Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic criteria, severity classification and guidelines of systemic sclerosis

Several effective drugs have been identified for the treatment of systemic sclerosis (SSc). However, in advanced cases, not only their effectiveness is reduced but they may be also harmful due to their side‐effects. Therefore, early diagnosis and early treatment is most important for the treatment of SSc. We established diagnostic criteria for SSc in 2003 and early diagnostic criteria for SSc in 2011, for the purpose of developing evaluation of each organ in SSc. Moreover, in November 2013, the American College of Rheumatology and the European Rheumatology Association jointly developed new diagnostic criteria for increasing their sensitivity and specificity, so we revised our diagnostic criteria and severity classification of SSc. Furthermore, we have revised the clinical guideline based on the newest evidence. In particular, the clinical guideline was established by clinical questions based on evidence‐based medicine according to the New Minds Clinical Practice Guideline Creation Manual (version 1.0). We aimed to make the guideline easy to use and reliable based on the newest evidence, and to present guidance as specific as possible for various clinical problems in treatment of SSc.
An Effective Joint Framework for Document Summarization

Document summarization is an important research issue and has attracted much attention from the academe. The approaches for document summarization can be classified as extractive and abstractive. In this work, we introduce an effective joint framework that integrates extractive and abstractive summarization models, which is much closer to the way human write summaries (first underlining important information). Preliminary experiments on real benchmark dataset demonstrate that our model is competitive with the state-of-the-art methods.
Coupling of replisome movement with nucleosome dynamics can contribute to the parent–daughter information transfer

Abstract Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich ‘phase diagram’ having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.
Detecting miRNA Mentions and Relations in Biomedical Literature

Introduction: MicroRNAs (miRNAs) have demonstrated their potential as post-transcriptional gene expression regulators, participating in a wide spectrum of regulatory events such as apoptosis, differentiation, and stress response. Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases. Dissection of miRNA-related associations are valuable for contemplating their mechanism in diseases, leading to the discovery of novel miRNAs for disease prognosis, diagnosis, and therapy. Motivation: Apart from databases and prediction tools, miRNA-related information is largely available as unstructured text. Manual retrieval of these associations can be labor-intensive due to steadily growing number of publications. Additionally, most of the published miRNA entity recognition methods are keyword based, further subjected to manual inspection for retrieval of relations. Despite the fact that several databases host miRNA-associations derived from text, lower sensitivity and lack of published details for miRNA entity recognition and associated relations identification has motivated the need for developing comprehensive methods that are freely available for the scientific community. Additionally, the lack of a standard corpus for miRNA-relations has caused difficulty in evaluating the available systems. We propose methods to automatically extract mentions of miRNAs, species, genes/proteins, disease, and relations from scientific literature. Our generated corpora, along with dictionaries, and miRNA regular expression are freely available for academic purposes. To our knowledge, these resources are the most comprehensive developed so far. Results: The identification of specific miRNA mentions reaches a recall of 0.94 and precision of 0.93. Extraction of miRNA-disease and miRNA-gene relations lead to an F 1 score of up to 0.76. A comparison of the information extracted by our approach to the databases miR2Disease and miRSel for the extraction of Alzheimer's disease related relations shows the capability of our proposed methods in identifying correct relations with improved sensitivity. The published resources and described methods can help the researchers for maximal retrieval of miRNA-relations and generation of miRNA-regulatory networks. Availability: The training and test corpora, annotation guidelines, developed dictionaries, and supplementary files are available at http://www.scai. fraunhofer.de/mirna-corpora.html
VIRTUAL AND PHYSICAL PROTOTYPING TO DEMONSTRATE DESIGN FEASIBILITY

Hybrid electric vehicle technology has become a preferred method for the automotive industry to reduce environmental impact and fuel consumption of their vehicles. However, the added cost of the hybrid electric system has hindered their sales. A more cost effective design of an electro-hydraulic braking system is presented. During the design process, emphasis was placed on demonstrating conceptual and system feasibility using virtual and physical prototyping. The role of prototyping in the design process is presented and discussed.
An efficient web search engine for noisy free information retrieval

The vast growth, various dynamic and low quality of the world wide web makes it very difficult to retrieve relevant information from internet during query search. To resolve this issue, various web mining techniques are being used. The biggest challenge in web mining is to remove noisy data information or unwanted information from the webpage such as banner, video, audio, images, hyperlinks etc. which are not associated to a user query. To overcome these issues, a novel custom search engine is proposed with efficient algorithm in this paper. The proposed Uniform Resource Locator (URL) pattern extractor algorithm will extract the all relevance index pages from the web and ranking the indexes based on user query. Then, Noisy Data Cleaner (NDC) algorithm is applied to remove the unwanted content from the retrieved web pages. The results show that the proposed URL Pattern Extractor (UPE)+NDC algorithm provides very promising results for different datasets with high precision and recall rate in comparison with the existing algorithms.
Firm performance and investment in R&D and intellectual property

This paper analyses the relationship between innovation - proxied by Research and Development (R&D), patent and trade mark activity - and profitability in a panel of Australian firms (1995 to 1998). Special attention is given to assessing the nature of competitive conditions faced by different firms, as the nature of competition is likely to affect the returns to innovation. The hypothesis is that lower levels of competition will imply higher returns to innovation. To allow for a time lag time before any return to innovation, the market value of the firms is used as a proxy for expected future profits. The results give some support for the main hypothesis: the market's valuation of R&D activity is higher in industries where competition is lower. However, the paper highlights the difficulty in assessing competitive conditions and finds a number of results that challenge the simple hypothesis.
In vitro tissue culture initiation from potted and garden Hydrangea macrophylla explants

Abstract The effect of sterilisation treatments on the initiation of the culture of three Hydrangea macrophylla genotypes in vitro was studied. The results indicated difference among different disinfection treatment; the consequence of treatments with dichloroisocyanuric acid, in combination with silver nitrate, was a significantly higher survival rate comparing to treatments based on NaOCl. Success of sterilisation was significantly influenced by studied genotypes. Two potted hydrangea genotypes (G2 and G3) showed higher survival rate (45.00 %, 55.00 %, respectively) comparing to the genotype 1 (originated from a local garden), which exhibited the highest percentage of contamination rate (58.75 %). Culturing the explants on a McCown woody plant medium supplemented with BAP at 2 mg/L and NAA at 0.005 mg/L produced the highest number of shoots with multiplication rate of 1.31 in 5 weeks. The highest rooting percentage (100.00 %) was obtained with the genotype 2 on a McCown woody plant medium supplemented with 0.5 mg/L IBA.
Spatial and temporal variability of CO2 and CH4 gas transfer velocities and quantification of the CH4 microbubble flux in mangrove dominated estuaries

Gas transfer velocities (k) of CO2 and CH4 were determined from 209 deployments of a newly designed floating chamber in six mangrove dominated estuaries in Australia and the United States to estimate mangrove system specific k. k600‐CO2 and k600‐CH4 (k normalized to the Schmidt number of 600) varied greatly within and between mangrove creeks, ranging from 0.9 cm h−1 to 28.3 cm h−1. The gas transfer velocity correlated well with current velocity at all study sites suggesting current generated turbulence was the main driver controlling k. An empirical relationship that accounts for current velocity and a linearly additive contribution of wind speed and water depth was a good predictor of k600‐CO2 (R2 = 0.67) and k600‐CH4 (R2 = 0.57) in the mangrove creeks in Australia. In a side‐by‐side study, good agreement was found between k determined from this new floating chamber and a 3He/SF6 dual tracer release experiment (∼5% discrepancy). k600‐CH4 correlated well with k600‐CO2 (R2 = 0.81), however, k600‐CH4 was on average 1.2 times higher than k600‐CO2, most likely reflecting a microbubble flux contribution. The microbubble flux contributed up to 73% of the total CH4 flux and was best predicted by a model that included CH4 supersaturation, temperature, and current velocity. A large overestimation was found for both CO2 and CH4 fluxes when calculated using empirically derived k models from previous studies in estuaries. The high temporal and spatial variabilities of kCO2 and kCH4 highlights the importance of site specific transfer velocity measurements in dynamic ecosystems such as mangrove estuaries.
Parenting stress and DNA methylation among African Americans in the InterGEN Study

Introduction General life stress has been associated with altered DNA methylation in individuals of African Ancestry, although the relationship between parenting stress and DNA methylation has not been described. The purpose of this study was to examine the relationship between maternal parenting stress and DNA methylation among African Ancestry mother-child dyads. Methods We evaluated epigenome-wide DNA methylation relative to parenting stress in 74 mother-child dyads using linear mixed models. Results Significant variation in maternal DNA methylation at 95 CpG sites was associated with level of parenting stress. Notably, we identified a change in DNA methylation associated with poly (ADP-ribose) polymerase-1, which plays a key role in stress signaling. We did not identify any significant variation in child DNA methylation related to maternal parenting stress. Conclusions However, DNA methylation patterns observed in children mirrored patterns observed in their mothers. The results suggest that differential maternal DNA methylation is associated with higher levels of parenting stress.
Empty Capsids in Production of Viral Vector: Separation and Reassembly

Viral vectors have become promising weapons against many illness, such as vaccine and gene therapy to cancer and genetic disorder disease. Production and purification of different viral vectors have been widely studied. In the production process of the virial vector, empty viral capsids, which do not contain nucleic acid material, were reported as an undesired by product in many gene therapy studies. Several groups have demonstrated the function of specific immunogenicity of empty capsids because of their integrated foreign antigens. Research studies have raised the point that empty capsids may act like a natural decoy rather than ‘contamination’ of the product [1]. Even though the potential function of the empty capsids, the ratio of empty capsids to full viral capsids is very difficult to control in the production process. The empty capsid can be produced more efficiently as virus-like particles, which are another type of on-purpose empty capsid, instead of being the side product. A rational process will be separation of the empty capsids first and mix them later at a certain ratio, if necessary. From a process development point of view, we discuss the efforts for separation, disassembly, and assembly of the empty capsids.
Processing Social Media Messages in Mass Emergency: Survey Summary

Millions of people use social media to share information during disasters and mass emergencies. Information available on social media, particularly in the early hours of an event when few other sources are available, can be extremely valuable for emergency responders and decision makers, helping them gain situational awareness and plan relief efforts. Processing social media content to obtain such information involves solving multiple challenges, including parsing brief and informal messages, handling information overload, and prioritizing different types of information. These challenges can be mapped to information processing operations such as filtering, classifying, ranking, aggregating, extracting, and summarizing. This work highlights these challenges and presents state of the art computational techniques to deal with social media messages, focusing on their application to crisis scenarios.
Taxonomic clarification and neotype designation for three Indian xyleborine species (Coleoptera: Curculionidae, Scolytinae).

Xyleborini currently consists of more than 1168 species in 36 genera, nearly all of which were described in Xyleborus (Hulcr et al. 2015; Smith 2017). The tribe has been the focus of considerable taxonomic attention over the last decade resulting in phylogenetically based revisions and the erection of new genera (e.g. Hulcr et al. 2007, Hulcr and Cognato 2010). However in the Old World these efforts have largely been restricted to faunas of particular countries such as Taiwan (Beaver and Liu 2010), Thailand (Beaver et al. 2014), and Papua New Guinea (Hulcr and Cognato 2008). The region's fauna was primarily described from the 1890s to the 1940s by three authors, W.F. H. Blandford, Hans Eggers and Karl Schedl. During the 1920s to the 1940s Eggers described numerous Xyleborus species from India and Myanmar (Burma), typically from single specimens or a small series, and deposited them in the Forest Research Institute (FRI) in Dehradun, Uttarakhand, India. Cotypes (paratypes), if present for the species, were kept in his collection. Upon his death, his collection was sent to the United States National Museum of Natural History but Schedl retained many of the types that are now at the Naturhistorisches Museum Wien (NHMW). In all, FRI houses 50 xyleborine holotypes, and most of these species are solely known from the holotype.
Contours and Kernels : The Art of Sketching

Given sketches of everyday objects, we seek to accomplish two goals. The first is to classify the object depicted within the sketch. The second is to study different styles and varied interpretations in the depictions of the same object category. We employ supervised learning algorithms as the main method of classifying sketches into their respective classes, with our fine-tuned multiclass SVM attaining 57.7% accuracy. To understand varied styles and portrayals of objects – concepts that inherently are subjective and contain more vague metrics – we use unsupervised learning algorithms to discover common structure in the data. We find that by clustering, we group sketches with stylistically or structurally similar features. These groupings yield important insight into how we can obtain computational interpretation of more general, subjective qualities.
Rapid behavioral transitions produce chaotic mixing by a planktonic microswimmer.

Despite their vast morphological diversity, many invertebrates have similar larval forms characterized by ciliary bands, innervated arrays of beating cilia that facilitate swimming and feeding. Hydrodynamics suggests that these bands should tightly constrain the behavioral strategies available to the larvae; however, their apparent ubiquity suggests that these bands also confer substantial adaptive advantages. Here, we use hydrodynamic techniques to investigate "blinking," an unusual behavioral phenomenon observed in many invertebrate larvae in which ciliary bands across the body rapidly change beating direction and produce transient rearrangement of the local flow field. Using a general theoretical model combined with quantitative experiments on starfish larvae, we find that the natural rhythm of larval blinking is hydrodynamically optimal for inducing strong mixing of the local fluid environment due to transient streamline crossing, thereby maximizing the larvae's overall feeding rate. Our results are consistent with previous hypotheses that filter feeding organisms may use chaotic mixing dynamics to overcome circulation constraints in viscous environments, and it suggests physical underpinnings for complex neurally-driven behaviors in early-divergent animals.
SENSITIVITY ANALYSIS OF INFLUENCING FACTORS ON PM 2 . 5 NITRATE SIMULATION

Fine particulate matter (PM2.5) has been of increasing concern because of its adverse effects on human health. The Ministry of the Environment of Japan introduced an air quality standard for PM2.5 in 2009. Although PM2.5 concentrations have decreased in recent years in Japan, the standard for PM2.5 is not attained in most urban areas in Japan. Although air quality models (AQMs) with reasonable accuracy are essential tools to develop and evaluate measures to attain the standard, current air quality models cannot adequately simulate atmospheric mass concentrations of PM2.5 and its components in the Kanto region of Japan (Morino et al., 2010). This study focused on secondary inorganic aerosols among major PM2.5 components. Air quality simulations were conducted in the Kanto region in winter 2010 and summer 2011 by using the Community Multiscale Air Quality modeling system (CMAQ) (Byun and Schere, 2006) with several configurations. Because large discrepancies occurred between observed and simulated NO3 concentrations as described in section 3, sensitivity analyses were conducted in order to investigate factors influencing the model performance for NO3 simulation.
Privacy Preserving Distributed Analysis of Social Networks

Social networks have been a popular choice of study, given the surge of online data on friendship networks, communication networks, collaboration networks etc. This popularity, however, is not true for all types of social networks. In the current work, we draw the reader's attention to a class of social networks which are investigated to a limited extent, classified as distributed sensitive social networks. It constitutes of networks where the presence or absence of edges in the network is distributedly known to a set of parties, who regard this information as their private data. Supply chain networks, informal networks such as trust network, advice network, enmity network, etc. are a few examples of the same. A major reason for the lack of any substantial study on these networks has been the unavailability of data. As a solution, we propose a privacy preserving approach to investigating these networks. We show the feasibility of using secure multiparty computation techniques to perform the required analysis, while preserving the privacy of every individual's data. The possible approaches that can be considered to ensure the design of efficient secure protocols are discussed such as efficient circuit design, ORAM based secure computation, use of oblivious data structures, etc. The results obtained in the direction of secure network analysis algorithms are also presented.
Prism-Based Surface Plasmon Resonance for Dual-Parameter Sensing

A simple method to construct a dual-channel in a prism-based surface plasmon resonance sensor for dual-parameter monitoring is proposed. The metal layer (sensing area), attached to the prism, is half-covered with a polymer in order to generate two individual sensing sections. In this paper, eight different sensor structures (prism/metal/polymer) were analyzed. The prisms are made of NSK16 or SF10 glass and coated with gold or silver films. Half section of the metal films is covered with Polydimethylsiloxane (PDMS) or Poly-methyl methacrylate. The sensor is based on angle interrogation, the laser beam is aligned to be incident upon the interface of the bare and polymer sections. The resonance conditions are different at each pad, due to the refractive index (RI) mismatch, thus the intensity of the reflected signal presents a pair of well-defined resonance dips in series. The sensitivity of these dips to RI and temperature (T) changes was numerically analyzed. Finally, to demonstrate the feasibility to monitor RI and T, simultaneously, a surface plasmon resonance sensor was constructed using a NSK16 glass prism coated with a thin gold film, which was half-covered with PDMS.
A Heuristic Approach to Social Network-based and Context-aware Mobile Services Recommendation

The rapid growth of the number of mobile services provides enormous potential for users to find mobile information of interest. How to use both social network analysis and contextual recommendation techniques to improve mobile services recommendation has received little notice. In this paper we introduce a new heuristic approach to search nearest neighbors for each mobile user based on both given contextual mobile user preferences and mobile social network relationships, and then predict unknown contextual mobile user preferences and finally generate contextual mobile recommendations. We evaluate it on a real-world data set and compare its performance with some classical baseline methods, showing improvements in terms of different evaluation metrics.
A clinical evaluation of non-invasive motor imagery-based brain-computer interface in stroke

This clinical study investigates whether the performance of hemiparetic stroke patients operating a non-invasive Motor Imagery-based Brain-Computer Interface (MI-BCI) is comparable to healthy subjects. The study is performed on 8 healthy subjects and 35 BCI-naïve hemiparetic stroke patients. This study also investigates whether the performance of the stroke patients in operating MI-BCI correlates with the extent of neurological disability. The performance is objectively computed from the 10×10-fold cross-validation accuracy of employing the Filter Bank Common Spatial Pattern (FBCSP) algorithm on their EEG measurements. The neurological disability is subjectively estimated using the Fugl-Meyer Assessment (FMA) of the upper extremity. The results show that the performance of BCI-naïve hemiparetic stroke patients is comparable to healthy subjects, and no correlation is found between the accuracy of their performance and their motor impairment in terms of FMA.