Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance of Molecular Approaches for Aspergillus Detection and Azole Resistance Surveillance in Cystic Fibrosis

Aspergillus fumigatus triazole resistance is an emerging concern for treating chronically infected/colonized patients. This study sought to evaluate the performance of PCR assays to detect Aspergillus fungi together with azole resistance in sputum samples from cystic fibrosis (CF) patients. In total, 119 sputum samples from 87 CF patients were prospectively processed for Aspergillus detection by means of mycological culture and four qPCR assays, 2 in-house methods and two commercial multiplex real-time PCR assays simultaneously detecting Aspergillus and the most relevant cyp51A gene mutations (MycoGENIE® and AsperGenius®). Azole susceptibility of A. fumigatus isolates was assessed using Etest® method and cyp51A gene mutation were characterized by sequencing. The overall rate of Aspergillus detection with the four qPCR assays ranged from 47.9 to 57.1%, contrasting with 42/119 (35.3%) positive cultures with A. fumigatus. The high sensitivity of PCR on sputum could then contribute to more effective grading of Aspergillus disease in CF patients. Five out of 41 isolated strains (12.2%) exhibited azole-resistant MIC patterns, three of which harbored cyp51A mutations and only 1/3 with the sequence TR34/L98H. Combined with culture, PCR assay achieved high sensitivity Aspergillus screening in CF samples. However, cyp51A targeting was only moderately effective for azole resistance monitoring, while Aspergillus resistance remains of great concern.
Supervised Classification of Aspectual Verb Classes in German - Subcategorization-Frame-Based vs Window-Based Approach: A Comparison

The present study examines the results of two experiments: the aspectual classification of German verbs within a window-based distributional framework and the classification within a subcategorization-frame-based framework. The predictive power of pure, unstructured co-occurrences of verbs is compared against that of linguistically motivated, well defined co-occurrences which we denote as informed distributional framework. Using a support vector machine classifier and a classification into an extended Vendler classification (Vendler, 1967) as the gold standard, we observe excellent results in both frameworks which perform almost on a par.
Using a high spatial resolution tactile sensor for intention detection

Intention detection is the interpretation of biological signals with the aim of automatically, reliably and naturally understanding what a human subject desires to do. Although intention detection is not restricted to disabled people, such methods can be crucial in improving a patient's life, e.g., aiding control of a robotic wheelchair or of a self-powered prosthesis. Traditionally, intention detection is done using, e.g., gaze tracking, surface electromyography and electroencephalography. In this paper we present exciting initial results of an experiment aimed at intention detection using a high-spatial-resolution, high-dynamic-range tactile sensor. The tactile image of the ventral side of the forearm of 9 able-bodied participants was recorded during a variable-force task stimulated at the fingertip. Both the forces at the fingertip and at the forearm were synchronously recorded. We show that a standard dimensionality reduction technique (Principal Component Analysis) plus a Support Vector Machine attain almost perfect detection accuracy of the direction and the intensity of the intended force. This paves the way for high spatial resolution tactile sensors to be used as a means for intention detection.
Barley root hair growth and morphology in soil, sand, and water solution media and relationship with nickel toxicity

Barley, Hordeum vulgare (Doyce), was grown in the 3 media of soil, hydroponic sand solution (sand), and hydroponic water solution (water) culture at the same environmental conditions for 4 d. Barley roots were scanned, and root morphology was analyzed. Plants grown in the 3 media had different root morphology and nickel (Ni) toxicity response. Root elongations and total root lengths followed the sequence soil > sand > water. Plants grown in water culture were more sensitive to Ni toxicity and had greater root hair length than those from soil and sand cultures, which increased root surface area. The unit root surface area as root surface area per centimeter of length of root followed the sequence water > sand > soil and was found to be related with root elongation. Including the unit root surface area, the difference in root elongation and 50% effective concentration were diminished, and percentage of root elongations can be improved with a root mean square error approximately 10% for plants grown in different media. Because the unit root surface area of plants in sand culture is closer to that in soil culture, the sand culture method, not water culture, is recommended for toxicity parameter estimation. Environ Toxicol Chem 2016;35:2125–2133. © 2016 SETAC
An in Silico Approach for Understanding the Complex Intercellular Interaction Patterns in Cancer Cells

Intercellular interaction allows cancer cells to preserve their malignance and through cell junctions to induce malignance in neighbouring cells and receive nutrients from them. The Wnt (wingless-related integration site) signalling pathway plays an important role in the formation of intercellular communications. In this work, we explore the complex interactions patterns of intercellular communication in cancer cells using an in silico modelling and simulation methodology developed by us. The proposed cellular signalling model, characterized by a multicompartmental nature, provides symbolic abstractions and accurate algorithms to model both intracellular and intercellular behaviours. In particular, in this work, we propose an in silico model and simulation of the formation of different communication channels, involving the Wnt signalling pathway. The final purpose of this study is to propose target molecules leading to break the communication between a cancer cell and surrounding normal cells. In this way, it is not necessary to carry out long series of different in vitro experiments, but only a few, because the focus should be only on the key molecules, which saves time and money. We observed, using in silico experiments, how the inhibition of Wnt signalling pathway prevents that the cells surrounding a cancerous cell are transformed.
Is my patient actually getting better? Application of the McNemar test for demonstrating the change at a single subject level

Abstract Purpose: The aim of the current work is to provide a novel method for demonstrating the modification of a single patient’s performance on questionnaires and scales. The minimal detectable change (MDC), a statistics indicating the minimal change in measure not attributable to random variation, is commonly used in rehabilitation for this purpose. However, the MDC has some important drawbacks (e.g. it cannot be calculated on scores from ordinal tests and it can be only used for full questionnaire). Method: Review of the MDC and its limitations and application of the McNemar test on simulated data from single subjects. Results: We propose to use the McNemar test to check if the proportion of test items affirmed by a patient after rehabilitation is significantly different from the same proportion before rehabilitation. A significant McNemar test would indicate a non-random modification of the patient’s score and thus a true modification of his/her performance. Conclusions: The application of the McNemar test to questionnaires and scales offers a simple method for demonstrating the modification of a single patient’s performance. This use of the McNemar test overcomes the weaknesses of the MDC and gives support to the clinician in assisting him/her to convincingly communicate a non-negligible modification of the patient’s status. IMPLICATIONS FOR REHABILITATION Measuring the change in patients’ status is of paramount importance in medicine and rehabilitation. However, tracking the change in rehabilitation is difficult. For example, the minimal detectable change cannot be calculated on scores from ordinal questionnaires and tests, which are widely used as rehabilitative outcome measures. We propose here to use a McNemar test to check if the proportion of test items affirmed or passed by is significantly different between two conditions (e.g. before vs. after rehabilitation). Similar to the minimal detectable change, the significant McNemar test would indicate a non-random modification of the patient’s test score. In addition, the McNemar test can be calculated on ordinal data, thus overcoming some of the minimal detectable change weaknesses.
Tracking Human Motions in Photographing

Due to the portability of smart phones, more and more people tend to take photos with smart phones. However, energy-saving continues to be a thorny problem, since photographing is a rather power hungry function. To extend the battery life of phones while taking photos, we propose a context-aware energy-saving scheme called “SenSave. ” SenSave senses the user’s activities during photographing and adopts suitable energy-saving strategies accordingly. SenSave works based on the observation that a lot of energy during photographing is wasted in preparations before shooting. By leveraging the low power-consuming embedded sensors, such as accelerometer and gyroscope, we can recognize the user’s activities and reduce unnecessary energy consumption. Besides, by maintaining an activity state machine, SenSave can determine the user’s activity progressively and improve the recognition accuracy. Experiment results show that SenSave can recognize the user’s activities with an average accuracy of 95.5% and reduce the energy consumption during photographing by 30.0%, when compared to the approach by frequently turning ON/OFF the camera or screen. Additionally, we enhance “SenSave” by introducing an extended Markov chain to predict the next activity state and adopt the energy-saving strategy in advance. Then, we can reduce the energy consumption during photographing by 36.1%.
Combined Phacoemulsification and Goniosynechialysis under an Endoscope for Chronic Primary Angle-Closure Glaucoma

Purpose To investigate the clinical efficacy and safety of combined phacoemulsification with goniosynechialysis (GSL) under an ophthalmic endoscope for chronic primary angle-closure glaucoma and coexisting cataract. Methods This is a retrospective study. The intraocular pressure (IOP), best-corrected visual acuity (BCVA), and number of glaucoma medications at baseline and each postoperative follow-up visit were recorded. Other measurements included supraciliochoroidal fluid measured by anterior segment optical coherence tomography, corneal endothelial cell density (ECD), and peripheral anterior synechia (PAS). All patients were followed for more than a year. Results Thirty-eight eyes of 31 patients were included. The mean follow-up duration was 16.3 ± 3.9 months. The IOP decreased from 22.2 ± 9.3 mmHg at baseline to 15.4 ± 4.2 mmHg at the last follow-up (P < 0.001). The mean number of glaucoma medications (0.1 ± 0.6) at the last follow-up was significantly lower than the preoperative number (2.3 ± 1.1) (P < 0.001). All patients achieved improved or stable visual acuity after surgery. All patients achieved a complete opened angle after GSL. The postoperative complications included hyphema (7.9%), exudation (5.3%), transiently elevated IOP (55.3%), and supraciliochoroidal fluid (40%). Conclusions Combined phacoemulsification and GSL under an endoscope can completely reopen PAS and is an effective and safe method for patients with chronic primary angle-closure glaucoma and coexisting cataract.
A DEVELOPMENTAL GRASP LEARNING SCHEME FOR HUMANOID

A DEVELOPMENTAL GRASP LEARNING SCHEME FOR HUMANOID ROBOTS Bozcuoğlu, Asil Kaan M.Sc., Department of Computer Engineering Supervisor : Assoc. Prof. Dr. Erol Şahin Co-Supervisor : Asst. Prof. Dr. Erhan Öztop September 2012, 64 pages While an infant is learning to grasp, there are two key processes that she uses for leading a successful development. In the first process, infants use an intuitional approach where the hand is moved towards the object to create an initial contact regardless of the object properties. The contact is followed by a tactile grasping phase where the object is enclosed by the hand. This intuitive grasping behavior leads an grasping mechanism, which utilizes visual input and incorporates this into the grasp plan. The second process is called scaffolding, a guidance by stating how to accomplish the task or modifying its behaviors by interference. Infants pay attention to such guidance and understand the indication of important features of an object from 9 months of age. This supervision mechanism plays an important role for learning how to grasp certain objects in a proper way. To simulate these behavioral findings, a reaching and a tactile grasping controller was implemented on iCub humanoid robot which allowed it to reach an object from different directions, and enclose its fingers to cover the object. With these, a human-like grasp learning for iCub is proposed. Namely, the first stage is an unsupervised learning where the robot is experimenting how to grasp objects. The second stage is supervised learning phase where a caregiver modifies the end-effector’s position when the robot is mistaken. iv By doing several experiments for two different grasping styles, we observe that the proposed methodology shows a better learning rate comparing to the scaffolding-only learning mechanism.
Blog Community Discovery and Evolution Based on Mutual Awareness Expansion

There are information needs involving costly decisions that cannot be efficiently satisfied through conventional Web search engines. Alternately, community centric search can provide multiple viewpoints to facilitate decision making. We propose to discover and model the temporal dynamics of thematic communities based on mutual awareness, where the awareness arises due to observable blogger actions and the expansion of mutual awareness leads to community formation. Given a query, we construct a directed action graph that is time-dependent, and weighted with respect to the query. We model the process of mutual awareness expansion using a random walk process and extract communities based on the model. We propose an interaction space based representation to quantify community dynamics. Each community is represented as a vector in the interaction space and its evolution is determined by a novel interaction correlation method. We have conducted experiments with a real-world blog dataset and have promising results for detection as well as insightful results for community evolution.
Charge-transfer complexes: new perspectives on an old class of compounds

The discovery of the organic metal TTF–TCNQ in 1973 led to an explosion of research conducted on organic charge-transfer complexes. While these materials have been studied intensely for several decades, the research was mostly aimed at the discovery of materials with high room-temperature conductivity or high-temperature superconductivity. Recently, attention has turned to technologically-relevant properties of charge-transfer complexes, such as ambipolar transport, metallicity, photoconductivity, ferroelectricity or magnetoresistance. This manuscript reviews the growth, structure and properties of charge-transfer complexes and underlines recent progress in their application in organic devices. Their prospects in future applications are discussed, as well as the challenges yet to be overcome to understand the fundamental parameters governing their operation.
High-fidelity phenotyping: richness and freedom from bias

Abstract Electronic health record phenotyping is the use of raw electronic health record data to assert characterizations about patients. Researchers have been doing it since the beginning of biomedical informatics, under different names. Phenotyping will benefit from an increasing focus on fidelity, both in the sense of increasing richness, such as measured levels, degree or severity, timing, probability, or conceptual relationships, and in the sense of reducing bias. Research agendas should shift from merely improving binary assignment to studying and improving richer representations. The field is actively researching new temporal directions and abstract representations, including deep learning. The field would benefit from research in nonlinear dynamics, in combining mechanistic models with empirical data, including data assimilation, and in topology. The health care process produces substantial bias, and studying that bias explicitly rather than treating it as merely another source of noise would facilitate addressing it.
Improved One-Way Hash Chain and Revocation Polynomial-Based Self-Healing Group Key Distribution Schemes in Resource-Constrained Wireless Networks

Self-healing group key distribution (SGKD) aims to deal with the key distribution problem over an unreliable wireless network. In this paper, we investigate the SGKD issue in resource-constrained wireless networks. We propose two improved SGKD schemes using the one-way hash chain (OHC) and the revocation polynomial (RP), the OHC&RP-SGKD schemes. In the proposed OHC&RP-SGKD schemes, by introducing the unique session identifier and binding the joining time with the capability of recovering previous session keys, the problem of the collusion attack between revoked users and new joined users in existing hash chain-based SGKD schemes is resolved. Moreover, novel methods for utilizing the one-way hash chain and constructing the personal secret, the revocation polynomial and the key updating broadcast packet are presented. Hence, the proposed OHC&RP-SGKD schemes eliminate the limitation of the maximum allowed number of revoked users on the maximum allowed number of sessions, increase the maximum allowed number of revoked/colluding users, and reduce the redundancy in the key updating broadcast packet. Performance analysis and simulation results show that the proposed OHC&RP-SGKD schemes are practical for resource-constrained wireless networks in bad environments, where a strong collusion attack resistance is required and many users could be revoked.
Takes Tutu to Ballet

Mirrors have been a core feature in ballet studios for over five hundred years. While physical mirrors provide real-time feedback, they do not inform dancers of their errors. Thus, technologies such as motion tracking have been used to augment what a physical mirror can provide. Current augmented mirrors, however, only implement one mode of communication, usually visual, and do not provide a holistic feedback to dancers that includes all the feedback elements commonly used in ballet classes. We conducted a mixed-method study with 16 novices and 16 expert dancers in which we compared two different modes of communication (visual and verbal), two different types of feedback (value and corrective) and two levels of guidance (mirror, or no mirror). Participants' ballet technique scores were evaluated by a remote teacher on eight ballet combinations (tendue, adagio, pirouette, saute, plié, degage, frappe and battement tendue). We report quantitative and qualitative results that show how the level of guidance, mode of communication, and type of feedback, needs to be tuned in different ways for novices and experts.
Improved interoceptive awareness in chronic low back pain: a comparison of Back school versus Feldenkrais method

Abstract Purpose: To determine the efficacy of the Feldenkrais method for relieving pain in patients with chronic low back pain (CLBP) and the improvement of interoceptive awareness. Method: This study was designed as a single-blind randomized controlled trial. Fifty-three patients with a diagnosis of CLBP for at least 3 months were randomly allocated to the Feldenkrais (mean age 61.21 ± 11.53 years) or Back School group (mean age 60.70 ± 11.72 years). Pain was assessed using the visual analog scale (VAS) and McGill Pain Questionnaire (MPQ), disability was evaluated with the Waddel Disability Index, quality of life was measured with the Short Form-36 Health Survey (SF-36), and mind–body interactions were studied using the Multidimensional Assessment of Interoceptive Awareness Questionnaire (MAIA). Data were collected at baseline, at the end of treatment, and at the 3-month follow-up. Results: The two groups were matched at baseline for all the computed parameters. At the end of treatment (Tend), there were no significant differences between groups regarding chronic pain reduction (p = 0.290); VAS and MAIA-N sub scores correlated at Tend (R = 0.296, p = 0.037). By the Friedman analysis, both groups experienced significant changes in pain (p < 0.001) and disability (p < 0.001) along the investigated period. Conclusions: The Feldenkrais method has comparable efficacy as Back School in CLBP. Implications for rehabilitation The Feldenkrais method is a mind–body therapy that is based on awareness through movement lessons, which are verbally guided explorations of movement that are conducted by a physiotherapist who is experienced and trained in this method. It aims to increase self-awareness, expand a person’s repertoire of movements, and to promote increased functioning in contexts in which the entire body cooperates in the execution of movements. Interoceptive awareness, which improves with rehabilitation, has a complex function in the perception of chronic pain and should be investigated further in future research. The efficacy of the Feldenkrais method is comparable with that of BS for nonspecific chronic low back pain. The physician can recommend a body–mind rehabilitation approach, such as the Feldenkrais method, or an educational and rehabilitation program, such as BS, to the patient, based on his individual needs. The 2 rehabilitation approaches are equally as effective in improving interoceptive awareness.
Learning Dutch Coreference Resolution

This paper presents a machine learning approach to the resolution of coreferential relations between nominal constituents in Dutch. It is the first significant automatic approach to the resolution of coreferential relations between nominal constituents for this language. The corpusbased strategy was enabled by the annotation of a substantial corpus (ca. 12,500 noun phrases) of Dutch news magazine text with coreferential links for pronominal, proper noun and common noun coreferences. Based on the hypothesis that different types of information sources contribute to a correct resolution of different types of coreferential links, we propose a modular approach in which a separate module is trained per NP type.
Efficacy and Safety of Targeted High‐Intensity Medium‐Band (304–312 nm) Ultraviolet B Light in Pediatric Vitiligo

Phototherapy is a commonly used treatment for vitiligo that has demonstrated safety and efficacy. High‐intensity targeted ultraviolet B (UVB) light (304–312 nm) delivered using a phototherapy device is a useful therapeutic option because it can induce repigmentation in a short time without global exposure to radiation, but information regarding this device in children is limited.