Miracle-dz/UniFAR-FTUs huggingface dataset:
β1-Adrenergic Receptor Contains Multiple IAk and IEk Binding Epitopes That Induce T Cell Responses with Varying Degrees of Autoimmune Myocarditis in A/J Mice

Myocarditis/dilated cardiomyopathy (DCM) patients can develop autoantibodies to various cardiac antigens and one major antigen is β1-adrenergic receptor (β1AR). Previous reports indicate that animals immunized with a β1AR fragment encompassing, 197–222 amino acids for a prolonged period can develop DCM by producing autoantibodies, but existence of T cell epitopes, if any, were unknown. Using A/J mice that are highly susceptible to lymphocytic myocarditis, we have identified β1AR 171–190, β1AR 181–200, and β1AR 211–230 as the major T cell epitopes that bind major histocompatibility complex class II/IAk or IEk alleles, and by creating IAk and IEk dextramers, we demonstrate that the CD4 T cell responses to be antigen-specific. Of note, all the three epitopes were found also to stimulate CD8 T cells suggesting that they can act as common epitopes for both CD4 and CD8 T cells. While, all epitopes induced only mild myocarditis, the disease-incidence was enhanced in animals immunized with all the three peptides together as a cocktail. Although, antigen-sensitized T cells produced mainly interleukin-17A, their transfer into naive animals yielded no disease. But, steering for T helper 1 response led the T cells reacting to one epitope, β1AR 181–200 to induce severe myocarditis in naive mice. Finally, we demonstrate that all three β1AR epitopes to be unique for T cells as none of them induced antibody responses. Conversely, animals immunized with a non-T cell activator, β1AR 201–220, an equivalent of β1AR 197–222, had antibodies comprising of all IgG isotypes and IgM except, IgA and IgE. Thus, identification of T cell and B cell epitopes of β1AR may be helpful to determine β1AR-reactive autoimmune responses in various experimental settings in A/J mice.
High prevalence of constipation and reduced quality of life in opioid-dependent patients treated with opioid substitution treatments

ABSTRACT Objectives To evaluate prevalence and severity of constipation and quality of life (QoL) in a cohort of opioid-addicted patients treated with opioid substitution treatments (OST). Methods: A total of 1057 heroin-dependent patients treated with methadone or buprenorphine were enrolled in a multicenter observational study. Constipation was assessed by Wexner Constipation Scoring System (Wexner CSS), QoL by General Health Questionnaire (GHQ-12). Results: 38.5% patients reported mild constipation, 33.3% reported moderate constipation, 14.8% severe constipation and 5.1% very severe constipation. Mean Wexner CSS score was 6.6 ± 4.8. 44.9% patients showed a GHQ-12 score ≥14; of these 18.3% patients showed a GHQ-12 score ≥20. Mean GHQ score was 13.8 ± 6.5. Mean Wexner CSS score was significantly higher in methadone patients (p = 0.004), in those taking psychoactive drugs (p = 0.0001) and in female (p < 0.0001) with respect to counterparts. Similarly, GHQ-12 mean scores were higher methadone group (p = 0.003), in those taking psychoactive drugs (p < 0.0001), and in female (p = 0.039) with respect to counterparts. ANOVA and ANCOVA showed a significant influence of methadone and female gender on Wexner CSS score while psychoactive drugs significantly influenced both tests. Conclusions: The present study shows that patients affected by opioid-dependence in OST with methadone and buprenorphine have a high prevalence of constipation and reduced QoL.
The mosaic of autoimmunity: prediction, autoantibodies, and therapy in autoimmune diseases--2008.

For more than two decades, the detection of serum autoanti-bodies has been used for the diagnosis and classification of autoimmune diseases. In addition, some autoantibodies have a prognostic significance or are used as markers for disease activity. In recent years a new piece in the mosaic of autoimmunity has clearly emerged – namely, the predictive value of autoantibodies. Indeed, many autoantibodies can be detected in the preclinical phase of autoimmune diseases many years before the disease becomes apparent; furthermore, they have a high diagnostic positive predictive value [1]. Among autoimmune rheumatic diseases, antibodies to RNP, Sm, dsDNA, cardiolipin, Ro and La have a PPV for systemic lupus erythematosus of 94–100%. According to the type of antibody, the appearance can precede clinical diagnosis by 7–10 years with a frequency that varies from 32% to 78% at the moment of
Molecular cloning and characterization of rat brain 2′, 3′ ‐cyclic nucleotide 3′ ‐phosphodiesterase isoform 2

We have isolated a cDNA coding for the larger isoform of the rat brain 2′,3′ ‐cyclic nucleotide 3′ ‐phosphodiesterase (CNP2), a protein associated with myelination in the central nervous system (CNS). The complete 420 amino acid sequence was deduced from the nucleotide sequence of the cDNA. Sequence comparisons show that rat CNP shares 96% homology with mouse, 84% with bovine, and 86% with human CNP. Errors in the published sequence of rat CNP1 have now been corrected. Comparisons with other proteins reveal several interesting conserved motifs, including two leucine repeat heptads, and two consensus motifs for phosphorylation in the N‐terminal domain of CNP2. © 1994 Wiley‐Liss, Inc.
Evidence behind the WHO guidelines: Hospital care for children: What is the most appropriate treatment for giardiasis?

The World Health Organization has produced guidelines for the management of common illnesses in hospitals with limited resources. This series reviews the scientific evidence behind WHO’s recommenda-tions. The WHO guidelines, and more reviews are available at: http://www.ichrc. org. This review addresses the question: What is the most appropriate treatment for giardiasis? The WHO Pocketbook of Hospital Care for Children (Pocketbook
Management of maxillofacial trauma in emergency: An update of challenges and controversies

Trauma management has evolved significantly in the past few decades thereby reducing mortality in the golden hour. However, challenges remain, and one such area is maxillofacial injuries in a polytrauma patient. Severe injuries to the maxillofacial region can complicate the early management of a trauma patient owing to the regions proximity to the brain, cervical spine, and airway. The usual techniques of airway breathing and circulation (ABC) management are often modified or supplemented with other methods in case of maxillofacial injuries. Such modifications have their own challenges and pitfalls in an already difficult situation.
Tiny ImageNet Challenge-Dissection of a convolutional neural network

In this project, we tried to achieve the best classification performance in the Tiny ImageNet Challenge using convolutional neural networks. Our constraint was a modest training infrastructure, as well as a limited time for training, which prompted us to try to get the most out of relatively shallow network architectures (compared to typical stateof-the-art networks). At the time of writing this report, our model achieved the fifth place in the class leaderboard, with a test accuracy of 44.0%. Another goal of this project was to see how different components of a network contributed to its performance. In order to achieve that, we evaluated different iterative versions of the same architecture, with increasing complexity. We then evaluated the validation accuracy of these different models so as to see how each added feature increased the accuracy. In particular, this analysis showed the importance of dropout units, especially in limiting overfitting.
Assessing the uncertainty of non-change in national-scale vegetation mapping using 3D wavelet transformed NDVI time series

The national or international mapping projects have usually long interval to update. To complement this long interval, satellite imagery obtained periodically and continuously is useful. This study is a preliminary step to generate annual spatial datasets comparable to the existing vegetation cover (EVC) layers using satellite imagery. We introduced and tested an approach based on 3D wavelet transform to analyze the multi-temporal satellite images. 3D wavelet transform based analysis was experimentally applied to NDVI images where identifying non-changed pixels. 3D wavelet transform can extract important patterns such as long term trends and short term events and analyze spatial and temporal relations with neighboring pixel. As a result, 3D wavelet transformed LLL values were much more stable across time than those of the original NDVI in non-changed areas. This study can provide fundamentals for image correction to ensure image comparability across years.
Influence of fiber delay fluctuation on a reference injection-locked optoelectronic oscillator

Optoelectronic oscillators (OEOs) are used to generate low phase noise microwave signals. A high performance OEO may act as a local oscillator that could lock the output of the absolute reference frequency, provided by the atomic transition. This study investigates the relationship between the phase shifts of a reference injection locked OEO and its fiber delay fluctuation. The impact of fiber delay fluctuation and the method to realize a good injection-locked OEO are discussed.
Surface Reconstruction from Points

This report surveys recent techniques for reconstructing surfaces from points. We describe four main ideas in the graphics literature: signed distance estimation, Voronoi-based reconstruction, implicit surface fitting, and moving least squares surfaces. The main challenges include reconstruction without surface normals, robustness to noise, accuracy to sharp features, and provable reconstruction guarantees. We compare various techniques and discuss possible avenues for future work. CR Categories: I.3. 5 [Computer Graphics]: Computational Geometry and Object Modeling—Curve, surface, solid, and object representations
Malnutrition and Clinical Outcome of 234 Head and Neck Cancer Patients who Underwent Percutaneous Endoscopic Gastrostomy

ABSTRACT Head and neck cancer (HNC) patients who underwent percutaneous endoscopic gastrostomy (PEG) present malnutrition risk and speech impairments. Their assessment relies on objective anthropometric/laboratory data. Focusing on HNC PEG patients, our aims were to evaluate: 1) outcome; 2) nutritional status when the patients underwent PEG; and 3) association of nutritional status/outcome, creating a survival predictive model. We evaluated the outcome based on NRS 2002, dietary assessment, body mass index (BMI), mid-upper arm circumference (MUAC), triceps skinfold thickness (TSF), mid-arm muscle circumference (MAMC), albumin, transferrin, and cholesterol on the day of gastrostomy. Using BMI, TSF, MAMC, and laboratory data, a survival predictive model was created. Of the 234 patients (cancer stages III–IV), 149 died, 33 were still PEG-fed, and 36 resumed oral intake (NRS-2002≥3, caloric needs <50% in all). BMI was 12.7–43. 189, 197, and 168 patients displayed, respectively, low MUAC, TSF, and MAMC. 91, 155, and 119 patients displayed low albumin, transferrin, and cholesterol. Albumin, cholesterol, and transferrin were strongly associated with the outcome. A predictive model was created, discriminating between short-term survivors (<4 months) and long-term survivors. HNC patients were malnourished. Using anthropometric/laboratory parameters, a predictive model provides discrimination between patients surviving PEG for <4 months and long-term survivors. Teams taking care of PEG patients may provide special support to potential short-term survivors.
Time-domain design of a linear antenna array for wideband shaped beams

This investigation reports a new design of a linear antenna array for wideband shaped patterns. The array consists of uniformly spaced antipodal Vivaldi elements. The proposed design process is based on the optimization of true-time delays by implementing a particle swarm algorithm. Simulation results show wideband shaped beam patterns of 15° and 30° degrees of coverage.
Risk factors associated with Salmonella enterica subsp. enterica contamination of chicken carcases in Senegal

1. The objective of this study was to identify the risk factors for Salmonella spp. contamination of Senegalese chicken carcases during slaughtering. One hundred and twenty traditional slaughterhouses were studied from January 2000 to December 2002 in and around Dakar. A questionnaire was administered to the slaughterers and samples of breast skin were taken to assess the Salmonella spp. status of chicken carcases. 2. Results showed that 43·3% of the chicken batches were contaminated with Salmonella spp. , with Salmonella Hadar and Salmonella Brancaster as the two main serovars. 3. Salmonella spp. contamination of the live birds before slaughtering was related to contamination of the carcases after slaughtering. Feed withdrawal before slaughtering and thorough cleaning and disinfection procedures decreased the risk of Salmonella contamination. One individual worker for each slaughtering stage was also associated with a decreased risk of Salmonella contamination. Using scalding water for plucking increased the risk of contamination. 4. These results will help slaughterers to produce safer products for local consumers.
Exploring the Human Connectome Topology in Group Studies

Visually comparing brain networks, or connectomes, is an essential task in the field of neuroscience. Especially relevant to the field of clinical neuroscience, group studies that examine differences between populations or changes over time within a population enable neuroscientists to reason about effective diagnoses and treatments for a range of neuropsychiatric disorders. In this paper, we specifically explore how visual analytics tools can be used to facilitate various clinical neuroscience tasks, in which observation and analysis of meaningful patterns in the connectome can support patient diagnosis and treatment. We conduct a survey of visualization tasks that enable clinical neuroscience activities, and further explore how existing connectome visualization tools support or fail to support these tasks. Based on our investigation of these tasks, we introduce a novel visualization tool, NeuroCave, to support group studies analyses. We discuss how our design decisions (the use of immersive visualization, the use of hierarchical clustering and dimensionality reduction techniques, and the choice of visual encodings) are motivated by these tasks. We evaluate NeuroCave through two use cases that illustrate the utility of interactive connectome visualization in clinical neuroscience contexts. In the first use case, we study sex differences using functional connectomes and discover hidden connectome patterns associated with well-known cognitive differences in spatial and verbal abilities. In the second use case, we show how the utility of visualizing the brain in different topological space coupled with clustering information can reveal the brain's intrinsic structure.
Provenance Trials in Alpine Range – Review and Perspectives for Applications in Climate Change

Effects of climate change on forest ecosystems and the mitigation of negative consequences to ecosystem functions and economic forest services are major challenges for current forest science and management [1-3]. Impact of climate change on forest ecosystems in Europe has been discussed controversially. It is generally agreed that increasing temperatures will lead to higher photosynthetic activity, faster growth and therefore higher forest net productivity, at least in large parts of central and northern Europe [4, 5]. However, increasing incidences of drought events and poor water supply are assumed to be limiting factors for tree growth in the future [6, 7], and the most productive coniferous species (e.g. Norway spruce) very likely cannot survive under future conditions in all parts of their natural range or cultivation area, respectively [8, 9]. This will have severe implications for forest management and the wood processing industry. For example, the financial effects of climate change due to biome shifts from productive coniferous forest to Mediterranean oak forests would result in a decrease of the expected value of European forest land between 14 and 50% [10].
A Risk Model of Requirements Change Impact Analysis

Software systems are critical assets to organisations as they support important business processes and workflow. To maintain the value of these assets, the requirements of software systems must evolve whenever there are changes in business needs. A key problem to organisations is implementing requirements change to the existing software systems. Such initiatives need proper analyses so that their effects could be determined before resources are spent. Impact analysis is therefore an important step in requirements change management. As a project, any change implementation involves risks. It is thus necessary for impact analysis to consider risk factors for implementing requirements change. However to date, the risk factors concerning requirement change are not much explored. This paper aims to identify the risk factors for implementing requirements change. The risk factors were identified through two qualitative approaches, namely a review of related work and a focus group study. The former involved fifty published articles and the latter concerned five domain experts. The collected risk factors from both studies were analysed by using content analysis. The risk factors form a risk model for analysing impacts of implementing requirements change. The model helps practitioners to assess the viability of requirements change requests.
Efficient video retrieval using index structure

Video retrieval remains a challenging problem since most of traditional query algorithms are ineffectual and time-consuming. In this article, we proposed a new video retrieval method, which segments the video stream by visual similarity between neighboring frames, and adopt the high-dimensional index structure to organize segments. Furthermore, a new similarity measure is brought forward to improve the query accuracy by synthetically taking into account the visual similarity and temporal order among video segments. Based on the similarity measure, we propose a novel video clip retrieval algorithm which achieves high query efficiency by using restricted sliding window to construct candidate video clips. Experimental results show that the proposed video retrieval method is efficient and effective. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 113–123, 2008
Effects of Feature-selective and Spatial Attention at Different Stages of Visual Processing

We investigated mechanisms of concurrent attentional selection of location and color using electrophysiological measures in human subjects. Two completely overlapping random dot kinematograms (RDKs) of two different colors were presented on either side of a central fixation cross. On each trial, participants attended one of these four RDKs, defined by its specific combination of color and location, in order to detect coherent motion targets. Sustained attentional selection while monitoring for targets was measured by means of steady-state visual evoked potentials (SSVEPs) elicited by the frequency-tagged RDKs. Attentional selection of transient targets and distractors was assessed by behavioral responses and by recording event-related potentials to these stimuli. Spatial attention and attention to color had independent and largely additive effects on the amplitudes of SSVEPs elicited in early visual areas. In contrast, behavioral false alarms and feature-selective modulation of P3 amplitudes to targets and distractors were limited to the attended location. These results suggest that feature-selective attention produces an early, global facilitation of stimuli having the attended feature throughout the visual field, whereas the discrimination of target events takes place at a later stage of processing that is only applied to stimuli at the attended position.
A Classification-System Improves the Intra- and Interobserver Reliability of Radiographic Diagnosis of “Pistol-Grip-Deformity”

Early detection of pistol-grip-deformity may be beneficial in optimising the outcome and the cost effectiveness of surgery. It is important to identify reliable radiographic parameters in assessing femoro-acetabular impingement (FAI) to develop a treatment algorithm. Radiographs of 47 patients ranging from “pistol grip deformity” to a normal head-neck-junction were measured for alpha angle and head ratio, and then classified by two different observers. The Bland-Altman plot was used for inter- and intraobserver agreement of alpha angle and head ratio. Inter- and intraobserver agreement for classification of “pistol grip deformity” was determined using weighted Cohen's kappa coefficient. Observer I achieved a kappa coefficient of 0.97. Observer II achieved a kappa coefficient of 0.92. An interobserver kappa coefficient between 0.87 and 0.92 was achieved by using a classification system. By testing for interobserver agreement, a bias of –0.004 with an upper limit of 0.461 and a lower limit of –0.47 was seen for the ratio and a bias of –3.7 with an upper limit of 17.2 and a lower limit of –24.6 for the alpha angle. Therefore, poor results were seen for intra- and interobserver reliability by using only a single plane for classification of “pistol grip deformity”. The strength of agreement could be improved by using a classification system (based on two planes).
Anomaly Detection and Fault Prognosis for Bearings

In this paper, a new bearing anomaly detection and fault prognosis method is proposed. The method detects bearing anomalies and then predicts its remaining useful life (RUL). To achieve these two goals, an autoregressive model, which is used to filter out fault-unrelated signals, is derived according to healthy bearing vibrational signals. A health index is developed to indicate bearing health conditions. Anomalies of bearings are detected by choosing an appropriate threshold with the aid of a Box-Cox transformation. A nonlinear model is built to track the bearings' degradation process and an extended Kalman filter is designed to model adaptation and RUL prediction. Finally, PRONOSTIA bearing data are used to demonstrate the effectiveness of the proposed method.
The angular apodization in coherent plane-wave compounding [Correspondence]

This article describes the relation between apodization in conventional focused imaging and apodization in coherent plane-wave compounding (CPWC). We pose the hypothesis that equivalent transmit beams can be produced with both methods if the transmit apodization is adequately transformed. We derive a relation between apodization in CPWC and in synthetic transmit aperture imaging (STAI), which we argue to be equivalent to conventional optimal multifocus imaging. We find that under certain conditions, the transformation of the apodization becomes trivial and the same window used in STAI can be applied for CPWC but extended to the whole angle sequence. We test the hypothesis with in silico data and find that the transformed apodization accurately mimics the objective transmit apodization, with differences in the lateral resolution between 3% and 6%.
Optical spectroscopy and microscopy of metallic nanostructures

OF DOCTORAL DISSERTATION HELSINKI UNIVERSITY OF TECHNOLOGY P.O. BOX 1000, FI-02015 TKK http://www.tkk. fi Author Name of the dissertation Manuscript submitted Manuscript revised Date of the defence Monograph Article dissertation (summary + original articles) Faculty Department Field of research Opponent(s) Supervisor Instructor Abstract