Miracle-dz/UniFAR-FTUs huggingface dataset:
Audio Word2Vec: Unsupervised Learning of Audio Segment Representations Using Sequence-to-Sequence Autoencoder

The vector representations of fixed dimensionality for words (in text) offered by Word2Vec have been shown to be very useful in many application scenarios, in particular due to the semantic information they carry. This paper proposes a parallel version, the Audio Word2Vec. It offers the vector representations of fixed dimensionality for variable-length audio segments. These vector representations are shown to describe the sequential phonetic structures of the audio segments to a good degree, with very attractive real world applications such as query-by-example Spoken Term Detection (STD). In this STD application, the proposed approach significantly outperformed the conventional Dynamic Time Warping (DTW) based approaches at significantly lower computation requirements. We propose unsupervised learning of Audio Word2Vec from audio data without human annotation using Sequence-to-sequence Audoencoder (SA). SA consists of two RNNs equipped with Long Short-Term Memory (LSTM) units: the first RNN (encoder) maps the input audio sequence into a vector representation of fixed dimensionality, and the second RNN (decoder) maps the representation back to the input audio sequence. The two RNNs are jointly trained by minimizing the reconstruction error. Denoising Sequence-to-sequence Autoencoder (DSA) is furthered proposed offering more robust learning.
Vascular Inflammation in Obesity and Sleep Apnea

Background— Unrecognized obstructive sleep apnea (OSA) is highly prevalent in obesity. Both obesity and OSA are associated with vascular endothelial inflammation and increased risk for cardiovascular diseases. We investigated directly whether the endothelial alterations that are attributed commonly to obesity are in fact related to OSA. Methods and Results— Seventy-one subjects with a body mass index ranging from normal to obese underwent attended polysomnography. To assess vascular inflammation and oxidative stress directly, we quantified the expression of nuclear factor-&kgr;B and nitrotyrosine by immunofluorescence in freshly harvested venous endothelial cells. To evaluate basal endothelial nitric oxide (NO) production and activity, we quantified the expression of endothelial NO synthase (eNOS) and phosphorylated eNOS. Vascular reactivity was measured by brachial artery flow-mediated dilation. Expression of eNOS and phosphorylated eNOS and flow-mediated dilation were significantly lower, whereas expression of nitrotyrosine was significantly greater in OSA patients (n=38) than in OSA-free subjects (n=33) regardless of central adiposity. Expression of nuclear factor-&kgr;B was greater in obese OSA patients than in obese OSA-free subjects (P=0.004). Protein expression and flow-mediated dilation were not significantly affected by increasing body mass index or central obesity in OSA patients and in OSA-free subjects. After 4 weeks of continuous positive airway pressure therapy, flow-mediated dilation and expression of eNOS and phosphorylated eNOS significantly increased whereas expression of nitrotyrosine and nuclear factor-&kgr;B significantly decreased in OSA patients who adhered to continuous positive airway pressure ≥4 hours daily. Conclusions— Untreated OSA rather than obesity is a major determinant of vascular endothelial dysfunction, inflammation, and elevated oxidative stress in obese patients.
Daily Sleep Patterns, Sleep Quality, and Sleep Hygiene Among Parent-Child Dyads of Young Children Newly Diagnosed With Juvenile Idiopathic Arthritis and Typically Developing Children.

OBJECTIVES Describe daily sleep patterns, sleep quality, and sleep hygiene in 2-5-year-old children newly diagnosed with juvenile idiopathic arthritis (JIA) and their parents in comparison with typically developing (TD) children and parents. METHODS Participants (13 JIA, 16 TD parent-child dyads) wore actigraphs for 10 days. Parents completed sleep diaries and sleep hygiene survey. RESULTS Children with JIA had significantly less total sleep time, lower sleep efficiency (SE), and longer naps than TD children. Parents of children with JIA had significantly earlier bedtimes, more wake after sleep onset (WASO) and lower SE than TD parents. Parent-child SE and WASO were interrelated in JIA dyads. Sleep hygiene practices were inconsistent in both groups of children. CONCLUSIONS Inadequate amounts of sleep and poor sleep quality were common in parent-child dyads. Early interventions to improve sleep duration and promote sleep hygiene practices may alleviate future sleep problems and improve parent and child well-being.
A unified framework for tree search decoding: rediscovering the sequential decoder

We consider receiver design for coded transmission over linear Gaussian channels. We restrict ourselves to the class of lattice codes and formulate the joint detection and decoding problem as a closest lattice point search (CLPS). Here, a tree search framework for solving the CLPS is adopted. In our framework, the CLPS algorithm is decomposed into the preprocessing and tree search stages. The role of the preprocessing stage is to expose the tree structure in a form matched to the search stage. We argue that the forward and feedback (matrix) filters of the minimum mean-square error decision feedback equalizer (MMSE-DFE) are instrumental for solving the joint detection and decoding problem in a single search stage. It is further shown that MMSE-DFE filtering allows for solving underdetermined linear systems and using lattice reduction methods to diminish complexity, at the expense of a marginal performance loss. For the search stage, we present a generic method, based on the branch and bound (BB) algorithm, and show that it encompasses all existing sphere decoders as special cases. The proposed generic algorithm further allows for an interesting classification of tree search decoders, sheds more light on the structural properties of all known sphere decoders, and inspires the design of more efficient decoders. In particular, an efficient decoding algorithm that resembles the well-known Fano sequential decoder is identified. The excellent performance-complexity tradeoff achieved by the proposed MMSE-DFE Fano decoder is established via simulation results and analytical arguments in several multiple-input multiple-output (MIMO) and intersymbol interference (ISI) scenarios.
Charting the proteome of Cryptosporidium parvum sporozoites using sequence similarity-based BLAST searching

Cryptosporidium (C.) spp. are important zoonotic parasites causing widespread diarrhoeal disease in man and animals. The recent release of the complete genome sequences for C. parvum and C. hominis has facilitated the comprehensive global proteome analysis of these opportunistic pathogens. The well-known approach for mass spectrometry (MS) based data analysis using the BLAST tool (MS BLAST) is a database search protocol for identifying unknown proteins by sequence similarity to homologous proteins using peptide sequences produced by mass spectrometry. We have used several complementary approaches to explore the global sporozoite proteome of C. parvum with available proteomic tools. To optimize the output of the MS data, a sequence similarity-based MS BLAST strategy was employed for bioinformatic analysis. Most significantly, almost all the constituents of glycolysis and several mitochondrion-related proteins were identified. In addition, many hypothetical Cryptosporidium proteins were validated by the identification of their constituent peptides. The MS BLAST approach was found to be useful during the study and could provide valuable information towards a complete understanding of the unique biology of Cryptosporidium.
Prevention of diabetes in NOD mice at a late stage by targeting OX40/OX40 ligand interactions

Autoreactive T cells play a major role in the development of insulin‐dependent diabetes mellitus, suggesting that costimulatory molecules that regulate T cell responses might be essential for disease progression. In NOD mice, CD28/B7 and CD40/CD40 ligand (L) interactions control the onset of diabetes from 2 to 4 weeks of age, but blocking these molecules has little effect after this time. Hence, it is possible that other ligand/receptor pairs control a later phase of disease. We now show that OX40 is expressed on CD4 and CD8 T cells several weeks prior to islet destruction, which is initiated around weeks 12–14, and that OX40L is present on dendritic cells in both secondary lymphoid organs and the pancreas from 11 to 13 weeks of age. Blocking OX40L at 6, 9, or 15 weeks after birth had little effect on disease; however, inhibiting OX40/OX40L interactions at week 12, or continuous treatment from week 12 onwards, significantly reduced the incidence of diabetes. Histological examination showed that islet destruction was prevented and insulitis reduced by targeting OX40L. These studies show that OX40/OX40L interactions form a late checkpoint in diabetes development and suggest that these molecules are realistic targets for therapeutic intervention.
Mycoremediation of congo red dye by filamentous fungi

Azo, anthroquinone and triphenylmethane dyes are the major classes of synthetic colourants, which are difficult to degrade and have received considerable attention. Congo red, a diazo dye, is considered as a xenobiotic compound, and is recalcitrant to biodegradative processes. Nevertheless, during the last few years it has been demonstrated that several fungi, under certain environmental conditions, are able to transfer azo dyes to non toxic products using laccases. The aim of this work was to study the factors influencing mycoremediation of Congo red. Several basidiomycetes and deuteromycetes species were tested for the decolourisation of Congo red (0.05 g/l) in a semi synthetic broth at static and shaking conditions. Poor decolourisation was observed when the dye acted as the sole source of nitrogen, whereas semi synthetic broth supplemented with fertilizer resulted in better decolourisation. Decolourisation of Congo red was checked in the presence of salts of heavy metals such as mercuric chloride, lead acetate and zinc sulphate. Decolourisation parameters such as temperature, pH, and rpm were optimized and the decolourisation obtained at optimized conditions varied between 29.25- 97.28% at static condition and 82.1- 100% at shaking condition. Sodium dodecyl sulphate polyacrylamide gel electrophoretic analysis revealed bands with molecular weights ranging between 66.5 to 71 kDa, a characteristic of the fungal laccases. High efficiency decolourisation of Congo red makes these fungal forms a promising choice in biological treatment of waste water containing Congo red.
ON THE CONVERGENCE OF PATTERN SEARCH ALGORITHMS

We introduce an abstract definition of pattern search methods for solving nonlinear unconstrained optimization problems. Our definition unifies an important collection of optimization methods that neither compute nor explicitly approximate derivatives. We exploit our characterization of pattern search methods to establish a global convergence theory that does not enforce a notion of sufficient decrease. Our analysis is possible because the iterates of a pattern search method lie on a scaled, translated integer lattice. This allows us to relax the classical requirements on the acceptance of the step, at the expense of stronger conditions on the form of the step, and still guarantee global convergence.
Patterns in helminth communities in freshwater fish in Great Britain: alternative strategies for colonization

SUMMARY Examples of the apparently stochastic nature of freshwater fish helminth communities illustrating the erratic and unpredictable occurrence and distribution of many species are provided for six species of fish from several localities throughout Britain. By focussing on parasite colonization strategies two categories of helminths are recognized: autogenic species which mature in fish and allogenic species which mature in vertebrates other than fish and have a greater colonization potential and ability. Three groups of fish are distinguished: salmonids, in which helminth communities are generally dominated by autogenic species which are also responsible for most of the similarity within and between localities; cyprinids, in which they are dominated by allogenic species which are also responsible for most of the similarity within and between localities; and anguillids, whose helminth communities exhibit intermediate features with neither category consistently dominating nor providing a clear pattern of similarity. Recognition and appreciation of the different colonization strategies of autogenic and allogenic helminths in respect of host vagility and ability to cross land or sea barriers and break down habitat isolation, and their period of residence in a locality, whether transient or permanent, provides an understanding of, and explanation for, the observed patchy spatial distribution of many helminths. Comparison with other parts of the world indicates that colonization is a major determinant of helminth community structure.
Genetic Associations in Classical Hodgkin Lymphoma: A Systematic Review and Insights into Susceptibility Mechanisms

Both targeted and genome-wide studies have revealed genetic associations for susceptibility, prognosis, and treatment-induced secondary malignancies and toxicities in classical Hodgkin lymphoma (cHL). This review gives a systematic and comprehensive overview of significant associations and places them into a biologic context. The strongest susceptibility polymorphisms have been found for the human leukocyte antigen (HLA) genes. These associations are specific for cHL overall or for subgroups based on tumor cell Epstein–Barr virus (EBV) status. These findings strongly suggest that EBV-specific immune responses influence cHL susceptibility in EBV+ cHL and that immune responses targeting other tumor-associated antigens are important in EBV− cHL. Accordingly, most of the numerous other susceptibility loci map to genes that affect functionality of the immune system, underscoring the crucial role of the immune system in cHL development. The number of association studies on cHL prognosis is limited with one consistent association for the drug-metabolizing UGT1A1 gene. PRDM1 is associated with radiation-induced secondary malignancies and a small number of genes are associated with treatment-related toxicities. In conclusion, most loci showing genetic associations in cHL harbor genes with a potential functional relevance for cHL susceptibility. Cancer Epidemiol Biomarkers Prev; 23(12); 2737–47. ©2014 AACR.
Magnetism of Amorphous and Nano-Crystallized Dc-Sputter-Deposited MgO Thin Films

We report a systematic study of room-temperature ferromagnetism (RTFM) in pristine MgO thin films in their amorphous and nano-crystalline states. The as deposited dc-sputtered films of pristine MgO on Si substrates using a metallic Mg target in an O2 containing working gas atmosphere of (N2 + O2) are found to be X-ray amorphous. All these films obtained with oxygen partial pressure (PO2) ~10% to 80% while maintaining the same total pressure of the working gas are found to be ferromagnetic at room temperature. The room temperature saturation magnetization (MS) value of 2.68 emu/cm3 obtained for the MgO film deposited in PO2 of 10% increases to 9.62 emu/cm3 for film deposited at PO2 of 40%. However, the MS values decrease steadily for further increase of oxygen partial pressure during deposition. On thermal annealing at temperatures in the range 600 to 800 °C, the films become nanocrystalline and as the crystallite size grows with longer annealing times and higher temperature, MS decreases. Our study clearly points out that it is possible to tailor the magnetic properties of thin films of MgO. The room temperature ferromagnetism in MgO films is attributed to the presence of Mg cation vacancies.
The Association between Antidepressant Medications and Coronary Heart Disease in Brazil: A Cross-Sectional Analysis on the Brazilian Longitudinal Study of Adult Health (ELSA-Brazil)

Background: Recent studies have highlighted associations between use of antidepressant medications and coronary heart disease (CHD). Tricyclic antidepressants (TCA) are not recommended in patients with CHD as they may increase morbidity and mortality. However, this class of antidepressants is freely prescribed in public health pharmacies, while access to other classes of antidepressants is restricted in Brazil. Here, we examine the associations between antidepressant use and prevalent CHD in a large cohort from Brazil. Methods: Participants included 14,994 civil servants aged 35–74 years from the baseline assessment of the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil). CHD (n = 710) included stable angina, myocardial infarction, and coronary revascularization. Univariate (unadjusted) and multivariate (adjusted) logistic regression analyses were conducted to estimate odds ratios and confidence intervals. Results: After full adjustment for covariates, TCA use (n = 156) was associated with a twofold increase in prevalent CHD, relative to non-use (n = 14,076). Additional sensitivity analysis revealed a threefold association for myocardial infarction (OR: 2.96, 95% CI: 1.41–6.21) and coronary revascularization (OR: 2.92, 95% CI: 1.28–6.66). There were no significant associations between antidepressant use and stable angina pectoris. Conclusion: Findings highlight a strong association between TCA use and prevalent CHD. While the cross-sectional design is an important limitation of the present study, findings have important implications for the treatment of cardiac patients in Brazil.
Phagocytosis of Borrelia burgdorferi and Treponema pallidum Potentiates Innate Immune Activation and Induces Gamma Interferon Production

ABSTRACT We examined the interactions of live and lysed spirochetes with innate immune cells. THP-1 monocytoid cells were activated to comparable extents by live Borrelia burgdorferi and by B. burgdorferi and Treponema pallidum lysates but were poorly activated by live T. pallidum. Because THP-1 cells poorly internalized live spirochetes, we turned to an ex vivo peripheral blood mononuclear cell system that would more closely reflect spirochete-mononuclear phagocyte interactions that occur during actual infection. In this system, B. burgdorferi induced significantly greater monocyte activation and inflammatory cytokine production than did borrelial lysates or T. pallidum, and only B. burgdorferi elicited gamma interferon (IFN-γ) from NK cells. B. burgdorferi was phagocytosed avidly by monocytes, while T. pallidum was not, suggesting that the enhanced response to live B. burgdorferi was due to phagocytosis of the organism. When cytochalasin D was used to block phagocytosis of live B. burgdorferi, cytokine production decreased to levels comparable to those induced by B. burgdorferi lysates, while the IFN-γ response was abrogated altogether. In the presence of human syphilitic serum, T. pallidum was efficiently internalized and initiated responses resembling those observed with live B. burgdorferi, including the production of IFN-γ by NK cells. Depletion of monocytes revealed that they were the primary source of inflammatory cytokines, while dendritic cells (DCs) directed IFN-γ production from innate lymphocytes. Thus, phagocytosis of live spirochetes initiates cell activation programs in monocytes and DCs that differ qualitatively and quantitatively from those induced at the cell surface by lipoprotein-enriched lysates. The greater stimulatory capacity of B. burgdorferi versus T. pallidum appears to be explained by the successful recognition and phagocytosis of B. burgdorferi by host cells and the ability of T. pallidum to avoid detection and uptake by virtue of its denuded outer membrane rather than by differences in surface lipoprotein expression.
IgG‐secreting lymphoplasmacytoid leukaemia: a B‐cell disorder with extensively mutated VH genes undergoing Ig isotype‐switching frequently associated with trisomy 12

We investigated 16 patients with elevated serum monoclonal IgG and a leukaemic B‐cell lymphocytic disorder different from multiple myeloma. Their clinical history was that of a non‐aggressive disease with dominant splenomegaly and long survival. Whereas abnormal blood and bone marrow cells were predominantly small lymphocytes with a few lymphoplasmacytoid cells, histopathological features included a lymphoplasmacytic infiltrate in eight cases. Most frequently, abnormal blood cells displayed a CD19+CD5−CD23+/– immunophenotype different from that of chronic lymphocytic leukaemia, except in two cases with a CD19+CD5+CD23+ phenotype. Interestingly, a coexistent serum monoclonal IgM and/or surface IgMG+ with identical light chain was identified in 10 patients, whereas in the remaining six patients only IgG expression was determined. VH gene analysis was performed in eight patients to investigate the clonal origins of tumour cells. All cases utilized the VH3 family, with evidence of extensive somatic mutations and intraclonal homogeneity in all cases. VH gene analysis indicated a clonal relationship between cells expressing IgM and IgG, with one case being biclonal. Cytogenetic evaluation showed a high incidence of trisomy 12 (60%) and 13q14 deletion (40%). In conclusion, we have described an unusual subset of low‐grade lymphoma with high‐serum IgG and frequent lymphoplasmacytoid features in which tumour cells derive from post‐follicular memory B cells undergoing isotype switching with some cases arrested at both the IgM and IgG stage and others as IgG‐positive cells only.
Optimal ESS Allocation for Benefit Maximization in Distribution Networks

Smart grids have been emerging nowadays as an initiative to operate modern distribution systems in a more economic and efficient way. Energy storage systems (ESSs) are one of the promising technologies that can achieve the goals of smart grids via facilitating the connection of renewable sources, improving system reliability, and controlling the net demand through peak load shaving, etc. In this paper, a comprehensive planning framework is introduced for ascertaining the most cost effective siting and sizing of ESSs that maximize their benefits in distribution networks. A probabilistic approach is further adopted that includes the consideration of the stochastic nature of system components. Such approach allows determining the optimal operation of ESS at each load state. Moreover, contingency planning decisions, in the form of load points to be shed during contingencies, are identified through the approach proposed.
An Extensible Framework for Verification of Numerical Claims

In this paper we present our automated fact checking system demonstration which we developed in order to participate in the Fast and Furious Fact Check challenge. We focused on simple numerical claims such as “population of Germany in 2015 was 80 million” which comprised a quarter of the test instances in the challenge, achieving 68% accuracy. Our system extends previous work on semantic parsing and claim identification to handle temporal expressions and knowledge bases consisting of multiple tables, while relying solely on automatically generated training data. We demonstrate the extensible nature of our system by evaluating it on relations used in previous work. We make our system publicly available so that it can be used and extended by the community.