Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncertainty Visualization of Stenotic Regions in Vascular Structures

Stenosis refers to the thinning of the inner surface (lumen) of vascular structures. Detecting stenoses and correctly estimating their degree is crucial in clinical settings for proper treatment planning. Such a planning involves a visual assessment, which in case of vascular structures is frequently based on 3D visual representations of the vessels. However, since vessel segmentation is affected by various sources of errors and noise in the imaging and image processing pipeline, it is crucial to capture and visually convey the uncertainty in a 3D visual representation. We propose a novel approach for visualizing the shape deviation of different probability levels in vascular data, where the probability levels are computed from a probabilistic segmentation approach.
Ultrastructure of spermatozoa in three cicada species from China (Hemiptera, Cicadomorpha, Cicadidae)

Abstract The ultrastructure of mature spermatozoa of three cicada species, Subpsaltria yangi, Karenia caelatata, and Platypleura kaempferi, was investigated using epifluorescence and transmission electron microscopies. This is the first investigation of the sperm ultrastructure of species in the subfamily Tibicininae and the tribe Sinosenini, represented by S. yangi and K. caelatata, respectively. The three species all produce two or three types of spermatozoa with various lengths, viz., polymegaly. The centriolar adjunct of spermatozoa in S. yangi shows a granular substructure, which is different from that of other cicada species, suggesting that spermatozoa in Tibicininae may have their own characteristics in comparison with other cicadas. The centriolar adjunct of spermatozoa of K. caelatata displays characteristics similar to that of the Cicadinae. Combined with other morphological characters, it is reasonable to remove K. caelatata and its allies (i.e., Sinosenini) from Cicadettinae to Cicadinae. The study of sperm ultrastructure, particularly in the species of Tibicininae and Sinosenini, expands the spermatological research of Cicadidae and provides more information for phylogenetic analysis of Cicadidae.
Grain dormancy genes responsible for preventing pre-harvest sprouting in barley and wheat

Pre-harvest sprouting (PHS) remains a long-standing problem for the production of barley (Hordeum vulgare) and wheat (Triticum aestivum) worldwide. Grain dormancy, a key trait for the prevention of PHS, controls the timing of germination. Discovery of the causal sequence polymorphisms (CSPs) that produce naturally occurring variation in dormancy will help improve PHS tolerance. The identification of CSPs for dormancy remains difficult, especially for barley and wheat, because they are the last major cereals to have their genomes sequenced. However, recent work has identified several important CSPs that play pivotal roles in fine-tuning the dormancy levels in barley and wheat cultivars. This review summarizes these recent advances, which can be directly applied in breeding programs to improve PHS tolerance. These recent findings indicate the possibility that barley and wheat cultivars grown in East Asia, where much rain falls during the harvest season, will be rich sources of alleles that confer strong dormancy, since these cultivars have been selected to cope with the regional climate. The newly discovered dormant alleles will be useful for improving PHS tolerance around the world, just as Reduced-height (Rht) alleles from Japanese wheat varieties contributed to yield increases for the Green Revolution.
Visual Text Analytics using Semantic Networks and Interactive 3D Visualization

Facing the growth of textual information, the analysis of unstructured text data remains a challenge for visual analytics. Most text visualizations are based on models that use word frequencies for text vectorization and representation. As semantics reveal from word relations, we propose an integrated visual text analytics approach that utilizes semantic networks in an interactive 3D workspace for exploration and analysis. Semantic networks act as an intermediary structure for data modeling and interactive visualization to support the visual analytics process. Focussing on the integration of text analysis and visualization, this paper describes our system design and its preliminary implementation. Discussing typical usage scenarios and a practical ﬁeld-test, we present a strategy for text exploration and analysis to illustrate the usage of our system in an exemplary use case. Categories and Subject Descriptors (according to ACM CCS) : Computer Graphics [I.3. 6]: Methodology and Techniques – Interaction techniques—Document and Text Processing [I.7. 0]: General—Information Interfaces and presentation [H.5. 2]: User interfaces—
Discovery and Validation of Salivary Extracellular RNA Biomarkers for Noninvasive Detection of Gastric Cancer.

BACKGROUND Biomarkers are needed for noninvasive early detection of gastric cancer (GC). We investigated salivary extracellular RNA (exRNA) biomarkers as potential clinical evaluation tools for GC. METHODS Unstimulated whole saliva samples were prospectively collected from 294 individuals (163 GC and 131 non-GC patients) who underwent endoscopic evaluation at the Samsung Medical Center in Korea. Salivary transcriptomes of 63 GC and 31 non-GC patients were profiled, and mRNA biomarker candidates were verified with reverse transcription quantitative real-time PCR (RT-qPCR). In parallel, microRNA (miRNA) biomarkers were profiled and verified with saliva samples from 10 GC and 10 non-GC patients. Candidate biomarkers were validated with RT-qPCR in an independent cohort of 100/100 saliva samples from GC and non-GC patients. Validated individual markers were configured into a best performance panel. RESULTS We identified 30 mRNA and 15 miRNA candidates whose expression pattern associated with the presence of GC. Among them, 12 mRNA and 6 miRNA candidates were verified with the discovery cohort by RT-qPCR and further validated with the independent cohort (n = 200). The configured biomarker panel consisted of 3 mRNAs (SPINK7, PPL, and SEMA4B) and 2 miRNAs (MIR140-5p and MIR301a), which were all significantly down-regulated in the GC group, and yielded an area under the ROC curve (AUC) of 0.81 (95% CI, 0.72-0.89). When combined with demographic factors, the AUC of the biomarker panel reached 0.87 (95% CI, 0.80-0.93). CONCLUSIONS We have discovered and validated a panel of salivary exRNA biomarkers with credible clinical performance for the detection of GC. Our study demonstrates the potential utility of salivary exRNA biomarkers in screening and risk assessment for GC.
Ga-Based Alloys in Microelectronic Interconnects: A Review

Gallium (Ga) and some of its alloys have a range of properties that make them an attractive option for microelectronic interconnects, including low melting point, non-toxicity, and the ability to wet without fluxing most materials—including oxides—found in microelectronics. Some of these properties result from their ability to form stable high melting temperature solid solutions and intermetallic compounds with other metals, such as copper, nickel, and aluminium. Ga and Ga-based alloys have already received significant attention in the scientific literature given their potential for use in the liquid state. Their potential for enabling the miniaturisation and deformability of microelectronic devices has also been demonstrated. The low process temperatures, made possible by their low melting points, produce significant energy savings. However, there are still some issues that need to be addressed before their potential can be fully realised. Characterising Ga and Ga-based alloys, and their reactions with materials commonly used in the microelectronic industry, are thus a priority for the electronics industry. This review provides a summary of research related to the applications and characterisation of Ga-based alloys. If the potential of Ga-based alloys for low temperature bonding in microelectronics manufacturing is to be realised, more work needs to be done on their interactions with the wide range of substrate materials now being used in electronic circuitry.
Decentralized Online Simultaneous Localization and Mapping for Multi-Agent Systems

Planning tasks performed by a robotic agent require previous access to a map of the environment and the position where the agent is located. This creates a problem when the agent is placed in a new environment. To solve it, the RA must execute the task known as Simultaneous Location and Mapping (SLAM) which locates the agent in the new environment while generating the map at the same time, geometrically or topologically. One of the big problems in SLAM is the amount of memory required for the RA to store the details of the environment map. In addition, environment data capture needs a robust processing unit to handle data representation, which in turn is reflected in a bigger RA unit with higher energy use and production costs. This article presents a design for a system capable of a decentralized implementation of SLAM that is based on the use of a system comprised of wireless agents capable of storing and distributing the map as it is being generated by the RA. The proposed system was validated in an environment with a surface area of 25 m2, in which it was capable of generating the topological map online, and without relying on external units connected to the system.
Estimation of Above Ground Biomass in a Tropical Mountain Forest in Southern Ecuador Using Airborne LiDAR Data

A reliable estimation of Above Ground Biomass (AGB) in Tropical Mountain Forest (TMF) is still complicated, due to fast-changing climate and topographic conditions, which modifies the forest structure within fine scales. The variations in vertical and horizontal forest structure are hardly detectable by small field plots, especially in natural TMF due to the high tree diversity and the inaccessibility of remote areas. Therefore, the present approach used remotely sensed data from a Light Detection and Ranging (LiDAR) sensor in combination with field measurements to estimate AGB accurately for a catchment in the Andes of south-eastern Ecuador. From the LiDAR data, information about horizontal and vertical structure of the TMF could be derived and the vegetation at tree level classified, differentiated between the prevailing forest types (ravine forest, ridge forest and Elfin Forest). Furthermore, topographical variables (Topographic Position Index, TPI; Morphometric Protection Index, MPI) were calculated by means of the high-resolution LiDAR data to analyse the AGB distribution within the catchment. The field measurements included different tree parameters of the species present in the plots, which were used to determine the local mean Wood Density (WD) as well as the specific height-diameter relationship to calculate AGB, applying regional scale modelling at tree level. The results confirmed that field plot measurements alone cannot capture completely the forest structure in TMF but in combination with high resolution LiDAR data, applying a classification at tree level, the AGB amount (Mg ha−1) and its distribution in the entire catchment could be estimated adequately (model accuracy at tree level: R2 > 0.91). It was found that the AGB distribution is strongly related to ridges and depressions (TPI) and to the protection of the site (MPI), because high AGB was also detected at higher elevations (up to 196.6 Mg ha−1, above 2700 m), if the site is situated in depressions (ravine forest) and protected by the surrounding terrain. In general, highest AGB is stored in the protected ravine TMF parts, also at higher elevations, which could only be detected by means of the remote sensed data in high resolution, because most of these areas are inaccessible. Other vegetation units, present in the study catchment (pasture and subparamo) do not contain large AGB stocks, which underlines the importance of intact natural forest stands.
Phosphocholine-Modified Lipooligosaccharides of Haemophilus influenzae Inhibit ATP-Induced IL-1β Release by Pulmonary Epithelial Cells

Phosphocholine-modified bacterial cell wall components are virulence factors enabling immune evasion and permanent colonization of the mammalian host, by mechanisms that are poorly understood. Recently, we demonstrated that free phosphocholine (PC) and PC-modified lipooligosaccharides (PC-LOS) from Haemophilus influenzae, an opportunistic pathogen of the upper and lower airways, function as unconventional nicotinic agonists and efficiently inhibit the ATP-induced release of monocytic IL-1β. We hypothesize that H. influenzae PC-LOS exert similar effects on pulmonary epithelial cells and on the complex lung tissue. The human lung carcinoma-derived epithelial cell lines A549 and Calu-3 were primed with lipopolysaccharide from Escherichia coli followed by stimulation with ATP in the presence or absence of PC or PC-LOS or LOS devoid of PC. The involvement of nicotinic acetylcholine receptors was tested using specific antagonists. We demonstrate that PC and PC-LOS efficiently inhibit ATP-mediated IL-1β release by A549 and Calu-3 cells via nicotinic acetylcholine receptors containing subunits α7, α9, and/or α10. Primed precision-cut lung slices behaved similarly. We conclude that H. influenzae hijacked an endogenous anti-inflammatory cholinergic control mechanism of the lung to evade innate immune responses of the host. These findings may pave the way towards a host-centered antibiotic treatment of chronic airway infections with H. influenzae.
Intraperitoneal dexmedetomidine as an adjuvant to bupivacaine for postoperative pain management in children undergoing laparoscopic appendectomy: A prospective randomized trial

Background and Aims: Intraperitoneal local anesthetic is an effective analgesic approach in laparoscopic appendectomy in adults. The aim of the study was to compare the postoperative pain when intraperitoneal bupivacaine is administered alone versus the addition of dexmedetomidine to it in children undergoing a laparoscopic appendectomy. Methods: In this prospective randomized trial, 52 children were randomly allocated to Group B who received intraperitoneal bupivacaine 0.25% (2 mg/kg) or Group BD who received intraperitoneal bupivacaine 0.25% (2 mg/kg) plus dexmedetomidine (1 mcg/kg) for postoperative analgesia in children undergoing laparoscopic appendectomy. Postoperative pethidine consumption at day 1 was recorded and considered the primary outcome of the study. Patients were evaluated for pain scores at 0, 2, 4, 6, 12, and 24 h, time to first request of pethidine, sedation scores at 0, 2, 4, and 6 h, length of hospital stay, and parents' satisfaction. Chi-square, Fisher's exact, Student's t-test, and Mann–Whitney U-tests were used for analysis. Results: Postoperative visual analog scale scores were lower in Group BD at 2, 4, and 6 h (mean = 3, 3, 3, respectively) compared with Group B (mean = 4, 5, 4, respectively) (P < 0.05). Patients in Group BD had more sedation scores at 0, 2, and 4 h (P < 0.05), longer time to first rescue analgesia (P = 0.03), lesser rescue analgesic consumption (P = 0.02), shorter length of hospital stay (P = 0.02), and higher parents' satisfaction (P = 0.01). Conclusion: Adding dexmedetomidine to intraperitoneal bupivacaine provides adequate postoperative analgesia in children undergoing laparoscopic appendectomy.
Student-Centered Microbioassay Laboratory Activity Utilizing Bioluminescent Bacteria †

Student-centered teaching allows students to be actively engaged in hands-on, minds-on activities that emphasize creativity and collaboration, enabling them to ask questions and design their own investigations to real-world problems. One such problem is water contamination, which causes human health and environmental issues. However, chemical water quality testing for pollutants can be timely and expensive. In addition to chemical testing, researchers have developed assays using unicellular organisms to determine which pollutants are present and in what concentrations. In this three-hour laboratory activity, high school students and undergraduate biology or microbiology students work in pairs to help a fictional company develop a water quality microbioassay. Students design their own laboratory protocols to test the reaction of a bioluminescent bacterial species (i.e., Photobacterium phosphoreum or Aliivibrio fischeri) to exposure of common aquatic pollutants such as fertilizer, household cleaners, and motor oil. During this laboratory activity, students apply previously learned components of experimental design, including positive and negative controls, constants, and experimental groups. In addition, students gain experience writing a scientific explanation for a recommendation regarding the bioluminescent bacteria’s suitability in a bioassay. Pre- and post-evaluation data revealed that students were successful in achieving the activity’s objectives as well as in designing their investigations and writing their protocols using scaffolds within the lesson.
Decomposing the Twitter data stream in healthcare: An information theory perspective

Recent research using Twitter as an information communication channel has shown how event organizers convey and disseminate their agendas across industries and disciplines. However, little research has been carried out on the user's choice of information components when composing a tweet through the lens of information theory. This research employs a comparative case study to examine how medical‐terminology hashtags and corresponding lay‐language hashtags have been used to help to communicate healthcare messages on the Twitter platform. The main result of this case study revealed patterns that both retweeting behavior and the use of a variety of components to construct a tweet contribute to higher entropy values which imply that these are more informative ways to communicate healthcare messages.
Legal information acquisition by the public: The role of personal and environmental factors

This paper reports a portion of the results of a 2016 mixed methods study on the acquisition of legal information by members of the public. While information acquisition by health information seekers has been extensively studied, similar studies of legal consumers are almost nonexistent. Even less research has focused on incidental encounters with legal information. Based upon established models of human information behavior, and informed by numerous studies of health information acquisition by consumers, this study examined the relationship of personal, contextual, affective and environmental factors with frequency of legal information acquisition. In one phase of the study, an online survey was administered to 385 adults without formal legal training. Reported frequency of legal information searching and incidental encountering (IE) of legal information were assessed for significant relationships with personal characteristics and environmental factors. Age, income and previous experience with the legal system were associated with greater legal search frequency. Age, race and previous experience with the legal system were associated with greater frequency of legal IE. Exposure to multiple information sources and multiple mass media sources were associated with greater frequency of both legal search and IE. The study was exploratory in nature, but it serves as a first step in assessing civil legal information acquisition by American adults without specialized legal training. It also explicitly ties legal consciousness, and legal access, to information acquisition practices.
Dynamic demethylation of the IL2RA promoter during in vitro CD4+ T cell activation in association with IL2RA expression

ABSTRACT IL2RA, a subunit of the high affinity receptor for interleukin-2 (IL2), plays a crucial role in immune homeostasis. Notably, IL2RA expression is induced in CD4+ T cells in response to various stimuli and is constitutive in regulatory T cells (Tregs). We selected for our study 18 CpGs located within cognate regulatory regions of the IL2RA locus and characterized their methylation in naive, regulatory, and memory CD4+ T cells. We found that 5/18 CpGs (notably CpG + 3502) show dynamic, active demethylation during the in vitro activation of naive CD4+ T cells. Demethylation of these CpGs correlates with appearance of IL2RA protein at the cell surface. We found no influence of cis located SNP alleles upon CpG methylation. Treg cells show constitutive demethylation at all studied CpGs. Methylation of 9/18 CpGs, including CpG +3502, decreases with age. Our data thus identify CpG +3502 and a few other CpGs at the IL2RA locus as coordinated epigenetic regulators of IL2RA expression in CD4+ T cells. This may contribute to unravel how the IL2RA locus can be involved in immune physiology and pathology.
Upper bound estimation of the spectral abscissa for switched linear systems via coordinate transformations

In this paper, we develop computational procedures to approximate the spectral abscissa of the switched linear system via square coordinate transformations. First, we design iterative algorithms to obtain a sequence of the least $\mu_1$ measure. Second, it is shown that this sequence is convergent and its limit can be used to estimate the spectral abscissa. Moreover, the stopping condition of Algorithm 1 is also presented. Finally, an example is carried out to illustrate the effectiveness of the proposed method.
Understanding User Preferences and Goals in Recommender Systems

Recommender systems typically use collaborative filtering: information from your preferences (i.e. your ratings) is combined with that of other users to predict what other items you might also like. Much of the research in the field has focused on building algorithms that provide recommendations based purely on predicted accuracy [5]. However, these models make strong assumptions about how preferences come about, how stable they are, and how they can be measured [4]. Having a background in decision psychology I have studied how the preference elicitation methods of recommender systems can be better understood and improved based on psychological insights. I will illustrate this with an example of new choice-based preference interfaces we have developed. Users are more satisfied with a method that measures their preferences through a series of choices than with a rating-based preference elicitation, because the rating-based is more effortful and provides more obscure movies [2]. However, a drawback is that recommendation lists of choice-based preference elicitation contain mostly popular movies, and further research has investigated that showing trailers can help to reduce this popularity effect a bit as users are able to use the trailer to inspect less well-known items [3]. Moreover, recommender systems should also align with user goals. Many reallife recommender systems are evaluated mostly on (implicit) behavioral data such as clicks streams and viewing times. However, such an approach has limitations and I will show how a user-centric approach can help better understand why users are satisfied or not, for example why users prefer diversify over prediction accuracy as it reduces choice difficulty [8]. The behaviorist approach to evaluation also misses that users' short term goals (i.e. their current behavior) might not be representative of the goals they want to attain (i.e. their desired behavior) [1]. This is especially relevant in health and life style domains [6] where people are in need of support while changing their current behavior. I will elaborate on an example in the energy recommendation domain, and show how a different type of recommender approach and interface might help users to save more energy [7].