Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA)

Background: Subtelomeric rearrangements contribute to idiopathic mental retardation and human malformations, sometimes as distinct mental retardation syndromes. However, for most subtelomeric defects a characteristic clinical phenotype remains to be elucidated. Objective: To screen for submicroscopic subtelomeric aberrations using multiplex ligation dependent probe amplification (MLPA). Methods: 210 individuals with unexplained mental retardation were studied. A new set of subtelomeric probes, the SALSA P036 human telomere test kit, was used. Results: A subtelomeric aberration was identified in 14 patients (6.7%) (10 deletions and four duplications). Five deletions were de novo; four were inherited from phenotypically normal parents, suggesting that these were polymorphisms. For one deletion, DNA samples of the parents were not available. Two de novo submicroscopic duplications were detected (dup 5qter, dup 12pter), while the other duplications (dup 18qter and dup 22qter) were inherited from phenotypically similarly affected parents. All clinically relevant aberrations (de novo or inherited from similarly affected parents) occurred in patients with a clinical score of ⩾3 using an established checklist for subtelomeric rearrangements. Testing of patients with a clinical score of ⩾3 increased the diagnostic yield twofold to 12.4%. Abnormalities with clinical relevance occurred in 6.3%, 5.1%, and 1.7% of mildly, moderately, and severely retarded patients, respectively, indicating that testing for subtelomeric aberrations among mildly retarded individuals is necessary. Conclusions: The value of MLPA is confirmed. Subtelomeric screening can be offered to all mentally retarded patients, although clinical preselection increases the percentage of chromosomal aberrations detected. Duplications may be a more common cause of mental retardation than has been appreciated.
Development of a Smartphone-Based System for Intrinsically Photosensitive Retinal Ganglion Cells Targeted Chromatic Pupillometry

Chromatic Pupillometry, used to assess Pupil Light Reflex (PLR) to a coloured light stimulus, has regained interest since the discovery of melanopsin in the intrinsically photosensitive Retinal Ganglion Cells (ipRGCs). This technique has shown the potential to be used as a screening tool for neuro-ophthalmological diseases; however, most of the pupillometers available are expensive and not portable, making it harder for them to be used as a widespread screening tool. In this study, we developed a smartphone-based system for chromatic pupillometry that allows targeted stimulation of the ipRGCs. Using a smartphone, this system is portable and accessible and takes advantage of the location of the ipRGCs in the perifovea. The system incorporates a 3D-printed support for the smartphone and an illumination system. Preliminary tests were carried out on a single individual and then validated on eleven healthy individuals with two different LED intensities. The average Post-Illumination Pupil Light Response 6 s after the stimuli offsets (PIPR-6s) showed a difference between the blue and the red stimuli of 9.5% for both intensities, which aligns with the studies using full-field stimulators. The results validated this system for a targeted stimulation of the ipRGCs for chromatic pupillometry, with the potential to be a portable and accessible screening tool for neuro-ophthalmological diseases.
TIGIT regulates CD4+ T cell immunity against polymicrobial sepsis

Background Sepsis is one of the major causes of death and increased health care burden in modern intensive care units. Immune checkpoints have been prompted to be key modulators of T cell activation, T cell tolerance and T cell exhaustion. This study was designed to investigate the role of the negative immune checkpoint, T cell immunoglobulin and ITIM domain (TIGIT), in the early stage of sepsis. Method An experimental murine model of sepsis was developed by cecal ligation and puncture (CLP). TIGIT and CD155 expression in splenocytes at different time points were assessed using flow cytometry. And the phenotypes of TIGIT-deficient (TIGIT-/-) and wild-type (WT) mice were evaluated to explore the engagement of TIGIT in the acute phase of sepsis. In addition, the characteristics were also evaluated in the WT septic mice pretreated with anti-TIGIT antibody. TIGIT and CD155 expression in tissues was measured using real-time quantitative PCR and immunofluorescence staining. Proliferation and effector function of splenic immune cells were evaluated by flow cytometry. Clinical severity and tissue injury were scored to evaluate the function of TIGIT on sepsis. Additionally, tissue injury biomarkers in peripheral blood, as well as bacterial load in peritoneal lavage fluid and liver were also measured. Results The expression of TIGIT in splenic T cells and NK cells was significantly elevated at 24 hours post CLP.TIGIT and CD155 mRNA levels were upregulated in sepsis-involved organs when mice were challenged with CLP. In CLP-induced sepsis, CD4+ T cells from TIGIT-/- mice shown increased proliferation potency and cytokine production when compared with that from WT mice. Meanwhile, innate immune system was mobilized in TIGIT-/- mice as indicated by increased proportion of neutrophils and macrophages with potent effector function. In addition, tissue injury and bacteria burden in the peritoneal cavity and liver was reduced in TIGIT-/- mice with CLP induced sepsis. Similar results were observed in mice treated with anti-TIGIT antibody. Conclusion TIGIT modulates CD4+ T cell response against polymicrobial sepsis, suggesting that TIGIT could serve as a potential therapeutic target for sepsis.
Filling in the details: Perceiving from low fidelity images

Humans perceive their surroundings in great detail even though most of our visual field is reduced to low-fidelity color-deprived (e.g. dichromatic) input by the retina. In contrast, most deep learning architectures are computationally wasteful in that they consider every part of the input when performing an image processing task. Yet, the human visual system is able to perform visual reasoning despite having only a small fovea of high visual acuity. With this in mind, we wish to understand the extent to which connectionist architectures are able to learn from and reason with low acuity, distorted inputs. Specifically, we train autoencoders to generate full-detail images from low-detail "foveations" of those images and then measure their ability to reconstruct the full-detail images from the foveated versions. By varying the type of foveation, we can study how well the architectures can cope with various types of distortion. We find that the autoencoder compensates for lower detail by learning increasingly global feature functions. In many cases, the learnt features are suitable for reconstructing the original full-detail image. For example, we find that the networks accurately perceive color in the periphery, even when 75\% of the input is achromatic.
Performance of blind equalization with higher order statistics in indoor radio environments

This paper analyzes the performance of blind equalization using the complex cepstrum of third-order moments applied to 4-QAM time division multiple access (TDMA) indoor radio communication systems. In particular, we have modeled a dispersive indoor channel with Rice statistics. We used the blind algorithms to estimate the channel-impulse response, and from this, we computed the equalizer coefficients using a classical minimum mean square error (MMSE) algorithm. In order to evaluate the system performance, we calculated the bit error rate (BER) of a decision feedback equalizer (DFE) that uses a tricepstrum algorithm to estimate the channel-impulse response. The results are compared with those obtained using a least sum of square errors (LSSE) algorithm as a channel estimator and considering the exact channel response. The results obtained show that this kind of blind equalizer performs better than the more classically trained equalizer when Rice channels with a strong direct path and signal-to-noise ratios (SNRs) lower than 20 dB are taken into account. However, some problems relating to the length of time needed for convergence must be solved.
An MR Brain Images Classifier System via Particle Swarm Optimization and Kernel Support Vector Machine

Automated abnormal brain detection is extremely of importance for clinical diagnosis. Over last decades numerous methods had been presented. In this paper, we proposed a novel hybrid system to classify a given MR brain image as either normal or abnormal. The proposed method first employed digital wavelet transform to extract features then used principal component analysis (PCA) to reduce the feature space. Afterwards, we constructed a kernel support vector machine (KSVM) with RBF kernel, using particle swarm optimization (PSO) to optimize the parameters C and σ. Fivefold cross-validation was utilized to avoid overfitting. In the experimental procedure, we created a 90 images dataset brain downloaded from Harvard Medical School website. The abnormal brain MR images consist of the following diseases: glioma, metastatic adenocarcinoma, metastatic bronchogenic carcinoma, meningioma, sarcoma, Alzheimer, Huntington, motor neuron disease, cerebral calcinosis, Pick's disease, Alzheimer plus visual agnosia, multiple sclerosis, AIDS dementia, Lyme encephalopathy, herpes encephalitis, Creutzfeld-Jakob disease, and cerebral toxoplasmosis. The 5-folded cross-validation classification results showed that our method achieved 97.78% classification accuracy, higher than 86.22% by BP-NN and 91.33% by RBF-NN. For the parameter selection, we compared PSO with those of random selection method. The results showed that the PSO is more effective to build optimal KSVM.
INDER : A Flexible Clustering Tool for Summarization

We present a statistical similarity measuring and clustering tool, SIMFINDER, that organizes small pieces of text from one or multiple documents into tight clusters. By placing highly related text units in the same cluster, SIMFINDER enables a subsequent content selection/generation component to reduce each cluster to a single sentence, either by extraction or by reformulation. We report on improvements in the similarity and clustering components of SIMFINDER, including a quantitative evaluation, and establish the generality of the approach by interfacing SIMFINDER to two very different summarization systems.
Mutations in Non-Acid Patch Residues Disrupt H2A.Z’s Association with Chromatin through Multiple Mechanisms

The incorporation of histone variants into nucleosomes is a critical mechanism for regulating essential DNA-templated processes and for establishing distinct chromatin architectures with specialised functions. H2A.Z is an evolutionarily conserved H2A variant that has diverse roles in transcriptional regulation, heterochromatin boundary definition, chromosome stability and DNA repair. The H2A.Z C-terminus diverges in sequence from canonical H2A and imparts unique functions to H2A.Z in the yeast S. cerevisiae. Although mediated in part through the acid patch-containing M6 region, many molecular determinants of this divergent structure-function relationship remain unclear. Here, by using an unbiased random mutagenesis screen of H2A.Z alleles, we identify point mutations in the C-terminus outside of the M6 region that disrupt the normal function of H2A.Z in response to cytotoxic stress. These functional defects correlate with reduced chromatin association, which we attribute to reduced physical stability within chromatin, but also to altered interactions with the SWR and INO80 chromatin remodeling complexes. Together with experimental data, computational modelling of these residue changes in the context of protein structure suggests the importance of C-terminal domain integrity and configuration for maintaining the level of H2A.Z in nucleosomes.
PHR1, an integral membrane protein of the inner ear sensory cells, directly interacts with myosin 1c and myosin VIIa

By using the yeast two-hybrid technique, we identified a candidate protein ligand of the myosin 1c tail, PHR1, and found that this protein can also bind to the myosin VIIa tail. PHR1 is an integral membrane protein that contains a pleckstrin homology (PH) domain. Myosin 1c and myosin VIIa are two unconventional myosins present in the inner ear sensory cells. We showed that PHR1 immunoprecipitates with either myosin tail by using protein extracts from cotransfected HEK293 cells. In vitro binding assays confirmed that PHR1 directly interacts with these two myosins. In both cases the binding involves the PH domain. In vitro interactions between PHR1 and the myosin tails were not affected by the presence or absence of Ca2+ and calmodulin. Finally, we found that PHR1 is able to dimerise. As PHR1 is expressed in the vestibular and cochlear sensory cells, its direct interactions with the myosin 1c and VIIa tails are likely to play a role in anchoring the actin cytoskeleton to the plasma membrane of these cells. Moreover, as both myosins have been implicated in the mechanotransduction slow adaptation process that takes place in the hair bundles, we propose that PHR1 is also involved in this process.
MESH-DHT APPROACH FOR EFFICIENT RESOURCE SHARING IN P 2 P BASED WIRELESS MESH NETWORK

Wireless Mesh Networks (WMN) is a popular communication paradigm due to its low cost and rapid deployment. A large-scale WMN needs a look-up structure to support storage, client mobility and generic services. A Distributed Hash Table (DHTs) spreads construction and maintenance load of abstract index infrastructure over participating nodes, providing simple data access interface. The existing Location aware chord protocol incorporates nodes locality in DHT construction. In addition to node locality, we have proposed MESH-DHT that considers the Link Quality, End to End Delay, Query Response time, Packet Delivery Ratio to improve the QoS parameters in a P2P based Wireless Mesh Network. As WMN’s Quality of Service (QoS) parameters are Non-Deterministic Polynomial (NP) hard problem, we have proposed Particle Swarm Optimization (PSO) to improve the QoS parameters of chord when deployed over a multihop environment like Wireless Mesh Networks.
Formal verification of logical link control and adaptation protocol

In this paper, we provide a formal verification of a configuration process in the Bluetooth logical link control and adaptation protocol (L2CAP). Formal verification has been carried out in a symbolic model checking framework. Hence, NuSMV has been chosen as a tool which enables the BDD-based model checking against CTL specifications. Formal description of the protocol is based on an interleaving semantics provided by the NuSMV. We checked the important system properties and described the problems related to its specification and verification.
A Market Test for the Positivity of Arrow-Debreu Prices

We derive tractable necessary and sufficient conditions for the absence of buy-and-hold arbitrage opportunities in a perfectly liquid, one period market. We formulate the positivity of Arrow-Debreu prices as a generalized moment problem to show that this no arbitrage condition is equivalent to the positive semidefiniteness of matrices formed by the market price of tradeable securities and their products. We apply this result to a market with multiple assets and basket call options.
Genetic Variations in Susceptibility to Traumatic Muscle Injuries and Muscle Pain among Brazilian High-Performance Athletes

Traumatic muscle injuries (TMIs) and muscle pain (MP) negatively impact athletes’ performance and quality of life. Both conditions have a complex pathophysiology involving the interplay between genetic and environmental factors. Yet, the existing data are scarce and controversial. To provide more insights, this study aimed to investigate the association of single-nucleotide polymorphisms (SNPs) previously linked to athletic status with TMI and MP after exercise among Brazilian high-performance athletes from different sports modalities (N = 345). The impact of important environmental determinants was also assessed. From the six evaluated SNPs (ACTN3 rs1815739, FAAH rs324420, PPARGC1A rs8192678, ADRB2 rs1042713, NOS3 rs1799983, and VDR rs731236), none was significantly associated with TMI. Regarding MP after exercise, ACTN3 rs1815739 (CC/CT vs. TT; adjusted odds ratio (aOR) = 1.90; 95% confidence interval (95%Cl), 1.01–3.57) and FAAH rs324420 (AA vs. AC/CC; aOR = 2.30; 95%Cl, 1.08–4.91) were independent predictors according to multivariate binomial analyses adjusted for age (≥23 vs. <23 years), sex (male vs. female), and tobacco consumption (yes vs. no). External validation is warranted to assess the predictive value of ACTN3 rs1815739 and FAAH rs324420. This could have implications for prophylactic interventions to improve athletes’ quality of life.
Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome

ABSTRACT We report here the draft genome sequences of Bifidobacterium strains N4G05 and N5G01, isolated from the human vaginal microbiome. Genome sequences were obtained by de novo assembly from high-quality reads. Both strains were closely related to Bifidobacterium kashiwanohense based on barcode marker sequences and average nucleotide identity analysis.
Walking and Playing with the Dog to Improve the Physical Activity Level of Adolescents: A Scoping Review

Background: In recent years, new technologies such as the introduction of the smartphone and the tablet in everyday life and habits have often made adolescents sedentary. It is becoming a serious problem in society. It is important to propose, as soon as possible, proper and feasible programs to modify this trend. A solution should be to increase physical activity, reducing sedentary behaviors. Adopting dogs and walking and playing with them could be a solution, and the population should be sensitized about this aspect. Consequently, the objective of this scoping revision of the literature is to analyze the association between physical activity in adolescents and the presence of a dog in the family. Methods: Three electronic databases were screened until 21 February 2024. The detected articles were screened against the eligibility criteria. The results were narratively discussed. Results: After the screening process, a total of four studies were included. The studies presented heterogeneity in the physical activity assessment. This made it hard to synthesize the results. Indicatively, there is a positive association between physical activity and dog ownership. Conclusions: walking and playing with the dog increase the physical activity level of adolescents. Therefore, a sensibilization campaign should highlight the importance of having dogs in families, especially in adolescence. It is fundamental to daily walk and play with them.
Further investigations on EMG-to-speech conversion

Our study deals with a Silent Speech Interface based on mapping surface electromyographic (EMG) signals to speech waveforms. Electromyographic signals recorded from the facial muscles capture the activity of the human articulatory apparatus and therefore allow to retrace speech, even when no audible signal is produced. The mapping of EMG signals to speech is done via a Gaussian mixture model (GMM)-based conversion technique. In this paper, we follow the lead of EMG-based speech-to-text systems and apply two major recent technological advances to our system, namely, we consider session-independent systems, which are robust against electrode repositioning, and we show that mapping the EMG signal to whispered speech creates a better speech signal than a mapping to normally spoken speech. We objectively evaluate the performance of our systems using a spectral distortion measure.
RNA Expression of MMP12 Is Strongly Associated with Inflammatory Bowel Disease and Is Regulated by Metabolic Pathways in RAW 264.7 Macrophages

Macrophage metalloelastase or matrix metalloproteinase-12 (MMP12) is a macrophage-specific proteolytic enzyme involved in the physiopathology of many inflammatory diseases, including inflammatory bowel disease. Although previously published data suggested that the modulation of MMP12 in macrophages could be a determinant for the development of intestinal inflammation, scarce information is available on the mechanisms underlying the regulation of MMP12 expression in those phagocytes. Therefore, in this study, we aimed to delineate the association of MMP12 with inflammatory bowel disease and the molecular events leading to the transcriptional control of this metalloproteinase. For that, we used publicly available transcriptional data. Also, we worked with the RAW 264.7 macrophage cell line for functional experiments. Our results showed a strong association of MMP12 expression with the severity of inflammatory bowel disease and the response to relevant biological therapies. In vitro assays revealed that the inhibition of mechanistic target of rapamycin complex 1 (mTORC1) and the stimulation of the AMP-activated protein kinase (AMPK) signaling pathway potentiated the expression of Mmp12. Additionally, AMPK and mTOR required a functional downstream glycolytic pathway to fully engage with Mmp12 expression. Finally, the pharmacological inhibition of MMP12 abolished the expression of the proinflammatory cytokine Interleukin-6 (Il6) in macrophages. Overall, our findings provide a better understanding of the mechanistic regulation of MMP12 in macrophages and its relationship with inflammation.
Exploratory Analysis of Concordance Between Clinician-Collected and Self-Sampled Human Papillomavirus Tests in a Small Cohort of Average- and High-Risk Patients

Objectives: Cervical cancer screening rates have stagnated, but self-sampling modalities have the potential to increase uptake. This study compares the test characteristics of self-sampled high-risk human papillomavirus (hrHPV) tests with clinician-collected hrHPV tests in average-risk (i.e., undergoing routine screening) and high-risk patients (i.e., receiving follow-up after abnormal screening results). Methods: In this cross-sectional study, a relatively small cohort of average-risk (n = 35) and high-risk (n = 12) participants completed both clinician-collected and self-sampled hrHPV testing, along with a brief phone survey. We assessed hrHPV positivity, concordance, positive predictive value (PPV), negative predictive value (NPV), sensitivity, and specificity across both methods (for types 16, 18, or other hrHPV). We also explored the relationship between test concordance and sociodemographic/behavioral factors. Results: Among average-risk participants, hrHPV positivity was 6% for both test methods (i.e., hrHPV-positive cases: n = 2), resulting in reported concordance, PPV, NPV, sensitivity, and specificity of 100%. Among high-risk participants, hrHPV positivity was 100% for clinician-collected tests but only 67% for self-sampled tests, showing varied concordance and sensitivity. Concordance was not associated with sociodemographic or behavioral factors. Conclusions: Self-sampled hrHPV testing demonstrated high accuracy for average-risk patients in this exploratory study. However, its performance was less consistent in high-risk patients who had already received an abnormal screening result, which could be attributed to spontaneous viral clearance over time. The limited number of participants, particularly HPV-positive cases, suggests caution in interpreting these results. Further research with larger cohorts is necessary to validate these findings and to explore the integration of self-sampled hrHPV testing into routine clinical care, particularly for patients with a history of cervical abnormalities. Clinical Trial Registration: NCT04591977, NCT04585243.