Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletion of Integron-Associated Gene Cassettes Impact on the Surface Properties of Vibrio rotiferianus DAT722

Background The integron is a genetic recombination system that catalyses the acquisition of genes on mobilisable elements called gene cassettes. In Vibrio species, multiple acquired gene cassettes form a cassette array that can comprise 1–3% of the bacterial genome. Since 75% of these gene cassettes contain genes encoding proteins of uncharacterised function, how the integron has driven adaptation and evolution in Vibrio species remains largely unknown. A feature of cassette arrays is the presence of large indels. Using Vibrio rotiferianus DAT722 as a model organism, the aim of this study was to determine how large cassette deletions affect vibrio physiology with a view to improving understanding into how cassette arrays influence bacterial host adaptation and evolution. Methodology/Principal Findings Biological assays and proteomic techniques were utilised to determine how artificially engineered deletions in the cassette array of V. rotiferianus DAT722 affected cell physiology. Multiple phenotypes were identified including changes to growth and expression of outer membrane porins/proteins and metabolic proteins. Furthermore, the deletions altered cell surface polysaccharide with Proton Nuclear Magnetic Resonance on whole cell polysaccharide identifying changes in the carbohydrate ring proton region indicating that gene cassette products may decorate host cell polysaccharide via the addition or removal of functional groups. Conclusions/Significance From this study, it was concluded that deletion of gene cassettes had a subtle effect on bacterial metabolism but altered host surface polysaccharide. Deletion (and most likely rearrangement and acquisition) of gene cassettes may provide the bacterium with a mechanism to alter its surface properties, thus impacting on phenotypes such as biofilm formation. Biofilm formation was shown to be altered in one of the deletion mutants used in this study. Reworking surface properties may provide an advantage to the bacterium’s interactions with organisms such as bacteriophage, protozoan grazers or crustaceans.
Applying FSL to the FIAC data: Model‐based and model‐free analysis of voice and sentence repetition priming

This article presents results obtained from applying various tools from FSL (FMRIB Software Library) to data from the repetition priming experiment used for the HBM'05 Functional Image Analysis Contest. We present analyses from the model‐based General Linear Model (GLM) tool (FEAT) and from the model‐free independent component analysis tool (MELODIC). We also discuss the application of tools for the correction of image distortions prior to the statistical analysis and the utility of recent advances in functional magnetic resonance imaging (FMRI) time series modeling and inference such as the use of optimal constrained HRF basis function modeling and mixture modeling inference. The combination of hemodynamic response function (HRF) and mixture modeling, in particular, revealed that both sentence content and speaker voice priming effects occurred bilaterally along the length of the superior temporal sulcus (STS). These results suggest that both are processed in a single underlying system without any significant asymmetries for content vs. voice processing. Hum Brain Mapp, 2006. © 2006 Wiley‐Liss, Inc.
Association between SORL1 and Alzheimer's disease in a genome-wide study

Several studies have reported an association of Alzheimer's disease (AD) with polymorphic markers in SORL1. Data from a recently published genome-wide association study in AD have been made publicly available. We tested the association of AD with SORL1 in this dataset (Translational Genomics Research Institute; TGEN), which included 31 SORL1 single nucleotide polymorphisms (SNPs), eight of which overlapped the original study. Six SNPs, near the 3′ region of SORL1 containing SNPs which were strongly associated with AD in previous studies, showed significant association in the TGEN dataset. These results provide an independent replication of the association between AD and SORL1.
Does Shared Decision Making in Cancer Treatment Improve Quality of Life? A Systematic Literature Review

Background. The growing consensus espousing the use of shared decision making (SDM) in cancer treatment has coincided with the rise of health care evaluation paradigms that emphasize quality of life (QOL) as a central outcome measure. This review systematically examines the association between treatment SDM and QOL outcomes in cancer. Methods. A range of bibliographic databases and gray literature sources was searched. The search retrieved 16,726 records, which were screened by title, abstract, and full text to identify relevant studies. The review included 17 studies with a range of study designs and populations. Data were extracted on study methods, participants, setting, study or intervention description, outcomes, main findings, secondary findings, and limitations. Quality appraisal was used, in conjunction with a narrative approach, to synthesize the evidence. Results. The review found weak, but suggestive, evidence for a positive association between perceived patient involvement in decision making, a central dimension of SDM, and QOL outcomes in cancer. The review did not find evidence for an inverse association between SDM and QOL. The poor methodological quality and heterogeneity of the extant literature constrained the derived conclusions. In addition, the literature commonly treated various subscales of QOL instruments as separate outcomes, increasing the probability of spurious findings. Conclusions. There is weak evidence that aspects of shared decision-making approaches are positively associated with QOL outcomes and very little evidence of a negative association. The extant literature largely assessed patient involvement, only capturing one aspect of the shared decision-making construct, and is of poor quality, necessitating robust studies examining the association.
The Functional Consequences of Variation in Transcription Factor Binding

One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This combination of data allowed us to infer functional TF binding. Using this approach, we found that only a small subset of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes. We found that functional TF binding is enriched in regulatory elements that harbor a large number of TF binding sites, at sites with predicted higher binding affinity, and at sites that are enriched in genomic regions annotated as “active enhancers. ”
Breit–Wigner formula at barrier tops

For noncritical energies, the asymptotic behavior of the scattering phase and of the time-delay are known to be described by a Weyl type formula and the Breit–Wigner formula, respectively. We consider here the case of critical energy levels in dimension 1. We obtain the semiclassical asymptotics of the scattering phase and of the time-delay, uniformly with respect to the energy in a neighborhood of a critical value.
Decoding of finger trajectory from ECoG using deep learning

Objective. Conventional decoding pipeline for brain–machine interfaces (BMIs) consists of chained different stages of feature extraction, time-frequency analysis and statistical learning models. Each of these stages uses a different algorithm trained in a sequential manner, which makes it difficult to make the whole system adaptive. The goal was to create an adaptive online system with a single objective function and a single learning algorithm so that the whole system can be trained in parallel to increase the decoding performance. Here, we used deep neural networks consisting of convolutional neural networks (CNN) and a special kind of recurrent neural network (RNN) called long short term memory (LSTM) to address these needs. Approach. We used electrocorticography (ECoG) data collected by Kubanek et al. The task consisted of individual finger flexions upon a visual cue. Our model combined a hierarchical feature extractor CNN and a RNN that was able to process sequential data and recognize temporal dynamics in the neural data. CNN was used as the feature extractor and LSTM was used as the regression algorithm to capture the temporal dynamics of the signal. Main results. We predicted the finger trajectory using ECoG signals and compared results for the least angle regression (LARS), CNN-LSTM, random forest, LSTM model (LSTM_HC, for using hard-coded features) and a decoding pipeline consisting of band-pass filtering, energy extraction, feature selection and linear regression. The results showed that the deep learning models performed better than the commonly used linear model. The deep learning models not only gave smoother and more realistic trajectories but also learned the transition between movement and rest state. Significance. This study demonstrated a decoding network for BMI that involved a convolutional and recurrent neural network model. It integrated the feature extraction pipeline into the convolution and pooling layer and used LSTM layer to capture the state transitions. The discussed network eliminated the need to separately train the model at each step in the decoding pipeline. The whole system can be jointly optimized using stochastic gradient descent and is capable of online learning.
Map building with RGB-D camera for mobil robot

The paper deals with the issues of the autonomous navigation of mobile robots. Nowadays several automatic operated vehicles, robots are used widely from the industry (storage system) to the everyday use (automatic parking system). The paper deals with the realization of a smaller sized robot vehicle which is capable for autonomous navigation. Within this framework we describe the realization of the vehicle, the developed board computer for navigation and the possible sensors as well. At the beginning of the paper some developments are presented which also dealt with the autonomous navigation of robots and mapping their environment. In knowledge of these works we started to develop our robot system. In a former paper we presented our robot vehicle and an early navigation algorithm. In the current paper it is summarized which sensors can detect the environment and the localization of the vehicle. The paper presents our experimental results about the accuracy of the Kinect sensor in more details.
Pace Yourself: Intraindividual Variability in Context Use Revealed by Self-paced Event-related Brain Potentials

Event-related brain potentials (ERPs) have revealed multiple mechanisms by which contextual constraints impact language processing. At the same time, little work has examined the trial-to-trial dynamics of context use in the brain. In the current study, we probed intraindividual variability in behavioral and neural indices of context processing during reading. In a concurrent self-paced reading and ERP paradigm, participants read sentences that were either strongly or weakly constraining completed with an expected or unexpected target word. Our findings revealed substantial within-subject variability in behavioral and neural responses to contextual constraints. First, context-based amplitude reductions of the N400, a component linked to semantic memory access, were largest among trials eliciting the slowest RTs. Second, the RT distribution of unexpected words in strongly constraining contexts was positively skewed, reflecting an increased proportion of very slow RTs to trials that violated semantic predictions. Among those prediction-violating trials eliciting faster RTs, a late sustained anterior positivity was observed. However, among trials producing the differentially slowed RTs to prediction violations, we observed a markedly earlier effect of constraint in the form of an anterior N2, a component linked to conflict resolution and the cognitive control of behavior. The current study provides the first neurophysiological evidence for the direct role of cognitive control functions in the volitional control of reading. Collectively, our findings suggest that context use varies substantially within individual participants and that coregistering behavioral and neural indices of online sentence processing offers a window into these single-item dynamics.
Mind the gap: MIND, the mental hygiene movement and the trapdoor in measurements of intellect.

BACKGROUND The National Association for Mental Health adopted the 'brand name' MIND as part of its transformation into a campaigning pressure group at the turn of the 1970s. This article examines the historical antecedents to key statements made by the organisation at this time regarding the relationship of mental health with, what was then called, 'mental handicap'. METHODS The National Association is placed within the historical context of the movement for mental hygiene. The article traces how the movement theorised mental health as critically related to intellect and emotionality. RESULTS The movement relegated people deemed 'mentally deficient' from therapeutic policies based on family relationships believed to promote mental health. However, a late 1950s experiment known as the Brooklands study subverted this discrimination. This was paradoxical since it built on mental hygiene theorising. CONCLUSIONS Theorisations of the relationship between intellect, emotion and mental health are still potentially discriminatory.
Doubly Hybrid Meta DFT: New Multi-Coefficient Correlation and Density Functional Methods for Thermochemistry and Thermochemical Kinetics

This paper presents two new multi-coefficient correlation and density functional methods based on mixing scaling-all-correlation (SAC) theory and hybrid meta density functional theory with empirical parameters. Both methods were optimized against a database of 109 atomization energies and 42 barrier heights. The resulting methods, called MC3BB and MC3MPW, were tested against a database of saddle point geometries, and scaling factors were optimized for calculating vibrational frequencies. The two new methods were compared to the methods that we have previously determined to be most efficient for thermochemistry and thermochemical kinetics, where the criterion is the average of the mean unsigned errors for bond energies and barrier heights. These comparisons show that MC3BB is more accurate than any other method that has comparable cost. Both new methods are well suited for direct dynamics calculations that require Hessians. The new approach is called doubly hybrid density functional theory if kinetic energy density is not included in the functional and doubly hybrid meta density functional theory if it is.
MovieReshape: tracking and reshaping of humans in videos

We present a system for quick and easy manipulation of the body shape and proportions of a human actor in arbitrary video footage. The approach is based on a morphable model of 3D human shape and pose that was learned from laser scans of real people. The algorithm commences by spatio-temporally fitting the pose and shape of this model to the actor in either single-view or multi-view video footage. Once the model has been fitted, semantically meaningful attributes of body shape, such as height, weight or waist girth, can be interactively modified by the user. The changed proportions of the virtual human model are then applied to the actor in all video frames by performing an image-based warping. By this means, we can now conveniently perform spatio-temporal reshaping of human actors in video footage which we show on a variety of video sequences.
Prospective Study of Chikungunya Virus Acute Infection in the Island of La Réunion during the 2005–2006 Outbreak

Background Chikungunya virus (CHIKV) is a recently re-emerged arthropod borne virus responsible for a massive outbreak in the Indian Ocean and India, and extended to Southeast Asia as well as Italy. CHIKV has adapted to Aedes albopictus, an anthropophilic mosquito species widely distributed in Asia, Europe, Africa and America. Our objective was to determine the clinical and biological features of patients at the acute phase of CHIKV infection. Methods and Findings A prospective study enrolled 274 consecutive patients with febrile arthralgia recorded at the Emergency Department of the Groupe Hospitalier Sud-Réunion between March and May 2006. Three groups were defined: one group of 180 viremic patients (positive CHIKV RT-PCR), one group of 34 patients with acute post-viremic infection (negative CHIKV RT-PCR, positive anti-CHIKV IgM and negative IgG), and one group of 46 uninfected patients (negative CHIKV RT-PCR, anti-CHIKV IgM and IgG). Bivariate analyses of clinical and biological features between groups were performed. Patients with CHIKV viremia presented typically with asymmetrical bilateral polyarthralgia (96.5%) affecting the lower (98%) and small joints (74.8%), as well as asthenia (88.6%), headache (70%), digestive trouble (63.3%), myalgia (59%), exanthems (47.8%), conjunctival hyperhemia (23%) and adenopathy (8.9%). Vertigo, cutaneous dysesthesia, pharyngitis and haemorrhages were seldom observed. So far unreported symptoms such as chondrocostal arthralgia (20%), entesopathies (1.6%), talalgia (14%) were also noted. Prurit was less frequent during the viremic than post-viremic phase (13.9% vs. 41.2%; p<0.001), whereas lymphopenia was more frequent (87.6% vs. 39.4%; p<0.001). Others biological abnormalities included leukopenia (38.3%), thrombocytopenia (37.3%), increased ASAT and ALAT blood levels (31.6 and 7.3%, respectively) and hypocalcemia (38.7%). Lymphopenia <1,000/mm3 was very closely associated with viremic patients (Yule coefficient 0.82, positive predictive value 92.3%). Age under 65 was associated with a benign course, as no patients younger than 65 had to be hospitalized (Yule coefficient 0.78). Conclusions The diagnosis of CHIKV infection in acute phase is based on commonly accepted clinical criteria (fever and arthralgia), however clinical and biological diffrences exist in acute phase depending on whether or not the patient is within the viremic phase of the infection.
High Affinity Nanobodies against the Trypanosome brucei VSG Are Potent Trypanolytic Agents that Block Endocytosis

The African trypanosome Trypanosoma brucei, which persists within the bloodstream of the mammalian host, has evolved potent mechanisms for immune evasion. Specifically, antigenic variation of the variant-specific surface glycoprotein (VSG) and a highly active endocytosis and recycling of the surface coat efficiently delay killing mediated by anti-VSG antibodies. Consequently, conventional VSG-specific intact immunoglobulins are non-trypanocidal in the absence of complement. In sharp contrast, monovalent antigen-binding fragments, including 15 kDa nanobodies (Nb) derived from camelid heavy-chain antibodies (HCAbs) recognizing variant-specific VSG epitopes, efficiently lyse trypanosomes both in vitro and in vivo. This Nb-mediated lysis is preceded by very rapid immobilisation of the parasites, massive enlargement of the flagellar pocket and major blockade of endocytosis. This is accompanied by severe metabolic perturbations reflected by reduced intracellular ATP-levels and loss of mitochondrial membrane potential, culminating in cell death. Modification of anti-VSG Nbs through site-directed mutagenesis and by reconstitution into HCAbs, combined with unveiling of trypanolytic activity from intact immunoglobulins by papain proteolysis, demonstrates that the trypanolytic activity of Nbs and Fabs requires low molecular weight, monovalency and high affinity. We propose that the generation of low molecular weight VSG-specific trypanolytic nanobodies that impede endocytosis offers a new opportunity for developing novel trypanosomiasis therapeutics. In addition, these data suggest that the antigen-binding domain of an anti-microbial antibody harbours biological functionality that is latent in the intact immunoglobulin and is revealed only upon release of the antigen-binding fragment.
Predictors of Technical Success and Rate of Complications of Image-Guided Percutaneous Transthoracic Lung Needle Biopsy of Pulmonary Tumors

Purpose To investigate predictors of technical success and complications of computed tomography (CT)-guided percutaneous transthoracic needle biopsy of potentially malignant pulmonary tumors. Material and Methods From 2008 to 2009, technical success and rate of complications of CT-guided percutaneous transthoracic lung needle biopsies of patients with suspicious pulmonary tumors were retrospectively evaluated. The influence on technical success and rate of complications was assessed for intervention-related predictors (lesion diameter, length of biopsy pathway, number of pleural transgressions, and needle size) and patient-related predictors (age, gender, reduced lung function). In addition, technical success and rate of complications were compared between different interventional radiologists. Results One hundred thirty-eight patients underwent biopsies by 15 interventional radiologists. The overall technical success rate was 84.1% and was significantly different between interventional radiologists (range 25%-100%; p<0.01). Intervention-related and patient-related predictors did not influence the technical success rate. The overall complication rate was 59.4% with 39.1% minor complications and 21.0% major complications. The rate of complications was influenced by lesion diameter and distance of biopsy pathway. Interventional radiologist-related rates of complications were not statistically different. Conclusions Technical success of percutaneous, transthoracic lung needle biopsies of pulmonary tumors is probably dependent on the interventional radiologist. In addition, lesion diameter and length of biopsy pathway are predictors of the rate of complications.