Miracle-dz/UniFAR-FTUs huggingface dataset:
Mindfulness-based cognitive therapy is effective as relapse prevention for patients with recurrent depression in Scandinavian primary health care.

This study examined the effectiveness of mindfulness-based cognitive therapy (MBCT) in primary care for patients with recurrent depression (major depressive disorder: MDD). According to the World Health Organization (WHO), MDD is now the leading cause of disease burden in middle- and high-income countries. Patients (N = 45) with three or more previous depressive episodes were recruited to participate in MBCT as a preventative intervention. Using a benchmarking approach, outcome data was compared with data from a recent efficacy study. The methodology is a rigorous approach to assessing effectiveness when evidence-based UK protocols are transferred into the existing Scandinavian service delivery. Additionally, a person-centred methodological approach was used to assess clinical significance on the Reliable Change Index (RCI). The analysis revealed comparable or larger effects from pre-test to post-test in reduced psychiatric symptoms, increased quality of life and level of mindfulness, and the effects were maintained over 14 months. Analysis of the relapse rate in the current study (16%) compared to the TAU in the efficacy study (68%) yielded an h value of 0.78, a moderate effect size. Only 13% dropped out of the treatment. According to the RCI findings, 65% to 67% of participants in the clinical group improved, no individual worsened, and women showed a significantly greater improvement of depression and anxiety than men. Therapeutic alliance and motivation had no impact on the outcome. The overall result suggests that MBCT can be implemented successfully in Scandinavian primary health care as a preventive intervention for patients with recurrent depression.
Influence of musical expertise and musical training on pitch processing in music and language.

PURPOSE We review a series of experiments aimed at studying pitch processing in music and speech. These studies were conducted with musician and non musician adults and children. We found that musical expertise improved pitch processing not only in music but also in speech. Demonstrating transfer of training between music and language has interesting applications for second language learning. We also addressed the issue of whether the positive effects of musical expertise are linked with specific predispositions for music or with extensive musical practice. Results of longitudinal studies argue for the later. Finally, we also examined pitch processing in dyslexic children and found that they had difficulties discriminating strong pitch changes that are easily discriminate by normal readers. These results argue for a strong link between basic auditory perception abilities and reading abilities. METHODS We used conjointly the behavioral method (Reaction Times and error rates) and the electrophysiological method (recording of the changes in brain electrical activity time-locked to stimulus presentation, Event-Related brain Potentials or ERPs). RESULTS A set of common processes may be responsible for pitch processing in music and in speech and these processes are shaped by musical practice. CONCLUSION These data add evidence in favor of brain plasticity and open interesting perspectives for the remediation of dyslexia using musical training.
Simulations of electrical properties of cylindrical 3d-trench electrical si detectors under different radiation fluences and mip incident position

In this work, we investigate the dependence of charge collection on the MIP(minimum ionizing particle) incident position for cylindrical 3D-Trench electrode Si detectors being irradiated to various fluences. Simulation results are: (1) For non-irradiated detectors, detector charge collection does not depend on the MIP incident position, i.e. the charge collection is always a constant, there is no effect of trapping; (2) For irradiated detectors, detector charge collection depends on the MIP incident position; (3) As radiation fluence increases, detector charge collection decreases, regardless of MIP incident position. This is due to the fact that charge trapping by radiation induced defects also increases with radiation fluences, resulting in less charge collection.
Predicting Protein Folding Pathways

A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence, in the conformational search. Pathway prediction, thus gives more insight into the folding process and is a valuable guiding tool to search the conformation space. In this paper, we propose a novel 'unfolding' approach to predict the folding pathway. We apply graph-based methods on a weighted secondary structure graph of a protein to predict the sequence of unfolding events. When viewed in reverse this yields the folding pathway. We demonstrate the success of our approach on several proteins whose pathway is partially known.
Indeterminate bone lesion: the diagnosis

The diagnostic approach is statistical[1,2]. Age is important: before 5 years old, malignant tumour is almost always metastatic neuroblastoma; between 5 and 15 years old, it is often osteosarcoma or Ewing’s sarcoma; after 40 years old, it tends to be metastasis or myeloma. Clinical symptoms vary little and are most often pain and swelling. Although fever suggests infection, it may also be found in Ewing’s sarcoma. The first step in the evaluation of a tumour is to determine its aggressiveness by conventional radiology. Important parameters include the tumour size, type of matrix, and periosteal reaction. Certain tumours are more common in particular bones. Adamantinoma, usually found in the adult, selectively involves the tibia and fibula. The most common epiphyseal tumour in childhood is the chondroblastoma. In addition, the aggressiveness of some tumours may relate to their location in the axial or appendicular skeleton: in the hand, cartilaginous tumours are almost always benign, whereas in the pelvis, they are often malignant. If necessary, multiple lesions may be estimated with bone scanning. Multiple lesions are seen in chondromas, osteochondromas, histiocytosis X and metastases. The first necessary step is to definitively diagnose benign lesions based on clinical and radiologic signs, and for which biopsy is not necessary. These lesions are fibrous cortical defect, non-ossifying fibroma, periosteal desmoid, fibrous dysplasia, osteochondroma or exostoses, chondroma, simple bone cyst, vertebral angiomas and myositis ossificans. Diagnosis may be difficult. In these cases, the next step is CT. Problems can result from bone locations which are difficult to evaluate on conventional X-ray (short, flat bones especially the pelvis, sacrum, sternum, and vertebrae). Sometimes, the study of the tumour matrix can provide features necessary for the diagnosis. It can be fluid density, small calcifications allowing diagnosis of cartilaginous tumour, osteoid matrix, or fat[3]. CT is the examination of choice in the diagnosis of the nidus of osteoid osteoma in dense bone[4]. Small lytic lesions of the cortex, localized involvement of the soft tissues and thin peripheral periosteal reaction can be seen; lesions with slow evolution which displace and expand the cortex peripherally can be distinguished from more aggressive lesions which cross the cortex. CT can show the tumour on both sides of the cortex before it is destroyed. This is the case for Ewing sarcomas and osteosarcomas[5]. CT allows measurement of the thickness of a non-calcified cuff of a cartilaginous tumour: the cuff is thin in benign lesions and thick (more than 3 cm) in chondrosarcomas[6,7]. In other cases, evidence favours a malignant lesion. Examination for metastases, and MRI examination before biopsy, must be performed.
The Airborne Metagenome in an Indoor Urban Environment

The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens.
Fennel and Raspberry Leaf as Possible Inhibitors of Acetaminophen Oxidation

In addition to CYP2E1, several CYP isoenzymes, notably CYP1A2, 2D6, and 3A4, are suggested to contribute in acetaminophen oxidation and formation of the hepatotoxic metabolite N‐acetyl‐p‐benzoquinone imine (NAPQI). The in vitro CYP2E1 inhibitory potentials of fennel and raspberry leaf, herbs previously found to inhibit CYP1A2, 2D6, and 3A4 activities in vitro, were investigated. Extracts from commercially available herbal products were incubated with recombinant cDNA‐expressed human CYP2E1. A validated LC/MS/MS methodology was applied for determination of 6‐hydroxychlorzoxazone formation with disulfiram used as a positive inhibitory control. CYP2E1 IC50 inhibition constants were found to be 23 ± 4 and 27 ± 5 µg/ml for fennel and raspberry leaf, respectively, constants significantly lower than those presented in the literature for other herbal extracts. Together with previous findings, the presented in vitro data for CYP2E1 inhibition suggest that fennel and raspberry leaf have a significant potential of inhibiting all the major metabolic pathways for acetaminophen oxidation and NAPQI formation. Both herbs should be further investigated for their in vivo ability of inhibiting acetaminophen oxidation and NAPQI formation. Copyright © 2014 John Wiley & Sons, Ltd.
Presenting parasitological data: the good, the bad and the error bar

SUMMARY Visual displays of data in the parasitology literature are often presented in a way which is not very informative regarding the distribution of the data. An example being simple barcharts with half an error bar on top to display the distribution of parasitaemia and biomarkers of host immunity. Such displays obfuscate the shape of the data distribution through displaying too few statistical measures to explain the spread of all the data and selecting statistical measures which are influenced by skewness and outliers. We describe more informative, yet simple, visual representations of the data distribution commonly used in statistics and provide guidance with regards to the display of estimates of population parameters (e.g. population mean) and measures of precision (e.g. 95% confidence interval) for statistical inference. In this article we focus on visual displays for numerical data and demonstrate such displays using an example dataset consisting of total IgG titres in response to three Plasmodium blood antigens measured in pregnant women and parasitaemia measurements from the same study. This tutorial aims to highlight the importance of displaying the data distribution appropriately and the role such displays have in selecting statistics to summarize its distribution and perform statistical inference.
Locating Salient Object Features

We present a method for locating salient object features. Salient features are those which have a low probability of being mis-classified with any other feature, and are therefore more easily found in a similar image containing an example of the object. The local image structure can be described by vectors extracted using a standard ‘feature extractor’ at a range of scales. We train statistical models for each feature, using vectors taken from a number of training examples. The feature models can then be used to find the probability of misclassifying a feature with all other features. Low probabilities indicate a salient feature. Results are presented showing that salient features can be relocated more reliably than features chosen using previous methods, including hand picked features.
Histopathological Evaluation of Pediatric Intestinal Pseudo-Obstruction: Quantitative Morphometric Analysis of Pathological Changes in the Enteric Nervous System

Background : This study was done to obtain comprehensive data on changes in the structural components of the enteric nervous system in pediatric patients with intestinal pseudo-obstruction (IPO). We evaluated routinely processed, in formalin-fixed tissues by quantitative morphometric analysis. In addition, we used formalin-fixed tissue to explore the possibility of using previously proposed diagnostic criteria to evaluate frozen serial sections for intestinal neuronal dysplasia (IND) type B and hypoganglionosis. Methods : We analyzed data for 19 IPO cases. Morphometric analysis for quantification of ganglia and ganglion cells (GCs) was done for the myentric and the submucous plexus. In addition, we determined the presence of immature GCs and the distribution of nerve fibers and interstitial cells of Cajal (ICC). Results : Nine patients showed combined hypoganglionosis, IND, and decreased ICC; others showed various combinations of these. Several morphometric factors were significantly different between patient groups as well as being different than the control group. Conclusions : Our pediatric IPO cases showed extensive overlapping of pathological findings. And the findings suggest the utility of using previously proposed morphometrically measured factors in multiple frozen sections as diagnostic criteria for IND type B and hypoganglionosis in formalin-fixed tissue.
Delegation Control in Control of Unmanned Aerial Systems (UAS)

Building on the development of the playbook® concept for control of Unmanned Aerial Systems developed by Smart Information Flow Technology (SIFT) (Miller, Goldman, Funk, Wu and Pate (2003), the Army Aeroflightdynamics directorate extended and tested this concept. Similar to a quarterback calling a play in football, the UAS operator can call a “play” that tasks multiple heterogeneous UAS simultaneously. This frees up the operator from having to input way-points and manually coordinate the UASs. Several simulations were run to test the boundaries and conditions under which this technique would be useful. Plays were consistently shown to result in better performance and lower operator workload. This was true even when a series of experiments were conducted that were specifically designed to look at plays in conditions where they might not be optimal. Following this work, flight demonstrations highlighted the technical maturity of the technique. A second flight demonstration flew tactically correct and high value plays as judged by Army UAS operators. Playbook® is a well-tested, mature technology; the next step should be development and transition of an operational system.
Single-stranded nucleic acid binding in Arabidopsis thaliana cold shock protein is cold shock domain dependent

Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. The CSPs have been shown to play important role in development and stress adaptation in various plant species. The objective of this study was to find out the possible nucleic acid-binding affinities of whole CSP as well as independent domains, so that role of each individual domain may be revealed in Arabidopsis thaliana, the model plant species. The structure of CSP 3 protein from A. thaliana was modeled by homology-based approach and docking was done with different nucleic acid types.
Macroscopic quantum tunneling in superconducting nanowire devices

Macroscopic quantum tunneling is a process by which a macroscopic object, rather than a single electron, tunnels between two macroscopically distinct quantum states. In this dissertation, we will present the study of macroscopic quantum tunneling of phase-slips in superconducting devices, including one-dimensional nanowires, quasi-two-dimensional superconducting strips and doubly connected superconducting devices composed of two nanowires connected in parallel. We observe macroscopic quantum tunneling in these devices by measuring switching current distributions. It is known that the standard deviation of switching current distributions can be measured on a single nanowire to reveal temperatures at which macroscopic quantum tunneling is responsible for phase-slips [1, 2]. Therefore we begin by studying higher moments of the switching current distributions, namely the skewness S (a measure of the asymmetry of a distribution) and kurtosis K (a measure of its peakedness). We find that the skewness and kurtosis of the switching current distributions obtained via the Kurkijärvi process on devices composed of single nanowires do not depend on whether the switching events are initiated by quantum or thermal phase-slips. Skewness and kurtosis deviate considerably from the values associated with a Gaussian distribution (S = 0 and K = 3). If, in an experiment these higher moments approach Gaussian values they indicate the existence of noise. Next we study macroscopic quantum tunneling of phase-slips in quasi-two-dimensional superconducting strips, which are commercially available devices used as single-photon detectors. These devices are composed of (∼250 μm) long, (∼120 nm) wide, meandering superconducting strips. Each time a photon with sufficient energy strikes the strip a voltage pulse is produced and counted. However, the accuracy of these detectors is limited by a rate of dark counts (false events). We find that at sufficiently low temperatures, the macroscopic quantum tunneling of a vortex through an edge barrier on the wire (which results in a phase-slip as the vortex crosses the wide wire) contributes a base-level dark count rate in these detectors which must be considered during operation at low enough temperatures. After studying tunneling in single one-dimensional nanowires and wide, quasi-two-dimensional strips, we move our focus to doubly connected superconducting samples composed of two nanowires connected in parallel. We characterize and model these devices, and show their applicability as nanometer-scale superconducting memory cells. We develop precise algorithms allowing
Liver cancer cells: targeting and prolonged-release drug carriers consisting of mesoporous silica nanoparticles and alginate microspheres

A new microsphere consisting of inorganic mesoporous silica nanoparticles (MSNs) and organic alginate (denoted as MSN@Alg) was successfully synthesized by air-dynamic atomization and applied to the intracellular drug delivery systems (DDS) of liver cancer cells with sustained release and specific targeting properties. MSN@Alg microspheres have the advantages of MSN and alginate, where MSN provides a large surface area for high drug loading and alginate provides excellent biocompatibility and COOH functionality for specific targeting. Rhodamine 6G was used as a model drug, and the sustained release behavior of the rhodamine 6G-loaded MSN@Alg microspheres can be prolonged up to 20 days. For targeting therapy, the anticancer drug doxorubicin was loaded into MSN@Alg microspheres, and the (lysine)4-tyrosine-arginine-glycine-aspartic acid (K4YRGD) peptide was functionalized onto the surface of MSN@Alg for targeting liver cancer cells, hepatocellular carcinoma (HepG2). The results of the 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay and confocal laser scanning microscopy indicate that the MSN@Alg microspheres were successfully uptaken by HepG2 without apparent cytotoxicity. In addition, the intracellular drug delivery efficiency was greatly enhanced (ie, 3.5-fold) for the arginine-glycine-aspartic acid (RGD)-labeled, doxorubicin-loaded MSN@Alg drug delivery system compared with the non-RGD case. The synthesized MSN@Alg microspheres show great potential as drug vehicles with high biocompatibility, sustained release, and targeting features for future intracellular DDS.
NOD2 (CARD15), the first susceptibility gene for Crohn's disease

“ This is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning . ” Sir Winston Churchill, 1942. A “working model” of the pathophysiology of Crohn's disease (CD) is of an abnormal immune response to enteric bacteria in genetically susceptible individuals. There is a greater concordance for CD in monozygotic than dizygotic twins (concordance for CD in monozygotic twins 37% compared with 7% for dizygotic twins), suggesting a major genetic contribution to the pathogenesis of CD. The risk to siblings of affected individuals relative to the general population (λs) is 15–40 for CD and the calculated heritability for CD is greater than that for schizophrenia or asthma and at least equal to that of type 1 diabetes.1 2 Evidence for the role of enteric bacteria in the pathogenesis of CD comes from data demonstrating that genetically modified mice utilised as models for inflammatory bowel disease/CD fail to manifest the disease in germ free environments and only develop disease when exposed to normal enteric commensal organisms. In addition, Crohn's colitis frequently improves when the faecal stream is diverted following formation of a loop ileostomy and symptoms from CD are transiently improved following administration of antibiotics. Geneticists have proposed that the genes for complex genetic diseases will be discovered by one or more of the following three methods: In 1996, Jean-Pierre Hugot et al published the first genome wide scan identifying a susceptibility locus for CD adjacent to the centromere on chromosome …
Automatic selection of relevant features using Rough Set Theory for real-time situation recognition based on fuzzy SOM-based CBR

This paper investigates feature selection to discard irrelevant features for dimensionality reduction and improving situation recognition process. A situation illustrating the internal structure of a system state and its related environment is based on a large set of characteristics (features). Real-time situation recognition is still a challenge because of dealing with incremental knowledge as well as imprecise, uncertain, and redundant data (features). Investigation of relevant and key situations features could effectively enhance the situation recognition performance in terms of accuracy and computational complexity. In this paper, Case-Based Reasoning (CBR) as a problem solving approach is used for situation recognition. A fuzzy SOM-based approach by integration of Situation-Operator Modeling (SOM) and Fuzzy Logic (FL) is provided for knowledge representation in CBR process. A feature selection is realized using Rough Set Theory (RST) for data mining and uncertainty management in real-time applications. Different feature selection algorithms based on RST are applied to fuzzy SOM-based CBR. An analysis of the performance of all resulting combinations is done in terms of feature reduction and situation recognition. Finally, the proposed CBR approach is realized using experiments based on driving maneuvers conducted by a professional driving simulator. This application shows the effectiveness as well as the accuracy of the introduced approach.