and efficiency of 95% is obtained. The antenna presentation is analyzed on the basis of size of antenna, VSWR, bandwidth, return loss and efficiency. The presented antenna is an excellent choice for WLAN and WiMAX. Improvements: As compared to conventional Microstrip Patch Antenna return loss is improved with 67% and area minimization of 63% has been attained.
Trauma-Responsive Care in a Pediatric Setting: Feasibility and Acceptability of Screening for Adverse Childhood Experiences.

Adverse childhood experiences (ACEs) have demonstrable negative effects on long-term physical and mental health. Low-income and ethnic minority communities face significant disparities in exposure to ACEs. Pediatric settings offer an opportune context to identify and address ACEs, with the potential to reduce barriers in access to resources and services. The current study examined the feasibility and acceptability of screening infants and their parents for ACEs at a community medical clinic. Feasibility data indicated that 151 (92%) of the 164 unique patients that presented for well-child visits for infants (4- to 12-months) across a 13-month period were screened for infant and parent ACEs. Of these 151 patients, 47% met eligibility (infants with 1 + ACEs, parents with 2 + ACEs) deemed intermediate risk and indicated referral to prevention services. The majority of referred families (77%) accepted prevention services, including appointments with bilingual and bicultural wellness navigators who provided a cultural bridge and access to resources that could address patients' social determinants of health. Qualitative interviews with providers expand upon screening acceptability. Implications for integrated behavioral health, ACEs screening, and trauma-responsive prevention in a pediatric setting are discussed.
Lamin A/C deficiency in CD4+ T‐cells enhances regulatory T‐cells and prevents inflammatory bowel disease

The mechanisms by which lamin A/C in CD4+ T‐cells control intestinal homeostasis and can cause inflammatory bowel disease (IBD) are unknown. Here, we explore lamin A/C in a mouse model of IBD. Adoptive transfer to Rag1−/− mice of Lmna−/− CD4+ T‐cells, which have enhanced regulatory T‐cells (Treg) differentiation and function, induced less severe IBD than wild‐type T‐cells. Lamin A/C deficiency in CD4+ T‐cells enhanced transcription of the Treg master regulator FOXP3, thus promoting Treg differentiation, and reduced Th1 polarization, due to epigenetic changes in the Th1 master regulator T‐bet. In mesenteric lymph nodes, retinoic acid (RA) released by CD103+ dendritic cells downregulated lamin A/C in CD4+ T‐cells, enhancing Treg differentiation. However, non‐RA‐producing CD103− dendritic cells predominated in peripheral lymph nodes, facilitating lamin A/C expression in CD4+ T‐cells and therefore Th1 differentiation. Our findings establish lamin A/C as a key regulator of Th differentiation in physiological conditions and show it as a potential immune‐regulatory target in IBD. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Intra-fraction motion prediction in MRI-guided radiation therapy using Markov processes

Internal organ motion during radiation delivery may lead to underdosing of cancer cells or overdosing of normal tissue, potentially causing treatment failure or normal-tissue toxicity. Organ motion is of particular concern in the treatment of lung and abdominal cancers, where breathing induces large tumor displacement and organ deformation. A new generation of radiotherapy devices is equipped with on-board MRI scanners to acquire a real-time movie of the patient’s anatomy during radiation delivery. The goal of this research is to develop, calibrate, and test motion predictive models that employ real-time MRI images to provide the short-term trajectory of respiration-induced anatomical motion during radiation delivery. A semi-Markov model predicts transitions between the phases of a respiratory cycle, and a Markov model predicts transitions to future respiratory cycles, leading to accurate motion forecasting over longer-term horizons. The intended application for this work is real-time tracking and re-optimization of intensity-modulated radiation delivery.
Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts

The DNA damage checkpoint response is controlled by the phosphatidylinositol 3-kinase-related kinases (PIKK), including ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR). ATR forms a complex with its partner ATRIP. In budding yeast, ATR and ATRIP correspond to Mec1 and Ddc2, respectively. ATRIP/Ddc2 interacts with replication protein A-bound single-stranded DNA (RPA-ssDNA) and recruits ATR/Mec1 to sites of DNA damage. Mec1 is stimulated by the canonical activators including Ddc1, Dpb11 and Dna2. We have characterized the ddc2-S4 mutation and shown that Ddc2 not only recruits Mec1 to sites of DNA damage but also stimulates Mec1 kinase activity. However, the underlying mechanism of Ddc2-dependent Mec1 activation remains to be elucidated. Here we show that Ddc2 promotes Mec1 activation independently of Ddc1/Dpb11/Dna2 function in vivo and through ssDNA recognition in vitro. The ddc2-S4 mutation diminishes damage-induced phosphorylation of the checkpoint mediators, Rad9 and Mrc1. Rad9 controls checkpoint throughout the cell-cycle whereas Mrc1 is specifically required for the S-phase checkpoint. Notably, S-phase checkpoint signaling is more defective in ddc2-S4 mutants than in cells where the Mec1 activators (Ddc1/Dpb11 and Dna2) are dysfunctional. To understand a role of Ddc2 in Mec1 activation, we reconstituted an in vitro assay using purified Mec1-Ddc2 complex, RPA and ssDNA. Whereas ssDNA stimulates kinase activity of the Mec1-Ddc2 complex, RPA does not. However, RPA can promote ssDNA-dependent Mec1 activation. Neither ssDNA nor RPA-ssDNA efficiently stimulates the Mec1-Ddc2 complex containing Ddc2-S4 mutant. Together, our data support a model in which Ddc2 promotes Mec1 activation at RPA-ssDNA tracts.
Investigation of ZnO-decorated CNTs for UV Light Detection Applications

Multi-walled carbon nanotubes (CNTs) decorated with zinc oxide nanoparticles (ZnO NPs) were prepared in isopropanol solution by a simple, room-temperature process and characterized from structural, morphological, electronic, and optical points of view. A strong interaction between ZnO and CNTs is fully confirmed by all the characterization techniques. ZnO-CNTs nanocomposites, with different weight ratios, were deposited as a dense layer between two electrodes, in order to investigate the electrical behaviour. In particular, the electrical response of the nanocomposite layers to UV light irradiation was recorded for a fixed voltage: As the device is exposed to the UV lamp, a sharp current drop takes place and then an increase is observed as the irradiation is stopped. The effect can be explained by adsorption and desorption phenomena taking place on the ZnO nanoparticle surface under irradiation and by charge transfer between ZnO and CNTs, thanks to the strong interaction between the two nanomaterials. The nanocomposite material shows good sensitivity and fast response to UV irradiation. Room temperature and low-cost processes used for the device preparation combined with room temperature and low voltage operational conditions make this methodology very promising for large scale UV detectors applications.
Disseminated toxoplasmosis associated with hemophagocytic syndrome after kidney transplantation: A case report and review

Disseminated toxoplasmosis is infrequent after kidney transplant transmission but life‐threatening because of a lack of diagnostic suspicion as well as specific chemoprophylaxis recommendations. Solid organ transplantation has resulted in few cases of disseminated toxoplasmosis presenting with associated hemophagocytic syndrome. Herein, we report, within the context of a donor/receiver mismatch, a case of a toxoplasmosis associated with hemophagocytic syndrome in a kidney transplant recipient. Molecular and serological investigations confirmed Toxoplasma gondii transmission through the kidney graft.
An Ultra-Area-Efficient 1024-Point In-Memory FFT Processor

Current computation architectures rely on more processor-centric design principles. On the other hand, the inevitable increase in the amount of data that applications need forces researchers to design novel processor architectures that are more data-centric. By following this principle, this study proposes an area-efficient Fast Fourier Transform (FFT) processor through in-memory computing. The proposed architecture occupies the smallest footprint of around 0.1 mm2 inside its class together with acceptable power efficiency. According to the results, the processor exhibits the highest area efficiency (FFT/s/area) among the existing FFT processors in the current literature.