Miracle-dz/UniFAR-FTUs huggingface dataset:
Setting measurable goals with young people: Qualitative feedback from the Goal Attainment Scale in youth mental health

Introduction Measuring occupational performance is an essential part of clinical practice; however, there is little research on service user perceptions of measures. The aim of this investigation was to explore the acceptability and utility of one occupational performance outcome measure, Goal Attainment Scaling, with young people (12–25 years old) seeking psychological help. Method Semi-structured interviews were conducted with ten young people seeking help from a youth mental health clinic. Interviews were audio taped and a field diary kept. Interviews were transcribed verbatim and analysed using content analysis. Results were verified by member checking. Results All participants were able to engage in using Goal Attainment Scaling to set goals for therapy, and reported the process to be useful. The participants identified the physical location and ownership of the scale was important to help motivate them to work on their goals. Conclusion Young help-seekers see Goal Attainment Scaling as an acceptable tool to facilitate the establishment of functional goals. Young service users were particularly keen to maintain control over the physical location of completed forms.
Soluble Respiratory Syncytial Virus Fusion Protein in the Fully Cleaved, Pretriggered State Is Triggered by Exposure to Low-Molarity Buffer

ABSTRACT The paramyxovirus fusion (F) glycoprotein is anchored in the virion membrane in a metastable, pretriggered form. Once triggered, the F protein undergoes a dramatic conformational extension that inserts its hydrophobic fusion peptide into the target cell membrane, then folds back on itself to bring the membranes together and initiate fusion. Unlike most other paramyxoviruses, the respiratory syncytial virus (RSV) F protein alone is sufficient to mediate membrane fusion and virus infection. To study the triggering mechanism of the RSV F protein, we have generated a soluble F (sF) protein by replacing the transmembrane and cytoplasmic tail domains with a 6His tag. The sF protein is secreted efficiently from 293T cells in a fully cleaved form. It is recognized by neutralizing monoclonal antibodies, appears spherical by electron microscopic analysis, and is not aggregated, all consistent with a native, pretriggered trimer. The sF protein was purified on a Ni+2 column and eluted with 50 mM phosphate buffer containing 500 mM NaCl and 250 mM imidazole. Dialysis against 10 mM buffer caused the sF protein to trigger, forming “hat pin”-shaped molecules that aggregated as rosettes, characteristic of the posttriggered form. Further dialysis experiments indicated that the efficiency of triggering correlated well with the reduction of buffer molarity. Reduction of buffer molarity by dilution also resulted in exposure of the fusion peptide, as detected by liposome association, confirming sF protein triggering. Mutation of the furin cleavage site adjacent to the fusion peptide prevented liposome association, further confirming that association is via the fusion peptide.
Multidrug resistance pump AcrAB-TolC is required for high-level, Tet(A)-mediated tetracycline resistance in Escherichia coli.

OBJECTIVES Starting from the observation that Escherichia coli tolC mutations severely reduced the high-level resistance to tetracycline afforded by Tn10- and plasmid-encoded Tet(A) pumps, we studied the mechanism of this susceptibility. METHODS The MIC of tetracycline for MC4100 tolC::Tn10 and several tolC mutants carrying the Tn10 in other sites on the chromosome (thr::Tn10) was determined. The effect of a tolC mutation on the level of expression of Tn10 tet(A) was examined by using a tet(A)::lacZ gene fusion. Influence of tolC mutations on tetracycline efflux and accumulation was quantified by spectrofluorometric assays. The contribution of the AcrAB multidrug efflux system to high-level tetracycline resistance was measured in a Tn10-carrying acrAB null mutant strain. RESULTS Tn10- and plasmid-encoded Tet(A) conferred 5- to 6-fold lower levels of tetracycline resistance in tolC mutants, as compared with control strain tolC+. Spectrofluorometric analyses showed that this resulted from a decrease in drug efflux in tolC mutants. Chlortetracycline resistance was also compromised by loss of TolC. Mutational loss of the AcrAB multidrug efflux transporter had the same effect as tolC mutations on tetracycline resistance. This indicated that tolC mutations act through inactivation of the AcrAB system. CONCLUSIONS Our results are compatible with the hypothesis that the AcrAB pump is an important component in the development of high levels of resistance to tetracycline in E. coli, perhaps by working in combination with Tet(A).
Entorhinal–hippocampal neuronal circuits bridge temporally discontiguous events

The entorhinal cortex (EC)–hippocampal (HPC) network plays an essential role for episodic memory, which preserves spatial and temporal information about the occurrence of past events. Although there has been significant progress toward understanding the neural circuits underlying the spatial dimension of episodic memory, the relevant circuits subserving the temporal dimension are just beginning to be understood. In this review, we examine the evidence concerning the role of the EC in associating events separated by time—or temporal associative learning—with emphasis on the function of persistent activity in the medial entorhinal cortex layer III (MECIII) and their direct inputs into the CA1 region of HPC. We also discuss the unique role of Island cells in the medial entorhinal cortex layer II (MECII), which is a newly discovered direct feedforward inhibitory circuit to CA1. Finally, we relate the function of these entorhinal cortical circuits to recent findings concerning hippocampal time cells, which may collectively activate in sequence to bridge temporal gaps between discontiguous events in an episode.
SIMPLE CHORD ESTIMATE : SUBMISSION TO THE MIREX CHORD ESTIMATION TASK

I present my submission MM1 to the Chord Estimation Task of the 2010 Music Information Retrieval Evaluation eXchange (MIREX 2010). The front-end chroma generation is based on a new implementation of NNLS Chroma as a Vamp plugin. The higher level model is very simple, and a very similar method is implemented as the nonHMM version of the Chordino plugin. These two plugins are now available at http://www.isophonics. net/nnls-chroma. The method has achieved the nextto highest chord overlap ratio (0.7963) among the participating methods.
Image denoising via adjustment of wavelet coefficient magnitude correlation

We describe a novel method of removing additive white noise of known variance from photographic images. The method is based on a characterization of the statistical properties of natural images represented in a complex wavelet decomposition. Specifically, we decompose the noisy image into wavelet subbands, estimate the autocorrelation of both the noise-free raw coefficients and their magnitudes within each subband, impose these statistics by projecting onto the space of images having the desired autocorrelations, and reconstruct an image from the modified wavelet coefficients. This process is applied repeatedly, and can be accelerated to produce optimal results in only a few iterations. Denoising results compare favorably to three reference methods, both perceptually and in terms of mean squared error.
Integrating noise estimation and factorization-based speech separation: A novel hybrid approach

We present a novel method to integrate noise estimates by unsupervised speech enhancement algorithms into a semi-supervised non-negative matrix factorization framework. A multiplicative update algorithm is derived to estimate a non-negative noise dictionary given a time-varying background noise estimate with a stationarity constraint. A large-scale, speaker-independent evaluation is carried out on spontaneous speech overlaid with the official CHiME 2011 Challenge corpus of realistic domestic noise, as well as music and stationary environmental noise corpora. In the result, the proposed method delivers higher signal-distortion ratio and objective perceptual measure than standard semi-supervised NMF or spectral subtraction based on the same noise estimation algorithm, and further gains can be expected by speaker adaptation.
A1 receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine selectively activates chloride efflux from human epithelial and mouse fibroblast cell lines expressing the cystic fibrosis transmembrane regulator delta F508 mutation.

Cystic fibrosis is an autosomal recessive disorder affecting chloride transport in pancreas, lung, and other tissues, which is caused by mutations in the cystic fibrosis transmembrane regulator (CFTR). The A1 receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (CPX) stimulates 36Cl- efflux from pancreatic CFPAC-1 cells which bear the delta F508 genotype common to most cases of cystic fibrosis [Eidelman et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5562-5566]. By contrast, correction of the cystic fibrosis defect by retrovirus-mediated gene transfer renders the resulting CFPAC-PLJ-CFTR cells insensitive to CPX. We now report that CPX also activates chloride efflux from the CF tracheal epithelial cell line IB3-1 bearing a delta F508 allele, but not if the IB3-1 cells have been repaired by transfection of the wild-type CFTR gene. Similar results were obtained with recombinant NIH 3T3 cells, in which CPX activates 36Cl- efflux from cells expressing the CFTR (delta F508) gene product but not from 3T3 cells expressing the wild-type CFTR. In all three cell types expressing CFTR (delta F508), CPX was found to activate 36Cl- efflux in a dose-dependent manner over the concentration range of 1-30 nM and then gradually lose potency at higher CPX concentrations. Six CPX analogues, A1 receptor antagonists of affinity similar to that of CPX, were found to be much less effective than CPX at activating 36Cl- efflux from CFPAC-1 cells. These included 2-thio-CPX. CPT (8-cyclopentyl-1,3-dimethylxanthine),3,4-dehydro-CPX,3-F-CPX,3-1-CPX, and KW-3902 (8-noradamantyl-1,3-dipropylxanthine). (ABSTRACT TRUNCATED AT 250 WORDS)
A Fast Clustering Based Feature Subset Selection Algorithm For High Dimensional Data

Identifying a subset of the most useful features that produces compatible results as the original entire set of features is involved in feature selection. A feature selection algorithm can be evaluated from efficiency and effectiveness points of view. The effectiveness is concerned to the quality of the subset of features, the efficiency is related to the time required to find a subset of features. Based on above criteria, a fast clustering-based feature selection algorithm (FAST) is proposed and experimentally evaluated in this paper. The FAST algorithm works in four steps. In the Step 1: The irrelevant features are removed. Step 2: Features are divided into cluster that posses features with redundant features. Step 3: the selection of most representative feature that is closely related to the target classes. Step 4: Feature is selected from each cluster to form the features subset. Features present in different clusters are relatively independent. By analysing the data from a huge collection, the relevant data can be separated out using FAST algorithm. The FAST has a high probability of producing a subset of useful and independent features because of its clustering-based strategy. The efficient minimum-spanning tree (MST) clustering method is adopted to ensure the efficiency of FAST.
Describing relevant indices from the resting state electrophysiological networks

The “Default Mode Network” concept was defined, in fMRI field, as a consistent pattern, involving some regions of the brain, which is active during resting state activity and deactivates during attention demanding or goal-directed tasks. Several fMRI studies described its features also correlating the deactivations with the attentive load required for the task execution. Despite the efforts in EEG field, aiming at correlating the spectral features of EEG signals with DMN, an electrophysiological correlate of the DMN hasn't yet been found. In this study we used advanced techniques for functional connectivity estimation for describing the neuroelectrical properties of DMN. We analyzed the connectivity patterns elicited during the rest condition by 55 healthy subjects by means of Partial Directed Coherence. We extracted some graph indexes in order to describe the properties of the resting network in terms of local and global efficiencies, symmetries and influences between different regions of the scalp. Results highlighted the presence of a consistent network, elicited by more than 70% of analyzed population, involving mainly frontal and parietal regions. The properties of the resting network are uniform among the population and could be used for the construction of a normative database for the identification of pathological conditions.
Tracking the motion of the outer tips of microtubules

Microtubules play numerous critical roles in a cell such as providing structural tracks for the anchoring and movement of vesicles and chromosomes. Also, the assembly of microtubules coordinates cell division and migration. Abnormal function of the assembly is involved in cancer. To date the study of the microtubule assembly dynamics has been done by visual inspection or manually. In this work we have developed a method to automatically track microtubule tips so as to enable high throughput quantitative studies. Our approach first estimates the region where a tip is expected to lie. In that region a tip feature is computed for all time and used to form the tip trajectory. Last, we evaluate our method with phantom data as well as real sequences of fluorescently tagged living cells
Mining Query Subtopics from Questions in Community Question Answering

This paper proposes mining query subtopics from questions in community question answering (CQA). The subtopics are represented as a number of clusters of questions with keywords summarizing the clusters. The task is unique in that the subtopics from questions can not only facilitate user browsing in CQA search, but also describe aspects of queries from a question-answering perspective. The challenges of the task include how to group semantically similar questions and how to find keywords capable of summarizing the clusters. We formulate the subtopic mining task as a non-negative matrix factorization (NMF) problem and further extend the model of NMF to incorporate question similarity estimated from metadata of CQA into learning. Compared with existing methods, our method can jointly optimize question clustering and keyword extraction and encourage the former task to enhance the latter. Experimental results on large scale real world CQA datasets show that the proposed method significantly outperforms the existing methods in terms of keyword extraction, while achieving a comparable performance to the state-of-the-art methods for question clustering.
High-pressure crystal chemistry of cubanite, CuFerS,

We have studied cubanite, CuFerS, (orthorhombic, space gtoup Pcmn, a: 6.46, b : 11.10, c : 6.22 A), using single-crystal X-ray diffraction in a diamond-anvil cell at room temperature from 0 to 3.68 GPa. Refinements were performed aI 0, 1.76, and 3.59 GPa, and cell parameters were measured at 20 pressures up to 3.68 GPa. The linear compressibilities of the a, b, and c crystal axes are 0.00513(5),0.00479(5), and 0.00575(4) GPa ', respectively. Compressibility data were fitted to a Birch-Murnaghan equation of state with parameters Ko : 55.3 + 1.7 GPa with Ko' constrained to be 4. High-pressure refinement data indicate that the principal response of the crystal structure to compression is a reduction in Cu-S bond lengths, whereas Fe-S bond lengths remain essentially unchanged. Results are compared to bulk moduli and polyhedral bulk moduli of other sulfides.
De Novo Transcriptome Sequencing and Analysis of the Cereal Cyst Nematode, Heterodera avenae

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.
An analysis of the timing behavior of CMOS digital blocks under Simultaneous Switching Noise conditions

This paper analyzes the impact of Simultaneous Switching Noise (SSN) on the timing behavior of CMOS digital blocks. The concept of Instantaneous Transfer Function is introduced to interpret noisy signals and perform timing measurements on such signals. It is shown that the average swing during switching is the key parameter to predict the noise impact on the delay of a logic path, whereas the peak of noise is not relevant. The influence of structural parameters such as the block topology is evaluated, and the unpredictable aspect of SSN impact on path delay is highlighted.
Electrophysiological observations in critically ill Guillain-Barre syndrome.

BACKGROUND Respiratory muscle paralysis is a serious complication of Guillain-Barre syndrome (GBS). Factors that govern duration and recovery from respiratory paralysis are unclear. AIM To correlate electrophysiological parameters in critically ill GBS with duration of mechanical ventilation and outcome at discharge. MATERIALS AND METHODS Data of a large cohort (n=93; M:F 59:34; mean age: 33.51+21.4 years) of critically-ill patients with GBS seen over one decade was retrospectively analyzed. RESULTS The duration of mechanical ventilation was <15 days (n = 38), 16-30 days (n = 24), and >30 days (n = 31). Majority of the patients had a demyelinating electrophysiology. Reduced amplitude or absent motor potentials correlated with requirement for longer duration of ventilation. Inexcitable sensory nerves were more common in patients who could be weaned off from the ventilator within 15 days. There was no relation between the conduction blocks in motor nerves and the duration of ventilation. Low amplitude of median nerve correlated with a poor outcome at hospital discharge as assessed by Hughes disability scale. CONCLUSION Distinct patterns of electrophysiological abnormalities are noted in patients and they correlate with the duration of mechanical ventilation. Future studies to unravel the underlying pathophysiological processes that govern the patterns of progression and recovery in the critically ill patients with GBS will pave way for the development of better and more potent therapies that will hasten recovery, when combined with the prevalent treatment modalities including plasmapheresis and intravenous immunoglobulin.
MYCN amplification confers enhanced folate dependence and methotrexate sensitivity in neuroblastoma

MYCN amplification occurs in 20% of neuroblastomas and is strongly related to poor clinical outcome. We have identified folate-mediated one-carbon metabolism as highly upregulated in neuroblastoma tumors with MYCN amplification and have validated this finding experimentally by showing that MYCN amplified neuroblastoma cell lines have a higher requirement for folate and are significantly more sensitive to the antifolate methotrexate than cell lines without MYCN amplification. We have demonstrated that methotrexate uptake in neuroblastoma cells is mediated principally by the reduced folate carrier (RFC; SLC19A1), that SLC19A1 and MYCN expression are highly correlated in both patient tumors and cell lines, and that SLC19A1 is a direct transcriptional target of N-Myc. Finally, we assessed the relationship between SLC19A1 expression and patient survival in two independent primary tumor cohorts and found that SLC19A1 expression was associated with increased risk of relapse or death, and that SLC19A1 expression retained prognostic significance independent of age, disease stage and MYCN amplification. This study adds upregulation of folate-mediated one-carbon metabolism to the known consequences of MYCN amplification, and suggests that this pathway might be targeted in poor outcome tumors with MYCN amplification and high SLC19A1 expression.
Shear fatigue micromechanics of the cement–bone interface: An in vitro study using digital image correlation techniques

Loss of fixation at the cement–bone interface is known to contribute to aseptic loosening, but little is known about the mechanical damage response of this interface. An in vitro study using cement–bone specimens subjected to shear fatigue loading was performed, and the progression of stiffness changes and creep damage at the interface was measured using digital image correlation techniques. Stiffness changes and creep damage were localized to the contact interface between cement and bone. Interface creep damage followed a three‐phase response with an initial rapid increase in creep, followed by a steady‐state increase, concluding in a final rapid increase in creep. The initial creep phase was accompanied by an increase in interface stiffness, suggesting an initial locking‐in effect at the interface. Interface stiffness decreased as creep damage progressed. Power law models were reasonably successful in describing the creep and stiffness damage response and were a function of loading magnitude, number of loading cycles, and contact area at the interface. More microcrack damage occurred to the cement when compared to the bone, and the damage was localized along the interface. These findings indicate that damage to the cement–bone interface could be minimized by improving cement–bone contact and by strengthening the fatigue resistance of the cement. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27:340–346, 2009
The Complexity and Algorithm for k-Duplicates Combinatorial Auctions with Submodular and Subadditive Bidders

In this paper, we study the problem of maximizing welfare in combinatorial auctions with k(> 1)duplicates of each item, where k is a fixed constant (i.e. k is not the part of the input) and bidders are submodular or subadditive. We exhibit some upper and lower approximation bounds for k-duplicates combinatorial auctions. First, we show that it is NP-hard to approximate the maximum welfare for k-duplicates combinatorial auctions with subadditive bidders within a factor of 2− where > 0 unless P = NP . Secondly, we propose a 2-approximation algorithm for kduplicates combinatorial auctions with submodular bidders.