Miracle-dz/UniFAR-FTUs huggingface dataset:
Copy‐number variation in the pathogenesis of autism spectrum disorder

Autism spectrum disorder is a neurodevelopmental disorder present in 1% of the population, characterized by impairments in reciprocal social interaction, communication deficits and restricted patterns of behavior. Approximately 10% of the autism spectrum disorder population is thought to have large chromosomal rearrangements. Copy‐number variations (CNV) alter the genome structure either by duplication or deletion of a chromosomal region. The association between CNV and autism susceptibility has become more apparent through the use of methods based on comparative genomic hybridization in screening CNV. The nature of the high CNV rate in the human genome is partly explained by non‐allelic homologous recombination between flanking repeated sequences derived from multiple copies of transposons or mobile genetic elements. There are hotspots for CNV in the human genome, such as 16p11.2 and 22q11.2. Genes involved in CNV are supposed to have copy‐number dose‐dependent effects on the behavior of affected individuals. Animal models give insight into the possible interactions between core genetic loci and additional factors contributing to the phenotypes of each individual. If affected genes code for cellular signaling molecules, reducing the dosage in the intracellular signaling pathway may result in the malfunction of the nervous system. The genetic background of autism spectrum disorder is highly heterogenic and most common or rare CNV do not lead to autism spectrum disorders in the majority of cases, but may occasionally increase the risk of developing an autism spectrum disorder.
MUSESCAPE: AN INTERACTIVE CONTENT-AWARE MUSIC BROWSER

Advances in hardware performance, network bandwidth and audio compression have made possible the creation of large personal digital music collections. Although, there is a significant body of work in image and video browsing, there has been little work that directly addresses the problem of audio and especially music browsing. In this paper, Musescape, a prototype music browsing system is described and evaluated. The main characteristics of the system are automatic configuration based on Computer Audition techniques and the use of continuous audio-music feedback while browsing and interacting with the system. The described ideas and techniques take advantage of the unique characteristics of music signals. A pilot user study was conducted to explore and evaluate the proposed user interface. The results indicate that the use of automatically extracted tempo information reduces browsing time and that continuous interactive audio feedback is appropriate for this particular domain.
Approaches to Addressing the Memory Wall

The memory wall is the predicted situation where improvements to processor speed will be masked by the much slower improvement in dynamic random access (DRAM) memory speed. Since the prediction was made in 1995, considerable progress has been made in addressing the memory wall. There have been advances in DRAM organization, improved approaches to memory hierarchy have been proposed, integrating DRAM onto the processor chip has been investigated and alternative approaches to organizing the instruction stream have been researched. All of these approaches contribute to reducing the predicted memory wall effect; some can potentially be combined. This paper reviews the approaches separately, and investigates the extent to which approaches can work together. The major finding is that an integrated approach is necessary, considering all aspects of system design which can impact on memory performance. Specific areas which need to be addressed include models for allowing alternative work to be scheduled while the processor is waiting for DRAM, design of virtual memory management with minimizing DRAM references a major goal, and making it possible to apply increasingly sophisticated strategies to managing the contents of caches, to minimize misses to DRAM.
H ∞ control for non-linear stochastic systems: the output-feedback case

The H ∞ output-feedback control problem for non-linear stochastic systems is considered. A solution for a large class of non-linear stochastic systems is introduced (including non-linear diffusion systems as a subclass). This solution is based on a bounded real lemma for non-linear stochastic systems that was previously established via a stochastic dissipativity concept. The theory yields sufficient conditions for the closed-loop system to possess a prescribed L 2-gain bound in terms of two Hamilton Jacobi inequalities: one that is associated with the state feedback part of the problem is n-dimensional (where n is the underlying system's state dimension) and the other inequality that stems from the estimation part is 2n-dimensional. Both stationary and non–stationary systems are considered. Stability of the closed-loop system is established, both in the mean-square and the in-probability senses. As the solution to the Hamilton Jacobi inequalities may, in general, lead to a non–realisable state estimator, a modification of the associated 2n-dimensional Hamilton Jacobi inequality is made in order to circumvent this realisation problem, while preserving the system's L 2-gain bound. For time-invariant systems, the problem of robust output-feedback is considered in the case of norm-bounded uncertainties. A solution is then derived in terms of linear state-dependent matrix inequalities.
Small World Networks as (Semi)-Structured Overlay Networks

Recent research has shown that small world network (SWN) is navigable. In this position paper, we propose that SWN, for example those which are social networks, have nice properties which make them attractive as overlay networks. Such networks occupy a space between structured and unstructured overlay networks. Our thesis is that SWN may be attractive enough to be a replacement for traditional structured overlay networks which are usually based on chord-style distributed hash tables. Preliminary experiment results show that without node failure, the performance of greedy routing in SWN works very well and with additional links in SWN the robustness in routing can be improved as well as the resilience against node/link failure.
Prognostic Role of High‐Sensitivity C‐Reactive Protein and B‐Type Natriuretic Peptide in Implantable Cardioverter‐Defibrillator Patients

Background: High‐sensitivity C‐reactive protein (hs‐CRP) and B‐type natriuretic peptide (BNP) are useful biomarkers for cardiovascular risk stratification. Little data are available regarding the prognostic value of hs‐CRP and BNP serum levels and future ventricular arrhythmic events triggering implantable cardioverter defibrillator (ICD) therapy.
A unified model for filter capacitor constraints in DC to DC switching converters design

This paper discusses a unified model for the determination of the constraint equations to be used in the selection of feasible capacitors for DC to DC converters. The model is based on a generalized waveform of the current flowing through capacitors, which provides the maximum acceptable ESR as a function of the capacitance C ensuring the compliance with ripple and constraints determined by the application. Design examples are presented regarding the application of the proposed model to boost, buck-boost and SEPIC topologies.
New protocol based on massive parallel sequencing for aneuploidy screening of preimplantation human embryos

ABSTRACT Novel next-generation sequencing procedures have rapidly emerged into the preimplantation genetic screening framework. This work presents the design and validation of a new low-coverage whole-genome sequencing assay for aneuploidy detection in single blastomeres and trophectodermal samples from preimplantation embryos. The validation ensures analytical sensitivity, specificity, robustness, precision, limit of detection, resolution, and reproducibility. Specific parameters to measure the performance are defined, and the results are compared with a standardized array-based method to stablish the concordance. From the single cell genomics point of view, the main novelties are the length of reads of the libraries (150 nucleotides) together with a paired-end strategy and the design of an original algorithm and copy number viewer. A total of 129 samples were included in six experimental runs using a MiSeq Illumina platform. Samples included: single amniocytes, single blastomeres (cleavage-stage embryos), trophectoderm samples (blastocyst), and diluted DNA. Sensitivity and specificity were calculated per chromosome yielding 96% and 99%, respectively. The percentage of concordant samples was 98.2% and all of the aneuploid samples were confirmed. In conclusion, the validation yields highly reliable and reproducible results, representing an accurate and cost-effective strategy for the routine detection of aneuploidy in human embryos.
Antimicrobial therapy of macrolide-resistant Mycoplasma pneumoniae pneumonia in children

ABSTRACT Introduction: Mycoplasma pneumoniae is an important cause of community-acquired pneumonia in children and young adolescents. Macrolides are recommended as the first-line therapy however, macrolide resistance rates in M. pneumoniae among children have been increasing substantially. Areas covered: This review focused on clinical characteristics and treatment of macrolide-resistant M. pneumoniae pneumonia in children. Expert commentary: Antibiotic choice should be based on in vitro activity, clinical efficacy and in consideration of potential adverse events. Macrolide resistance did not contribute to the clinical severity of M. pneumoniae pneumonia, but resistance may be an aggravating factor. Antibiotics may not be required for treatment in mild cases due to the self-resolving nature of M. pneumonia infection, regardless of macrolide resistance. In contrast, antibiotic treatment of severe cases of M. pneumoniae pneumonia is complicated. The clinical benefit of tetracyclines and fluoroquinolones has been shown in terms of shortening duration of symptoms and rapid defervescence in some reports. However, due to safety concerns regarding these two alternative antibiotics, clinicians should weigh the risks and benefits when choosing treatment options. Alternative antibiotics may be considered when patients remain febrile or when chest x-rays show deterioration at least 48-72 hours after macrolide treatment.
Analysis of protein complex formation , microtubules and cytoskeleton

1. Background Determination of the sedimentation coefficient of a protein, traditionally in a 5-20% sucrose gradient, in order to determine its molecular mass, is a technique that was developed many years ago. Although alternative methods, notably polyacrylamide gel electrophoresis, have achieved a wide popularity, there are certain situations that are better suited to density gradients, for example the analysis of heavily glycosylated proteins, which run anomalously on gels. Another area that may be better suited to density gradient analysis is the study of protein-protein interactions.
[Information about the medicines and adherence to high activity antiretroviral treatment in patients with HIV/AIDS in a hospital of Lima, Peru].

OBJECTIVES Determine the association between the information received on high activity antiretroviral treatment (HAART) and the adherence to this treatment in patients with HIV / AIDS of a hospital of Lima, Peru. MATERIALS AND METHODS Cross-sectional analytical study. Through interviews were applied the questionnaire SIMS (Satisfaction with Information about Medicines Scale) to measure satisfaction with information received about medications and SMAQ (Simplified Medication Adherence Questionnaire) to determine adherence to HAART. By reviewing medical records sociodemographic and clinical data were collected. RESULTS 364 patients were interviewed. Satisfaction with the information received about drugs was not associated with adherence to HAART (p = 0.611). Factors associated with the satisfaction with information were: female (ORa = 0.52; 95% CI 0.30 to 0.90); level of higher education (ORa = 0.45; 95% CI 0.27 to 0.75) and age (ORa = 1.05; 95% CI 1.02 to 1.08). There were more satisfaction with the information received on the action and drug use compared with information about potential adverse events (48.9% vs. 43.1%; p = 0.0291). CONCLUSIONS Satisfaction with information received about drugs was not associated with adherence to HAART. This satisfaction increases with age and is lower in females and in the degree of higher education. There are desires for further information on the potential adverse reactions to HAART.
Treating Insomnia, Amnesia, and Acalculia in Regular Expression Matching

Regular expressions provide a flexible means for matching strings and they are often used in data-intensive applications. They are formally equivalent to either deterministic finite automata (DFAs) or nondeterministic finite automata (NFAs). Both DFAs and NFAs are affected by two problems known as amnesia and acalculia, and DFAs are also affected by a problem known as insomnia. Existing techniques require an automata conversion and compaction step that prevents the use of existing automaton databases and hinders the maintenance of the resulting compact automata. In this paper, we propose Parallel Finite State Machines (PFSMs), which are able to run any DFA- or NFA-like state machines without a previous conversion or compaction step. PFSMs report, online, all the matches found within an input string and they solve the three aforementioned problems. Parallel Finite State Machines require quadratic time and linear memory and they are distributable. Parallel Finite State Machines make very fast distributed regular expression matching in data-intensive applications feasible.
A communication disturbance observer with a band-pass filter for delay time compensation

A delay time in a feedback control system deteriorates stability and performance. So, Smith predictor or communication disturbance observer (CDOB) has been proposed to compensate the dead time. However, Smith predictor requires the models of a plant and a dead time. Although the CDOB does not require the model of the dead time, the modeling error of the plant causes a steady state error against a step input. To avoid the steady state error, this paper proposes a novel CDOB using a band-pass filter. The proposal method has an effect to reduce the error against a step input, ramp input, or acceleration input.
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance.
Colony-stimulating factors for chemotherapy-induced febrile neutropenia: a meta-analysis of randomized controlled trials.

PURPOSE Current treatment for febrile neutropenia (FN) includes hospitalization for evaluation, empiric broad-spectrum antibiotics, and other supportive care. Clinical trials have reported conflicting results when studying whether the colony-stimulating factors (CSFs) improve outcomes in patients with FN. This Cochrane Collaboration review was undertaken to further evaluate the safety and efficacy of the CSFs in patients with FN. METHODS An exhaustive literature search was undertaken including major electronic databases (CANCERLIT, EMBASE, LILACS, MEDLINE, SCI, and the Cochrane Controlled Trials Register). All randomized controlled trials that compare CSFs plus antibiotics versus antibiotics alone for the treatment of established FN in adults and children were sought. A meta-analysis of the selected studies was performed. RESULTS More than 8,000 references were screened, with 13 studies meeting eligibility criteria for inclusion. The overall mortality was not influenced significantly by the use of CSF (odds ratio [OR] = 0.68; 95% CI, 0.43 to 1.08; P = .1). A marginally significant result was obtained for the use of CSF in reducing infection-related mortality (OR = 0.51; 95% CI, 0.26 to 1.00; P = .05). Patients treated with CSFs had a shorter length of hospitalization (hazard ratio [HR] = 0.63; 95% CI, 0.49 to 0.82; P = .0006) and a shorter time to neutrophil recovery (HR = 0.32; 95% CI, 0.23 to 0.46; P < .00001). CONCLUSION The use of the CSFs in patients with established FN caused by cancer chemotherapy reduces the amount of time spent in hospital and the neutrophil recovery period. The possible influence of the CSFs on infection-related mortality requires further investigation.
Automatic recognition of emotion evoked by general sound events

Without a doubt there is emotion in sound. So far, however, research efforts have focused on emotion in speech and music despite many applications in emotion-sensitive sound retrieval. This paper is an attempt at automatic emotion recognition of general sounds. We selected sound clips from different areas of the daily human environment and model them using the increasingly popular dimensional approach in the emotional arousal and valence space. To establish a reliable ground truth, we compare mean and median of four annotators with their evaluator weighted estimator. We discuss human labelers' consistency, feature relevance, and automatic regression. Results reach correlation coefficients of . 61 (arousal) and . 49 (valence).
Oligomerization of the integrin αIIbβ3: Roles of the transmembrane and cytoplasmic domains

Integrins are a family of α/β heterodimeric membrane proteins, which mediate cell–cell and cell–matrix interactions. The molecular mechanisms by which integrins are activated and cluster are currently poorly understood. One hypothesis posits that the cytoplasmic tails of the α and β subunits interact strongly with one another in a 1:1 interaction, and that this interaction is modulated in the course of the activation of αIIbβ3 [Hughes, P. E. , et al. (1996) J. Biol. Chem. 271, 6571–6574]. To examine the structural basis for this interaction, protein fragments encompassing the transmembrane helix plus cytoplasmic tails of the α and β subunits of αIIbβ3 were expressed and studied in phospholipid micelles at physiological salt concentrations. Analyses of these fragments by analytical ultracentrifugation, NMR, circular dichroism, and electrophoresis indicated that they had very little or no tendency to interact with one another. Instead, they formed homomeric interactions, with the α- and β-fragments forming dimers and trimers, respectively. Thus, these regions of the protein structure may contribute to the clustering of integrins that accompanies cellular adhesion.
The Economic Value of Ecological Services Provided by Insects

Abstract In this article we focus on the vital ecological services provided by insects. We restrict our focus to services provided by “wild” insects; we do not include services from domesticated or mass-reared insect species. The four insect services for which we provide value estimates—dung burial, pest control, pollination, and wildlife nutrition—were chosen not because of their importance but because of the availability of data and an algorithm for their estimation. We base our estimations of the value of each service on projections of losses that would accrue if insects were not functioning at their current level. We estimate the annual value of these ecological services provided in the United States to be at least $57 billion, an amount that justifies greater investment in the conservation of these services.
Combining antithrombotic and fibrinolytic agents: can it be done?

More than half of ischemic stroke patients who are treated with IV recombinant tissue-type plasminogen activator (rtPA) remain disabled at 3 months.1,2 The reasons are many. The IV rtPA rate of recanalizing occluded arteries is not as high as we would like, especially for large arterial occlusions, which are opened only 30% to 40% of the time.3–6 When rtPA does effectively lyse a thrombus, it is sometimes too late; permanent tissue injury may have already occurred.7,8 Moreover, even when rtPA restores blood flow expeditiously, reocclusion occurs in ≈20% to 30% of patients.9–11 Enhancing thrombolysis with adjunctive agents is a logical next step. Strategies under investigation include increasing recanalization rates through endovascular therapies or ultrasound assistance, increasing the resilience of ischemic tissue using neuroprotective strategies, and limiting the likelihood of reocclusion (and possibly improving recanalization) by adding antithrombotics, such as antiplatelet or anticoagulant agents. Definitive studies have been disappointing to date. The first strategy was recently addressed by the phase III Interventional Management of Stroke (IMS III) Trial, which demonstrated interim futility of adjunctive endovascular therapy compared with IV rtPA alone in a broad population of moderate and severe acute ischemic stroke subjects.12 Detailed results, including subgroup analyses, are pending. The second strategy was recently addressed by the phase III Albumin in Acute Ischemic Stroke (ALIAS) Trial of albumin, which also demonstrated interim futility (personal communication, Michael D. Hill, unpublished data, 2012), and detailed results are pending for this as well. Another phase III trial of neuroprotection strategy to enhance …
Role of Matrix Metalloproteinases in Photoaging and Photocarcinogenesis

Matrix metalloproteinases (MMPs) are zinc-containing endopeptidases with an extensive range of substrate specificities. Collectively, these enzymes are able to degrade various components of extracellular matrix (ECM) proteins. Based on their structure and substrate specificity, they can be categorized into five main subgroups, namely (1) collagenases (MMP-1, MMP-8 and MMP-13); (2) gelatinases (MMP-2 and MMP-9); (3) stromelysins (MMP-3, MMP-10 and MMP-11); (4) matrilysins (MMP-7 and MMP-26); and (5) membrane-type (MT) MMPs (MMP-14, MMP-15, and MMP-16). The alterations made to the ECM by MMPs might contribute in skin wrinkling, a characteristic of premature skin aging. In photocarcinogenesis, degradation of ECM is the initial step towards tumor cell invasion, to invade both the basement membrane and the surrounding stroma that mainly comprises fibrillar collagens. Additionally, MMPs are involved in angiogenesis, which promotes cancer cell growth and migration. In this review, we focus on the present knowledge about premature skin aging and skin cancers such as basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and melanoma, with our main focus on members of the MMP family and their functions.