Miracle-dz/UniFAR-FTUs huggingface dataset:
An automatic speech recognition system using neural networks and linear dynamic models to recover and model articulatory traces

We describe a speech recognition system which uses articulatory parameters as basic features and phone-dependent linear dynamic models. The system ﬁrst estimates articulatory trajectories from the speech signal. Estimations of x and y coordinates of 7 actual articulator positions in the midsagittal plane are produced every 2 milliseconds by a recurrent neural network, trained on real articulatory data. The output of this network is then passed to a set of linear dynamic models, which perform phone recognition.
Colorectal and interval cancers of the Colorectal Cancer Screening Program in the Basque Country (Spain)

AIM To assess proportions, related conditions and survival of interval cancer (IC). METHODS The programme has a linkage with different clinical databases and cancer registers to allow suitable evaluation. This evaluation involves the detection of ICs after a negative faecal inmunochemical test (FIT), interval cancer FIT (IC-FIT) prior to a subsequent invitation, and the detection of ICs after a positive FIT and confirmatory diagnosis without colorectal cancer (CRC) detected and before the following recommended colonoscopy, IC-colonoscopy. We conducted a retrospective observational study analyzing from January 2009 to December 2015 1193602 invited people onto the Programme (participation rate of 68.6%). RESULTS Two thousand five hundred and eighteen cancers were diagnosed through the programme, 18 cases of IC-colonoscopy were found before the recommended follow-up (43542 colonoscopies performed) and 186 IC-FIT were identified before the following invitation of the 769200 negative FITs. There was no statistically significant relation between the predictor variables of ICs with sex, age and deprivation index, but there was relation between location and stage. Additionally, it was observed that there was less risk when the location was distal rather than proximal (OR = 0.28, 95%CI: 0.20-0.40, P < 0.0001), with no statistical significance when the location was in the rectum as opposed to proximal. When comparing the screen-detected cancers (SCs) with ICs, significant differences in survival were found (P < 0.001); being the 5-years survival for SCs 91.6% and IC-FIT 77.8%. CONCLUSION These findings in a Population Based CRC Screening Programme indicate the need of population-based studies that continue analyzing related factors to improve their detection and reducing harm.
miR-21-5p regulates type II alveolar epithelial cell apoptosis in hyperoxic acute lung injury

Hyperoxia-induced acute lung injury (HALI) as one of the most common complications in patents on mechanical ventilation, and there are no efficient methods to overcome this at present. It was hypothesized that microRNA 21-5p(miR-21-5p) can promote the survival of type II alveolar epithelial cells (AECII), alleviating HALI. The present study aimed to combine gene chip analysis with the overexpression miR-21-5p to develop a novel therapeutic option for HALI. It was found that AECII apoptosis was an important pathogenic event in the development of HALI, and the overexpression of miR-21-5p prevented HALI, associated with reducing AECII apoptosis. These results were obtained using adenoviral/lentiviral vectors, which overexpressed miR-21-5p, to transfect AECII cells in vitro and in vivo. It was found that the overexpression of miR-21-5p reduced the apoptotic rate of the AECII cells. In addition, miR-21-5p decreased the ratio of B-cell lymphoma 2 (Bcl-2)-associated X protein/Bcl-2 and the expression of caspase-3. It was also revealed that the overexpression of miR-21-5p alleviated acute lung injury in adult rats exposed to a hyperoxic environment. These results suggest that miR-21-5p may become a novel therapeutic option for patients with HALI, by protecting AECII cells from apoptosis.
Neuroimaging in frontotemporal dementia

Abstract The term frontotemporal dementia (FTD) refers to a group of neurodegenerative disorders that are associated with atrophy of the frontal and temporal lobes, and present clinically with impairments of behaviour or language. Three main subtypes are described, behavioural variant FTD (bvFTD) and two subtypes of the language presentation (known as primary progressive aphasia or PPA) called semantic variant of PPA and non-fluent variant of PPA. Most imaging studies of FTD have used volumetric T1 magnetic resonance imaging (MRI) or positron emissions tomography imaging to identify patterns of grey matter atrophy or hypometabolism in these different subtypes, but more recently newer imaging techniques have been used to help define abnormalities in structural connectivity (white matter tract integrity using diffusion tensor imaging), functional connectivity (resting state networks using resting state functional MRI) and perfusion (using arterial spin labelling perfusion MRI) in FTD. These techniques have the potential to improve the differential diagnosis of FTD from other disorders and to provide more informative imaging signatures of FTD syndromes.
Analyzing Uncertainty in Neural Machine Translation

Machine translation is a popular test bed for research in neural sequence-to-sequence models but despite much recent research, there is still a lack of understanding of these models. Practitioners report performance degradation with large beams, the under-estimation of rare words and a lack of diversity in the final translations. Our study relates some of these issues to the inherent uncertainty of the task, due to the existence of multiple valid translations for a single source sentence, and to the extrinsic uncertainty caused by noisy training data. We propose tools and metrics to assess how uncertainty in the data is captured by the model distribution and how it affects search strategies that generate translations. Our results show that search works remarkably well but that models tend to spread too much probability mass over the hypothesis space. Next, we propose tools to assess model calibration and show how to easily fix some shortcomings of current models. As part of this study, we release multiple human reference translations for two popular benchmarks.
Lower Limb Force, Velocity, Power Capabilities during Leg Press and Squat Movements

Abstract The aim was to compare lower-limb power, force, and velocity capabilities between squat and leg press movements. Ten healthy sportsmen performed ballistic lower-limb push-offs against 5-to-12 different loads during both the squat and leg press. Individual linear force-velocity and polynomial power-velocity relationships were determined for both movements from push-off mean force and velocity measured continuously with a pressure sensor and linear encoder. Maximal power output, theoretical maximal force and velocity, force-velocity profile and optimal velocity were computed. During the squat, maximal power output (17.7±3.59 vs. 10.9±1.39 W·kg−1), theoretical maximal velocity (1.66±0.29 vs. 0.88±0.18 m·s−1), optimal velocity (0.839±0.144 vs. 0.465±0.107 m·s−1), and force-velocity profile (−27.2±8.5 vs. −64.3±29.5 N·s·m−1·kg−1) values were significantly higher than during the leg press (p=0.000, effect size=1.72–3.23), whereas theoretical maximal force values (43.1±8.6 vs. 51.9±14.0 N·kg−1, p=0.034, effect size=0.75) were significantly lower. The mechanical capabilities of the lower-limb extensors were different in the squat compared with the leg press with higher maximal power due to much higher velocity capabilities (e.g. ability to produce force at high velocities) even if moderately lower maximal force qualities.
The Effects of a Bottleneck on Inbreeding Depression and the Genetic Load

We study the effects of a population bottleneck on the inbreeding depression and genetic load caused by deleterious mutations in an outcrossing population. The calculations assume that loci have multiplicative fitness effects and that linkage disequilibrium is negligible. Inbreeding depression decreases immediately after a sudden reduction of population size, but the drop is at most only several percentage points, even for severe bottlenecks. Highly recessive mutations experience a purging process that causes inbreeding depression to decline for a number of additional generations. On the basis of available parameter estimates, the absolute fall in inbreeding depression may often be only a few percentage points for bottlenecks of 10 or more individuals. With a very high lethal mutation rate and a very slow population growth, however, the decline may be on the order of 25%. We examine when purging might favor a switch from outbreeding to selfing and find it occurs only under very limited conditions unless population growth is very slow. In contrast to inbreeding depression, a bottleneck causes an immediate increase in the genetic load. Purging causes the load to decline and then overshoot its equilibrium value. The changes are typically modest: the absolute increase in the total genetic load will be at most a few percentage points for bottlenecks of size 10 or more unless the lethal mutation rate is very high and the population growth rate very slow.
Experimental pain phenotype profiles in a racially and ethnically diverse sample of healthy adults.

OBJECTIVE To examine patterns of interindividual variability in experimental pain responses emerging from multiple experimental pain measures in a racially/ethnically diverse sample of healthy adults and to examine the association between the derived phenotype profiles with demographic, psychological, and health-related measures. METHODS Two hundred and ninety-one participants underwent heat, cold, pressure, and ischemic pain assessments, and completed several psychological and health-related assessments. The experimental pain measures were subjected to a principal component analysis and factor scores were used to compute Pain Sensitivity Index scores. The scores were subsequently submitted to a cluster analysis to identify patterns of pain sensitivity across experimental pain modalities. RESULTS The sample was equally composed of non-Hispanic whites, African Americans, and Hispanic whites. Sensitivity scores were computed for heat pain, pressure pain, cold pain, ischemic pain, and temporal summation of heat pain. Five distinct clusters were characterized by high heat pain sensitivity, low ischemic pain sensitivity, low cold pain sensitivity, low pressure pain sensitivity, and high temporal summation. Cluster membership was significantly different by sex as well as somatic reactivity and catastrophizing, although cluster differences were most pronounced between the heat pain-sensitive individuals vs the cold pain-insensitive individuals. CONCLUSIONS Our findings highlight the importance of phenotyping individuals to account for interindividual differences in pain responses. Our findings also replicate previously reported pain phenotypes, which are not solely related to demographic, psychosocial, or health-related factors in our healthy participants. Future studies designed to elucidate the biological underpinnings of pain sensitivity profiles would be of substantial value.
The Need for Standardized Assessment of Muscle Quality in Skeletal Muscle Function Deficit and Other Aging-Related Muscle Dysfunctions: A Symposium Report

A growing body of scientific literature suggests that not only changes in skeletal muscle mass, but also other factors underpinning muscle quality, play a role in the decline in skeletal muscle function and impaired mobility associated with aging. A symposium on muscle quality and the need for standardized assessment was held on April 28, 2016 at the International Conference on Frailty and Sarcopenia Research in Philadelphia, Pennsylvania. The purpose of this symposium was to provide a venue for basic science and clinical researchers and expert clinicians to discuss muscle quality in the context of skeletal muscle function deficit and other aging-related muscle dysfunctions. The present article provides an expanded introduction concerning the emerging definitions of muscle quality and a potential framework for scientific inquiry within the field. Changes in muscle tissue composition, based on excessive levels of inter- and intra-muscular adipose tissue and intramyocellular lipids, have been found to adversely impact metabolism and peak force generation. However, methods to easily and rapidly assess muscle tissue composition in multiple clinical settings and with minimal patient burden are needed. Diagnostic ultrasound and other assessment methods continue to be developed for characterizing muscle pathology, and enhanced sonography using sensors to provide user feedback and improve reliability is currently the subject of ongoing investigation and development. In addition, measures of relative muscle force such as specific force or grip strength adjusted for body size have been proposed as methods to assess changes in muscle quality. Furthermore, performance-based assessments of muscle power via timed tests of function and body size estimates, are associated with lower extremity muscle strength may be responsive to age-related changes in muscle quality. Future aims include reaching consensus on the definition and standardized assessments of muscle quality, and providing recommendations to address critical clinical and technology research gaps within the field.
Intramyocellular Ceramides: Subcellular Concentrations and Fractional De Novo Synthesis in Postabsorptive Humans

We investigated the relationship between insulin resistance markers and subsarcolemmal (SS) and intramyofibrillar (IMF) ceramide concentrations, as well as the contribution of plasma palmitate (6.5-h infusion of [U-13C]palmitate) to intramyocellular ceramides. Seventy-six postabsorptive men and women had muscle biopsies 1.5, 6.5, and 24 h after starting the tracer infusion. Concentrations and enrichment of muscle ceramides were measured by liquid chromatography-tandem mass spectrometry. We found that HOMA of insulin resistance, plasma insulin, and triglyceride concentrations were positively correlated with SS C16:0 and C18:1 ceramide, but not SS C14:0-Cer, C20:0-Cer, C24:0-Cer, and C24:1-Cer concentrations; IMF ceramide concentrations were not correlated with any metabolic parameters. The fractional contribution of plasma palmitate to 16:0 ceramide was greater in SS than IMF (SS, 18.2% vs. IMF, 8.7%; P = 0.0006). Plasma insulin concentrations correlated positively with the fractional contribution of plasma palmitate to SS 16:0 ceramide. The fractional contribution of plasma palmitate to intramyocellular SS 16:0 ceramide was positively correlated with SS C16:0 ceramide concentrations (γ = 0.435; P = 0.002). We conclude that skeletal muscle SS ceramides, especially C16 to C18 chain lengths and the de novo synthesis of intramyocellular ceramide from plasma palmitate are associated with markers of insulin resistance.
Effects of Enrichment on Three‐Level Food Chains with Omnivory

Although omnivory (the consumption of resources from more than one trophic level) is widespread, this fundamental limitation to the applicability of food chain theory to real communities has received only limited treatment. We investigated effects of enrichment (increasing carrying capacity, K, of the resource) on a system consisting of a resource (R), an intermediate consumer (N), and an omnivore (P) using a general mathematical model and tested the relevance of some of its predictions to a laboratory system of mixed bacteria (=R) and the ciliates Tetrahymena (=N) and Blepharisma (=P). The model produced six major predictions. First, N may facilitate or inhibit P. Enrichment may revert the net effect of N on P from facilitation to inhibition. Second, along a gradient of K, up to four regions of invasibility and stable coexistence of N and P may exist. At the lowest K, only R is present. At somewhat higher K, N can coexist with R. At intermediate K, either N and P coexist, or either consumer excludes the other depending on initial conditions. At the highest K, N may be excluded through apparent competition and only R and P can coexist. The pattern of persistence of Tetrahymena and Blepharisma along an enrichment gradient conformed fairly well to the scenario allowing coexistence at intermediate K. Third, for stable equilibria of the omnivory system, R always increases and N always decreases with K. The abundances of bacteria and Tetrahymena were suggestive of such a pattern but did not allow a strict test because coexistence occurred at only one level of enrichment. Fourth, an omnivore can invade an R‐N system at a lower K than an otherwise identical specialist predator of N. Fifth, an omnivore can always invade a food chain with such a specialist predator. Sixth, over ranges of K where both omnivory systems and otherwise identical three‐level food chains are feasible, N is always less abundant in the omnivory system, whereas the relative abundances of R and P in omnivory systems compared to food chains may change with K. It is thus possible that total community biomass at a given K is lower in an omnivory system than in a food chain. Both the model and the experimental results caution that patterns of trophic‐level abundances in response to enrichment predicted by food chain theory are not to be expected in systems with significant omnivory.
Thermal acclimation of photosynthesis and respiration of southern and northern white spruce seed sources tested along a regional climatic gradient indicates limited potential to cope with temperature warming

Abstract Background and Aims Knowledge of thermal acclimation of physiological processes of boreal tree species is necessary to determine their ability to adapt to predicted global warming and reduce the uncertainty around the anticipated feedbacks of forest ecosystems and global carbon cycle to climate change. The objective of this work was to examine the extent of thermal acclimation of net photosynthesis (An) and dark respiration (Rd) of two distant white spruce (Picea glauca) seed sources (from south and north of the commerial forest zone in Québec) in response to latitudinal and seasonal variations in growing conditions. Methods The temperature responses of An, its biochemical and biophysical limitations, and Rd were measured in 1-year-old needles of seedlings from the seed sources growing in eight forest plantations along a regional thermal gradient of 5.5 °C in Québec, Canada. Key Results The average optimum temperature (Topt) for An was 19 ± 1.2 °C and was similar among seed sources and plantation sites along the thermal gradient. Net photosynthesis at Topt (Aopt) varied significantly among plantation sites and was quadratically related to the mean July temperature (MJT) of plantation sites. Topt for mesophyll conductance, maximum electron transport rate and maximum rate of carboxylation were 28, 22 and 30 °C, respectively. Basal respiration rate (Rd at 10 °C) was linearly and negatively associated with MJT. Q10 of Rd (the rate of change in Rd with a 10 °C increase in temperature) did not show any significant relationship with MJT and averaged 1.5 ± 0.1. The two seed sources were similar in their thermal responses to latitudinal and seasonal variations in growing conditions. Conclusions The results showed moderate thermal acclimation of respiration and no evidence for thermal acclimation of photosynthesis or local genetic adaptation for traits related to thermal acclimation. Therefore, growth of local white spruces may decline in future climates.
A natural history study of X-linked myotubular myopathy

Objective: To define the natural history of X-linked myotubular myopathy (MTM). Methods: We performed a cross-sectional study that included an online survey (n = 35) and a prospective, 1-year longitudinal investigation using a phone survey (n = 33). Results: We ascertained data from 50 male patients with MTM and performed longitudinal assessments on 33 affected individuals. Consistent with existing knowledge, we found that MTM is a disorder associated with extensive morbidities, including wheelchair (86.7% nonambulant) and ventilator (75% requiring >16 hours of support) dependence. However, unlike previous reports and despite the high burden of disease, mortality was lower than anticipated (approximate rate 10%/y). Seventy-six percent of patients with MTM enrolled (mean age 10 years 11 months) were alive at the end of the study. Nearly all deaths in the study were associated with respiratory failure. In addition, the disease course was more stable than expected, with few adverse events reported during the prospective survey. Few non–muscle-related morbidities were identified, although an unexpectedly high incidence of learning disability (43%) was noted. Conversely, MTM was associated with substantial burdens on patient and caregiver daily living, reflected by missed days of school and lost workdays. Conclusions: MTM is one of the most severe neuromuscular disorders, with affected individuals requiring extensive mechanical interventions for survival. However, among study participants, the disease course was more stable than predicted, with more individuals surviving infancy and early childhood. These data reflect the disease burden of MTM but offer hope in terms of future therapeutic intervention.
Background and episodic breathlessness in advanced cancer patients followed at home

Abstract Background: The aim of this study was to assess the phenomenon of episodic breathlessness in advanced cancer patients followed by palliative care services at home. Methods: A consecutive sample of patients with advanced cancer, admitted to home care for a period of six months, was surveyed. The presence of background breathlessness and episodic breathlessness, their intensity, and drugs used for their treatment were collected. Factors inducing episodic breathlessness, and its influence on daily activities were investigated. Results: Three hundred forty-seven advanced cancer patients admitted to home palliative care were surveyed. The prevalence of breathlessness was 35.3%. The mean intensity of breathlessness was 3.8 (SD 1.96), out of a maximum score of 10 for worst imaginable. Sixty patients (49.2%) were receiving drugs for background breathlessness. In the multivariate analysis the risk of breathlessness increased with cardiovascular disease, chronic obstructive pulmonary disease, and lung cancer while it decreased in patients with a better performance status. The prevalence of episodic breathlessness in patients with background breathlessness was 79.5% and its mean intensity was 7.1 (SD 1.5, range 2–10). The mean duration of episodic breathlessness was 28.6 minutes (SD 47.1, range 1–300 minutes). Forty-three patients (44.3%) were receiving one or more drugs as needed. The majority of episodic breathlessness events were triggered by activity. Episodic breathlessness was interfering with daily activities in 65 patients (67%). Episodic breathlessness wasn’t associated with any variable taken into consideration. Conclusion: This study showed that episodic breathlessness frequently occurs in advanced cancer patients admitted to home care, is severe in intensity, is triggered in most cases by activity, and is characterized by a short duration which requires rapid measures.