Miracle-dz/UniFAR-FTUs huggingface dataset:
How to tackle chemical communication? Relative proportions versus semiquantitative determination of compounds in lizard chemical secretions

Abstract Knowledge about chemical communication in some vertebrates is still relatively limited. Squamates are a glaring example of this, even when recent evidences indicate that scents are involved in social and sexual interactions. In lizards, where our understanding of chemical communication has considerably progressed in the last few years, many questions about chemical interactions remain unanswered. A potential reason for this is the inherent complexity and technical limitations that some methodologies embody when analyzing the compounds used to convey information. We provide here a straightforward procedure to analyze lizard chemical secretions based on gas chromatography coupled to mass spectrometry that uses an internal standard for the semiquantification of compounds. We compare the results of this method with those obtained by the traditional procedure of calculating relative proportions of compounds. For such purpose, we designed two experiments to investigate if these procedures allowed revealing changes in chemical secretions 1) when lizards received previously a vitamin dietary supplementation or 2) when the chemical secretions were exposed to high temperatures. Our results show that the procedure based on relative proportions is useful to describe the overall chemical profile, or changes in it, at population or species levels. On the other hand, the use of the procedure based on semiquantitative determination can be applied when the target of study is the variation in one or more particular compounds of the sample, as it has proved more accurate detecting quantitative variations in the secretions. This method would reveal new aspects produced by, for example, the effects of different physiological and climatic factors that the traditional method does not show.
A Chair–Based Unobtrusive Cuffless Blood Pressure Monitoring System Based on Pulse Arrival Time

In this paper, we present an unobtrusive cuffless blood pressure (BP) monitoring system based on pulse arrival time (PAT) for facilitating long-term home BP monitoring. The proposed system consists of an electrocardiograph (ECG), a photoplethysmograph (PPG), and a control circuit with a Bluetooth module, all of which are mounted on a common armchair to measure ECG and PPG signals from users while sitting on the armchair in order to calculate continuous PAT. Considering the good linear correlation of systolic BP (SBP) and the nonlinear correlation of diastolic BP (DBP) with PAT, a new BP estimation method was proposed. Ten subjects underwent BP monitoring experiments involving stationary sitting on a chair, lying on a bed, and pedaling using an ergometer in order to assess the accuracy of the estimated BP. A cuff-type BP monitor was used as reference in the experiments. Results showed that the mean difference of the estimated SBP and DBP was within 0.2 ± 5.8 mmHg ($p$ < 0.00001) and 0.4 ± 5.7 mmHg ($p$ < 0.00001), respectively, and the mean absolute difference of the estimated SBP and DBP were 4.4 and 4.6 mmHg, respectively, compared to references. Additionally, five subjects participated in data collections consisting of sitting on a chair twice a day for one month. Compared to the reference, the difference did not obviously increase along with time, even though individualized calibration was executed only once at the beginning. These results suggest that the proposed system has quite the potential for long-term home BP monitoring.
"One‐Pot" Sample Processing Method for Proteome‐Wide Analysis of Microbial Cells and Spores

Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles.
A Novel Polymorphism in the Promoter of the CYP4A11 Gene Is Associated with Susceptibility to Coronary Artery Disease

Enzymes CYP4A11 and CYP4F2 are involved in biosynthesis of vasoactive 20-hydroxyeicosatetraenoic acid and may contribute to pathogenesis of coronary artery disease (CAD). We investigated whether polymorphisms of the CYP4A11 and CYP4F2 genes are associated with the risk of CAD in Russian population. DNA samples from 1323 unrelated subjects (637 angiographically confirmed CAD patients and 686 age- and sex-matched healthy individuals) were genotyped for polymorphisms rs3890011, rs9332978, and rs9333029 of CYP4A11 and rs3093098 and rs1558139 of CYP4F2 by using the Mass-ARRAY 4 system. SNPs rs3890011 and rs9332978 of CYP4A11 were associated with increased risk of CAD in women: OR = 1.26, 95% CI: 1.02–1.57, P = 0.004, and Q = 0.01 and OR = 1.45, 95% CI: 1.13–1.87, P = 0.004, and Q = 0.01, respectively. Haplotype G-C-A of CYP4A11 was associated with increased risk of CAD (adjusted OR = 1.41, 95% CI: 1.12–1.78, and P = 0.0036). Epistatic interactions were found between rs9332978 of CYP4A11 and rs1558139 of CYP4F2 (P interaction = 0.025). In silico analysis allowed identifying that SNP rs9332978 is located at a binding site for multiple transcription factors; many of them are known to regulate the pathways involved in the pathogenesis of CAD. This is the first study in Europeans that reported association between polymorphism rs9332978 of CYP4A11 and susceptibility to coronary artery disease.
Elevated seminal plasma myeloperoxidase is associated with a decreased sperm concentration in young men

Myeloperoxidase is a major neutrophil protein which generates oxidants that are highly reactive, and if present in seminal fluid, could be potentially damaging to spermatozoa. We recruited young males aged 18–35 years, unscreened for fertility status, for a pilot study measuring seminal plasma myeloperoxidase. On three occasions, over a 3‐month period, we measured parameters of semen quality and correlated these with seminal myeloperoxidase protein and activity. After baseline measurement, participants were supplemented daily with 250 mg of vitamin C, a potent scavenger of reactive oxygen species with antiinflammatory activities. Seminal plasma from eight of the 12 participants had measurable concentrations of myeloperoxidase protein, across a broad range (15–250 ng/mL). Median myeloperoxidase protein concentrations were ~45‐fold higher in semen samples with low vs. high sperm concentrations. Seminal plasma myeloperoxidase protein concentration was inversely correlated with the percentage of rapidly motile spermatozoa assessed by computer‐assisted sperm analysis, and the total number of spermatozoa per ejaculate, but positively correlated with sperm maturity, measured by DNA staining ability. We measured an inverse correlation between semen vitamin C concentration and seminal plasma myeloperoxidase protein concentration, although vitamin C supplementation had no effect on semen quality. Our pilot data suggest that high concentrations of myeloperoxidase were present in the seminal plasma of many of our young participants, and that this may be associated with decreases in semen quality. A larger study is required to confirm these findings.
Primary, secondary and compensated hypogonadism: a novel risk stratification for infertile men

Recently, the cohort of men from the European Male Ageing Study has been stratified into different categories distinguishing primary, secondary and compensated hypogonadism. A similar classification has not yet been applied to the infertile population. We performed a cross‐sectional study enrolling 786 consecutive Caucasian‐European infertile men segregated into eugonadal [normal serum total testosterone (≥3.03 ng/mL) and normal luteinizing hormone (≤9.4 mU/mL)], secondary (low total testosterone, low/normal luteinizing hormone), primary (low total testosterone, elevated luteinizing hormone) and compensated hypogonadism (normal total testosterone; elevated luteinizing hormone). In this cross‐sectional study, logistic regression models tested the association between semen parameters, clinical characteristics and the defined gonadal status. Eugonadism, secondary, primary and compensated hypogonadism were found in 80, 15, 2, and 3% of men respectively. Secondary hypogonadal men were at highest risk for obesity [OR (95% CI): 3.48 (1.98–6.01)]. Primary hypogonadal men were those at highest risk for azoospermia [24.54 (6.39–161.39)] and testicular volume <15 mL [12.80 (3.40–83.26)]. Compensated had a similar profile to primary hypogonadal men, while their risk of azoospermia [5.31 (2.25–13.10)] and small testicular volume [8.04 (3.17–24.66)] was lower. The risk of small testicular volume [1.52 (1.01–2.33)] and azoospermia [1.76 (1.09–2.82)] was increased, although in a milder fashion, in secondary hypogonadal men as well. Overall, primary and compensated hypogonadism depicted the worst clinical picture in terms of impaired fertility. Although not specifically designed for infertile men, European Male Ageing Study categories might serve as a clinical stratification tool even in this setting.
Repression of YAP by NCTD disrupts NSCLC progression

The efficacy of available lung cancer therapeutic interference is significantly limited by various resistance mechanisms to those drugs. Activation of the oncogene YAP underlying the initiation, progression, and metastasis of lung cancer associates with poor prognosis and confers drug resistance against targeted therapy. In this study, we evaluated the specificity of norcantharidin (NCTD) in repressing YAP to inhibit non-small cell lung carcinoma (NSCLC) progression. Our study revealed that YAP signal pathways were aberrantly activated in lung cancer tissues and cells which rendered more proliferative and invasive phenotypes to human lung cancer cells. We confirmed that NCTD specifically repressed YAP signaling pathway to interfere the YAP-mediated non-small cell lung carcinoma progression and metastasis via arresting cell cycle, enhancing apoptosis and inducing senescence. We also found NCTD-mediated repression of YAP decreased epithelial-to-mesenchymal transition (EMT) and reduced the motile and invasive cellular phenotype in vitro via enhancing E-cadherin and decreasing fibronectin/vimentin. Mechanistic investigations revealed that NCTD transcriptionally downregulated YAP and post-translationally modulated the subcellular redistribution of YAP between nucleus and cytoplasm. Collectively, our results indicated that NCTD is a novel therapeutic drug candidate for NSCLC which specifically and sensitively target YAP signal pathway.
Medical Image Retrieval via Histogram of Compressed Scattering Coefficients

The features used in many current medical image retrieval systems are usually low-level hand-crafted features. This limitation may adversely affect the retrieval performance. To address this problem, this paper proposes a simple yet discriminative feature, called histogram of compressed scattering coefficients (HCSC), for medical image retrieval. In the proposed work, the scattering transform, a particular variation of deep convolutional networks, is first performed to yield more abstract representations of a medical image. A projection operation is then conducted to compress the obtained scattering coefficients for efficient processing. Finally, a bag-of-words (BoW) histogram is derived from the compressed scattering coefficients as the features of the medical image. The proposed HCSC takes the advantages of both scattering transform and BoW model. Experiments on three benchmark medical computer tomography image databases demonstrate that HCSC outperforms several state-of-the-art features.
Attending Multiple Items Decreases the Selectivity of Population Responses in Human Primary Visual Cortex

Multiple studies have documented an inverse relationship between the number of to-be-attended or remembered items in a display (“set size”) and task performance. The neural source of this decline in cognitive performance is currently under debate. Here, we used a combination of fMRI and a forward encoding model of orientation selectivity to generate population tuning functions for each of two stimuli while human observers attended either one or both items. We observed (1) clear population tuning functions for the attended item(s) that peaked at the stimulus orientation and decreased monotonically as the angular distance from this orientation increased, (2) a set-size-dependent decline in the relative precision of orientation-specific population responses, such that attending two items yielded a decline in selectivity of the population tuning function for each item, and (3) that the magnitude of the loss of precision in population tuning functions predicted individual differences in the behavioral cost of attending an additional item. These findings demonstrate that attending multiple items degrades the precision of perceptual representations for the target items and provides a straightforward account for the associated impairments in visually guided behavior.
Second‐order quasi‐likelihood for spatial point processes

Applications of spatial point processes for large and complex data sets with inhomogeneities as encountered, example, in tropical rain forest ecology call for estimation methods that are both statistically and computationally efficient. We propose a novel second‐order quasi‐likelihood procedure to estimate the parameters for a second‐order intensity reweighted stationary spatial point process. Our approach is to derive first‐ and second‐order estimating functions and then combine them linearly using appropriate weight functions. In the stationary case, we argue that the asymptotically optimal weight functions are respectively a constant and a function of lags between distinct locations in the observation window. This leads to a considerable gain in computational efficiency. We further exploit this simplification in the nonstationary case. Simulations show that, when compared with several existing approaches, our method can achieve significant gains in statistical efficiency. An application to a tropical rain forest data set further illustrates the advantages of our procedure.
Can long-term historical data from electronic medical records improve surveillance for epidemics of acute respiratory infections? A systematic evaluation

Background As the deployment of electronic medical records (EMR) expands, so is the availability of long-term datasets that could serve to enhance public health surveillance. We hypothesized that EMR-based surveillance systems that incorporate seasonality and other long-term trends would discover outbreaks of acute respiratory infections (ARI) sooner than systems that only consider the recent past. Methods We simulated surveillance systems aimed at discovering modeled influenza outbreaks injected into backgrounds of patients with ARI. Backgrounds of daily case counts were either synthesized or obtained by applying one of three previously validated ARI case-detection algorithms to authentic EMR entries. From the time of outbreak injection, detection statistics were applied daily on paired background+injection and background-only time series. The relationship between the detection delay (the time from injection to the first alarm uniquely found in the background+injection data) and the false-alarm rate (FAR) was determined by systematically varying the statistical alarm threshold. We compared this relationship for outbreak detection methods that utilized either 7 days (early aberrancy reporting system (EARS)) or 2–4 years of past data (seasonal autoregressive integrated moving average (SARIMA) time series modeling). Results In otherwise identical surveillance systems, SARIMA detected epidemics sooner than EARS at any FAR below 10%. The algorithms used to detect single ARI cases impacted both the feasibility and marginal benefits of SARIMA modeling. Under plausible real-world conditions, SARIMA could reduce detection delay by 5–16 days. It also was more sensitive at detecting the summer wave of the 2009 influenza pandemic. Conclusion Time series modeling of long-term historical EMR data can reduce the time it takes to discover epidemics of ARI. Realistic surveillance simulations may prove invaluable to optimize system design and tuning.
GIRLS AND COMPUTING IN LOWER SECONDARY EDUCATION: The surprisingly unsurprising results of a Norwegian exploratory study

The low percentage of women pursuing Information Technology (IT) education is a concern in many countries worldwide. This exploratory study is motivated by the experimental introduction of an elective programming course in a selected number of Norwegian Lower Secondary schools, now recently extended to include any interested school. Though there is a growing body of knowledge in the area, we believe this study is important to understand the situation in a moment of great change in the national curriculum. Given the nature of our investigation, we have adopted multiple methods to collect a variety of data and get an overview of the practice. The main reasons not to choose IT education include: the poor reputation of programming, lack of information about the course, lack of knowledge about programming and technology and what it could be used for, the impression that programming is not useful to help society, the negative influence of parents and friends, and the disinterest in programming. To a large extent, these results are not surprising in that they confirm results from similar studies worldwide. However, the results are unexpected considering the social and economic conditions of Norway. This paper mainly wants to act as a warning pointing out that despite the high gender balance in Norwegian society, this does not automatically solve the gender gap in IT education, with important consequences on the longer term for the job market.
Nuclear mRNA degradation tunes the gain of the unfolded protein response in Saccharomyces cerevisiae

Abstract Unfolded protein response (UPR) is triggered by the accumulation of unfolded proteins in the endoplasmic reticulum (ER), which is accomplished by a dramatic induction of genes encoding ER chaperones. Activation of these genes involves their rapid transcription by Hac1p, encoded by the HAC1 precursor transcript harboring an intron and a bipartite element (3′-BE) in the 3′-UTR. ER stress facilitates intracellular targeting and recruitment of HAC1 pre-mRNA to Ire1p foci (requiring 3′-BE), leading to its non-spliceosomal splicing mediated by Ire1p/Rlg1p. A critical concentration of the pre-HAC1 harboring a functional 3′-BE element is governed by its 3′→5′ decay by the nuclear exosome/DRN. In the absence of stress, pre-HAC1 mRNA undergoes a rapid and kinetic 3′→5′ decay leading to a precursor pool, the majority of which lack the BE element. Stress, in contrast, causes a diminished decay, thus resulting in the production of a population with an increased abundance of pre-HAC1 mRNA carrying an intact BE, which facilitates its more efficient recruitment to Ire1p foci. This mechanism plays a crucial role in the timely activation of UPR and its prompt attenuation following the accomplishment of homeostasis. Thus, a kinetic mRNA decay provides a novel paradigm for mRNA targeting and regulation of gene expression.
Coarse to fine non-rigid registration: a chain of scale-specific neural networks for multimodal image alignment with application to remote sensing

We tackle here the problem of multimodal image non-rigid registration, which is of prime importance in remote sensing and medical imaging. The difficulties encountered by classical registration approaches include feature design and slow optimization by gradient descent. By analyzing these methods, we note the significance of the notion of scale. We design easy-to-train, fully-convolutional neural networks able to learn scale-specific features. Once chained appropriately, they perform global registration in linear time, getting rid of gradient descent schemes by predicting directly the deformation. We show their performance in terms of quality and speed through various tasks of remote sensing multimodal image alignment. In particular, we are able to register correctly cadastral maps of buildings as well as road polylines onto RGB images, and outperform current keypoint matching methods.
Assessment of 1-year Outcomes in Survivors of Severe Acute Respiratory Distress Syndrome Receiving Extracorporeal Membrane Oxygenation or Mechanical Ventilation: A Prospective Observational Study

Background: Little is known about the long-term outcomes of severe acute respiratory distress syndrome (ARDS) patients requiring extracorporeal membrane oxygenation (ECMO). This study aimed to investigate the 1-year outcomes of these patients or patients receiving mechanical ventilation (MV) and compare their health-related quality of life (HRQoL) to the general population. Methods: Severe ARDS survivors admitted to two ICUs in China between January 2012 and January 2014 were enrolled. Of the severe ARDS survivors enrolled, 1-year postdischarge, HRQoL assessment using the Short-Form 36 (SF-36) and EuroQol questionnaire dimensions, 6-min walking distance, chest computed tomography scan, pulmonary function, and arterial blood gas analysis were compared for ARDS patients with or without ECMO. Results: ARDS patients receiving ECMO had a significantly higher Acute Physiology and Chronic Health Evaluation II score (30.3 ± 6.7 vs. 26.5 ± 7.3, P = 0.036), lung injury score (3.3 ± 0.4 vs. 2.8 ± 0.5, P = 0.000), Sequential Organ Failure Assessment score (10.8 ± 3.5 vs. 7.9 ± 3.1, P = 0.000), lower PaO2/FiO2 ratio ([mmHg, 1 mmHg = 0.133 kPa], 68.3 ± 16.1 vs. 84.8 ± 16.5, P = 0.000), and increased extrapulmonary organ failure (2 [1, 3] vs. 1 [1, 1], P = 0.025) compared with patients not receiving ECMO. ECMO and non-ECMO survivors showed similar pulmonary function, morphological abnormalities, resting arterial blood gas values, and 6-min walking distance. Mild pulmonary dysfunction and abnormal morphology were observed in a few survivors. In addition, ECMO and non-ECMO survivors showed a similar quality of life. ECMO survivors showed lower SF-36 physical functioning and role-physical domain scores (minimum clinically significant difference at least 5 points), and non-ECMO survivors had similar outcome. Conclusions: One-year posthospital discharge, severe ARDS survivors receiving ECMO or MV demonstrated comparable outcomes. Compared with the general population, ARDS survivors showed reduced HRQoL. Pulmonary function and lung morphology revealed sufficient recovery with minor lung impairment.
Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip

Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.