Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of neocortical interneurons using affinity propagation

In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.
Brain's change detection elicited by emotional facial expressions in depressed and non-depressed individuals

Brain’s change detection elicited by emotional facial expressions in depressed and non-depressed individuals Author: Kirsti Hannikainen Supervisor: Piia Astikainen Master’s thesis in psychology University of Jyväskylä February 2009 31 pages Previous research has shown that people suffering from depression typically have deficits in emotional information processing. These deficits can be seen in the level of behavior and also in the brain processes. The aim of our study was to investigate with event-related potentials, whether depressed individuals have differences in their brain processes compared to nondepressed individuals when emotional facial expressions are used as stimuli. We applied an oddball paradigm in order to elicit visual mismatch negativity and thus investigate brain’s change detection. The brain reacts to infrequently presented stimuli and recognizes the change in the pattern. We also investigated whether short psychotherapy (Acceptance and Commitment Therapy, ACT) alters the brain processes of depressed individuals. Individuals were shown pictures of human faces. In 80% of the faces, the expression was neutral. In the rest of the faces, the expression was emotional. Half of the pictures depicted fearful expression. The other half depicted happy expression. Pictures were presented in quasi-random order on a computer screen. Twenty depressed and ten non-depressed individuals participated in the study. During the experiment, a participant’s EEG was recorded with electrodes attached to their scalp. Depressed individuals were randomized in to two groups. The first group received therapy immediately. The second group received therapy after six weeks from the first EEG recording. Those in the immediate treatment group had their EEG recorded twice. Those in the delayed treatment group had EEGs recorded three times. The non-depressed group had an EEG recorded only once. Stimuli were the same in each recording session. The results suggested that depressed and nondepressed individuals processed emotional facial expressions differently. Non-depressed individuals were able to differentiate emotional and neutral expression from one another. In the depressed group, this differentiation did not occur. The P240 component’s discriminative power seemed to be lateralized to the posterior parts of right hemisphere, whereas N240’s discriminative power was localized in fronto-parietal regions. Component N170 seemed to be the best to reflect a visual mismatch negativity. N170 was able to differentiate between the two emotional expressions which components P240 and N240 were not able to do. These results were in line with previous research which has shown that depression is often characterized by the dysfunctional processing of emotional information.
Dental Anxiety among Medical and Paramedical Undergraduate Students of Malaysia

Aim. To assess the dental anxiety level among dental, medical, and pharmacy students of MAHSA University, Malaysia. Materials and Methods. A cross-sectional questionnaire study was conducted among 1500 undergraduate students of MAHSA University. The Modified Dental Anxiety Scale (MDAS) was used to measure dental anxiety among the study population. The responses were assessed by 5-point likert scale ranging from 1 to 5. The level of anxiety was categorized into lowly anxious (5–11), moderately anxious (12–18), and severely anxious ≥19. Out of 1500 students enrolled, 1024 students (342 males and 682 females) completed and returned the questionnaire having response rate of 68.26%. Results. There was a statistically significant difference (P < 0.001) when the mean dental anxiety scores were compared among the three faculties and dental students had lowest mean score (11.95 ± 4.21). The fifth year (senior) dental students scored significantly (P = 0.02) lower mean anxiety score as compared to the first dental students (junior). The students were anxious mostly about tooth drilling and local anesthetic injection. Conclusions. Dental students have a significantly low level of dental anxiety as compared with medical and pharmacy students. Incorporation of dental health education in preuniversity and other nondental university curriculums may reduce dental anxiety among the students.
UAS-Based Change Detection of the Glacial and Proglacial Transition Zone at Pasterze Glacier, Austria

Glacier-related applications of unmanned aircraft systems (UAS) in high mountain regions with steep topography are relatively rare. This study makes a contribution to the lack of UAS applications in studying alpine glaciers in the European Alps. We transferred an established workflow of UAS-based change detection procedures to Austria’s largest glacier, the Pasterze Glacier. We focused on a selected part of the glacier tongue and its proglacial vicinity to obtain detailed knowledge of (i) the behavior of a lateral crevasse field, (ii) the evolution of glacier surface structures and velocity fields, (iii) glacier ablation behavior and the current glacier margin, and (iv) proglacial dead ice conditions and dead ice ablation. Based on two UAS flight campaigns, accomplished in 2016 (51 days apart), we produced digital elevation models (DEMs) and orthophotos with a ground sampling distance (GSD) of 0.15 m using Structure-from-Motion (SfM) photogrammetry. Electrical resistivity tomography (ERT) profiling was additionally conducted in the proglacial area. Results indicate distinct changes in the crevasse field with massive ice collapses, rapid glacier recession, surface lowering (mean of −0.9 m), and ice disintegration at the margins, calculated degree day factors on the order of −7 to −11 mm d−1·°C−1 for clean ice parts, and minimal changes of the debris-covered dead ice in the proglacial area. With this contribution we highlight the benefit of UAS in comparison to commonly used terrestrial methods and satellite-related approaches.
A Structural and Psychometric Evaluation of a Situational Judgment Test: The Workplace Skills Survey

Some basic but desirable employability skills are antecedents of job performance. The Workplace Skills Survey (WSS) is a 48-item situational judgment test (SJT) used to assess non-technical workplace skills for both entry-level and experienced workers. Unfortunately, the psychometric evidence for use of its scores is far from adequate. The purpose of current study was two-fold: (a) to examine the proposed structure of WSS scores using confirmatory factor analysis (CFA), and (b) to explore the WSS item functioning and performance using item response theory (IRT). A sample of 1,018 Jamaican unattached youth completed the WSS instrument as part of a longitudinal study on the efficacy of a youth development program in Jamaica. Three CFA models were tested for the construct validity of WSS scores. Parameter estimations of item difficulty, item discrimination, and examinee’s proficiency estimations were obtained with item response theory (IRT) and plotted in item characteristics curves (ICCs) and item information curves (IICs). Results showed that the WSS performed quite well as a whole and provided precise measurement especially for respondents at latent trait levels of -0.5 and +1.5. However, some modifications of some items were recommended. CFA analyses showed supportive evidence of the one-factor construct model, while the six-factor model and higher-order model were not achieved. Several directions for future research are suggested.
Human papillomavirus type 18 E5 oncogene supports cell cycle progression and impairs epithelial differentiation by modulating growth factor receptor signalling during the virus life cycle

Deregulation of proliferation and differentiation-dependent signalling pathways is a hallmark of human papillomavirus (HPV) infection. Although the manipulation of these pathways by E6 and E7 has been extensively studied, controversies surround the role of the E5 oncoprotein during a productive virus life cycle. By integrating primary keratinocytes harbouring wild type or E5 knockout HPV18 genomes with pharmacological and gain/loss of function models, this study aimed to provide molecular information about the role of E5 in epithelial proliferation and differentiation. We show that E5 contributes to cell cycle progression and unscheduled host DNA synthesis in differentiating keratinocytes. E5 function correlates with increased EGFR activation in differentiating cells and blockade of this pathway impairs differentiation-dependent cell cycle progression of HPV18 containing cells. Our findings provide a functional requirement of enhanced EGFR signalling for suprabasal cellular DNA synthesis during the virus life cycle. They also reveal an unrecognised contribution of E5 towards the impaired keratinocyte differentiation observed during a productive HPV infection. E5 suppresses a signalling axis consisting of the keratinocyte growth factor receptor (KGFR) pathway. Inhibition of this pathway compensates for the loss of E5 in knockout cells and re-instates the delay in differentiation. The negative regulation of KGFR involves suppression by the EGFR pathway. Thus our data reveal an unappreciated role for E5-mediated EGFR signalling in orchestrating the balance between proliferation and differentiation in suprabasal cells.
GazeArchers: playing with individual and shared attention in a two-player look&shoot tabletop game

Gaze can complement touch on surfaces for fast target selection and occlusion-free input. In this work, we look beyond single-user application of gaze and touch and explore how gaze can be leveraged for collaborative use. We present the design of a two-player shooter game in which targets are gaze-aware and able to react differently to attention by one of the players versus shared attention of both players. The game-play, evaluated in a study with 14 users, encourages users to adopt different strategies switching between individual and shared attention to achieve their collaborative goal.
Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation.

The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this technique to an activated microglia cell system to examine changes in the intracellular and extracellular proteomes. Microglia become activated when their homeostatic microenvironment is disrupted. There are varying degrees of microglial activation, and we chose to focus on the proinflammatory reactive state that is induced by exposure to such stimuli as lipopolysaccharide (LPS) and interferon-gamma (IFN-γ). Using an improved shotgun proteomics approach, we identified 5497 proteins in the whole-cell proteome and 4938 proteins in the secretome that were associated with the activation of BV2 mouse microglia by LPS or IFN-γ. Of the differentially expressed proteins in stimulated microglia, we classified pathways that were related to immune-inflammatory responses and metabolism. Our label-free parallel reaction monitoring (PRM) approach made it possible to comprehensively measure the hyper-multiplex quantitative value of each protein by high-resolution mass spectrometry. Over 450 peptides that corresponded to pathway proteins and direct or indirect interactors via the STRING database were quantified by label-free PRM in a single run. Moreover, we performed a longitudinal quantification of secreted proteins during microglial activation, in which neurotoxic molecules that mediate neuronal cell loss in the brain are released. These data suggest that latent pathways that are associated with neurodegenerative diseases can be discovered by constructing and analyzing a pathway network model of proteins. Furthermore, this systematic quantification platform has tremendous potential for applications in large-scale targeted analyses. The proteomics data for discovery and label-free PRM analysis have been deposited to the ProteomeXchange Consortium with identifiers and , respectively.
Existence of confinement phase in quantum electrodynamics

We show that the four-dimensional U(1) gauge theory in the continuum formulation has a confining phase (exhibiting area law of the Wilson loop) in the strong coupling region above a critical coupling gc. This result is obtained by taking into account topological non-trivial sectors in U(1) gauge theory. The derivation is based on the reformulation of gauge theory as a deformation of a topological quantum field theory and subsequent dimensional reduction of the D-dimensional topological quantum field theory to the (D-2)-dimensional nonlinear sigma model. The topological quantum field theory part of the four-dimensional U(1) gauge theory is exactly equivalent to the two-dimensional O(2) nonlinear sigma model. The confining (resp. Coulomb) phase of U(1) gauge theory corresponds to the high (resp. low) temperature phase of O(2) nonlinear sigma model and the critical point gc is determined by the BerezinskiiKosterlitz-Thouless phase transition temperature. The quark (charge) confinement in the strong coupling phase is caused by the vortex condensation. Thus the continuum gauge theory has the direct correspondence to the compact formulation of lattice gauge theory.
Modulation of buccal muscle contractility by serotonergic metacerebral cells in Aplysia: evidence for a role of cyclic adenosine monophosphate.

SUMMARY AND CONCLUSIONS 1. Experiments were performed to test the hypothesis that cyclic adenosine mono- phosphate (CAMP) may mediate the effects of serotonin and the metacerebral cell (MCC) on contractility of the accessory radula closer muscle (ARC) of Aplysia. 2. A cell-free homogenate of the ARC muscle showed a dose-related increase in the rate of accumulation of CAMP in the presence of serotonin. Serotonin did not reduce phos- phodiesterase activity in the muscle homog- enate. These results, therefore, indicate that the ARC contains a serotonin-sensitive adenylate cyclase. 3. The intact ARC muscle showed a dose- related increase in the synthesis (accumula- tion of radioactive precursor) and total levels of CAMP in the presence of serotonin. 4. Firing of a single MCC cell (mean, 297 spikes) produced a statistically significant increase of the synthesis of CAMP. The mean synthesis was 3.5 times higher in experimen- tal compared to paired control muscles from the same animal. This represents an 8% in- crease per MCC spike. 5. Two eighth position analogs of CAMP (8-BT CAMP and 8-PCPT CAMP) enhanced ARC muscle contractions elicited by fixed bursts of motor neuron spikes. The potentia- tion occurred in spite of the fact that the CAMP analogs reduced the size of the EJPs in the muscle. 6. The effect of the MCC in enhancing contractions of ARC muscle was enhanced in magnitude and duration by the phospho- diesterase inhibitor RO 20- 1724. 7. The data support the hypothesis that the modulatory action of serotonin at buccal muscle is mediated by CAMP.
Reliability of the Radiographic Sagittal and Frontal Tibiotalar Alignment after Ankle Arthrodesis

Background Accurate measurement of the tibiotalar alignment is important in radiographic outcome assessment of ankle arthrodesis (AA). In studies, various radiological methods have been used to measure the tibiotalar alignment leading to facultative misinterpretation of results. However, to our knowledge, no previous study has investigated the reliability of tibiotalar alignment measurement in AA. We aimed to investigate the reliability of four different methods of measurement of the frontal and sagittal tibiotalar alignment after AA, and to further clarify the most reliable method for determining the longitudinal axis of the tibia. Methods Thirty-eight weight bearing anterior to posterior and lateral ankle radiographs of thirty-seven patients who had undergone AA with a two screw fixation technique were selected. Three observers measured the frontal tibiotalar angle (FTTA) and the sagittal tibiotalar angle (STTA) using four different methods. The methods differed by the definition of the longitudinal tibial axis. Method A was defined by a line drawn along the lateral tibial border in anterior to posterior radiographs and along the posterior tibial border in lateral radiographs. Method B was defined by a line connecting two points in the middle of the proximal and the distal tibial shaft. Method C was drawn „freestyle”along the longitudinal axis of the tibia, and method D was defined by a line connecting the center of the tibial articular surface and a point in the middle of the proximal tibial shaft. Intra- and interobserver correlation coefficients (ICC) and repeated measurement ANOVA were calculated to assess measurement reliability and accuracy. Results All four methods showed excellent inter- and intraobserver reliability for the FTTA and the STTA. When the longitudinal tibial axis is defined by connecting two points in the middle of the proximal and the distal tibial shaft, the highest interobserver reliability for the FTTA (ICC: 0.980; CI 95%: 0.966–0.989) and for the STTA (ICC: 0.997; CI 95%: 0.996–0.999) is provided. Intergroup analysis for FTTA measurements revealed a statistically significant difference between the method in which the lateral border of the tibia was used to determine the longitudinal axis of the tibia, and the other methods in which the longitudinal axis was defined by bisecting the tibia. Conclusions When the longitudinal axis of the tibia is defined by connecting two points in the middle of the proximal and the distal tibial shaft for measuring the FTTA and STTA, the most favorable interobserver reliability is provided. Therefore, this method can be recommended for evaluating the frontal and the sagittal alignment on anterior to posterior and lateral radiographs after ankle arthrodesis.
Effective simulation model reuse: a case study for AMHS modeling

The application of simulation as a performance estimation tool in automated material handling system design is well documented, as is the amount of time required to build, debug, and analyze a typical AMHS simulation model. In the rapid growth, high technology industry, it is infeasible to continually employ sufficient staff to create unique models of all of the possible scenarios that require examination. Typically, the model is not complete before the project requirements have been modified. An alternative to unique model creation is to reuse an existing generic model. Generic models are similar to a group of software tools called simulators: software packages that contain a pre-programmed model. Investigation has indicated that a special purpose reusable generic model, designed to address the set of issues faced by a specific commercial entity, is efficient and necessary for fast model turnaround. If correctly developed, the generic model could be reused, thereby reducing model building time as well as increasing simulation accuracy. The paper discusses the use of such a model and illustrates the improvement to model build cycle time.
Immunogenicity of Intranasally Administered Meningococcal Native Outer Membrane Vesicles in Mice

ABSTRACT Colonization of the human nasopharyngeal region by Neisseria meningitidis is believed to lead to natural immunity. Although the presence of bactericidal antibody in serum has been correlated with immunity to meningococcal disease, mucosal immunity at the portal of entry may also play an important role. This study was undertaken to examine in mice the possibility of safely using native outer membrane vesicles (NOMV) not exposed to detergent as an intranasal (i.n.) vaccine. The mucosal and systemic responses of mice to intranasal and intraperitoneal (i.p.) vaccination with NOMV were compared over a range of doses from 0.1 to 20 μg. Intranasal vaccination of mice with NOMV induced a strong systemic bactericidal antibody response, as well as a strong local immunoglobulin A immune response in the lung as determined by assay of lung lavage fluid by enzyme-linked immunosorbent assay and lung antibody secreting cells by enzyme-linked immunospot assay. However, 8- to 10-fold-higher doses of NOMV were required i.n. compared to i.p. to elicit an equivalent bactericidal antibody response in serum. Some NOMV vaccine was aspirated into the lungs of mice during i.n. immunization and resulted in an acute inflammatory response that peaked at 1 to 2 days postimmunization and was cleared by day 7. These results indicate that i.n. delivery of meningococcal NOMV in mice is highly effective in eliciting the production of both a mucosal immune response and a systemic bactericidal antibody response.
Sparse appearance based modeling for robot localization

In appearance based robot localization a new image is matched with every image in the database. In this paper we describe how to reduce the number of images in this database with minimal loss of information and thereby increasing the efficiency of localization significantly. First we build an appearance based model consisting of a graph in which the nodes denote images and links denote relations between images. This graph is then pruned using the connected dominating set algorithm. The method is tested on an image set acquired by a mobile robot equipped with an omnidirectional camera driving around in an office environment, as well as sets of images taken while driving through a real furnished home environment