Miracle-dz/UniFAR-FTUs huggingface dataset:
Urinary Metabolomic Profile of Preterm Infants Receiving Human Milk with Either Bovine or Donkey Milk-Based Fortifiers

Fortification of human milk (HM) for preterm and very low-birth weight (VLBW) infants is a standard practice in most neonatal intensive care units. The optimal fortification strategy and the most suitable protein source for achieving better tolerance and growth rates for fortified infants are still being investigated. In a previous clinical trial, preterm and VLBW infants receiving supplementation of HM with experimental donkey milk-based fortifiers (D-HMF) showed decreased signs of feeding intolerance, including feeding interruptions, bilious gastric residuals and vomiting, with respect to infants receiving bovine milk-based fortifiers (B-HMF). In the present ancillary study, the urinary metabolome of infants fed B-HMF (n = 27) and D-HMF (n = 27) for 21 days was analyzed by 1H NMR spectroscopy at the beginning (T0) and at the end (T1) of the observation period. Results showed that most temporal changes in the metabolic responses were common in the two groups, providing indications of postnatal adaptation. The significantly higher excretion of galactose in D-HMF and of carnitine, choline, lysine and leucine in B-HMF at T1 were likely due to different formulations. In conclusion, isocaloric and isoproteic HM fortification may result in different metabolic patterns, as a consequence of the different quality of the nutrients provided by the fortifiers.
Evaluating the Implementation and Effectiveness of the SWITCH–MS: An Ecological, Multi-Component Adolescent Obesity Prevention Intervention

Background: The purpose of this study was to evaluate the implementation and effectiveness of an ecological, multi-component adolescent obesity prevention intervention called School Wellness Integration Targeting Child Health–Middle School (SWITCH–MS). Methods: Following the effectiveness-implementation hybrid type 3 quasi-experimental design, seven middle schools (377 students) in Iowa, United States, were stratified into “experienced” (n = 3; 110 students) or “inexperienced” (n = 4; 267 students) groups to receive the 12-week SWITCH–MS intervention. To evaluate implementation, school informants (n = 10) responded to a survey and students completed behavioral tracking in the classroom on a website. For effectiveness evaluation, students in 6th, 7th, and 8th grades completed a validated questionnaire before and after intervention, to measure behaviors of physical activity (PA; “Do”), screen-based activity (“View”), and fruits and vegetable consumption (“Chew”). Results: The two groups of schools showed similar levels of implementation for best practices, awareness, and engagement. Behavioral tracking rate favored the experienced schools early on (47.5% vs. 11.7%), but differences leveled off in weeks 3–12 (sustained at 30.1–44.3%). Linear mixed models demonstrated significant time effects for “Do” (at school and out of school; p < 0.01) and “View” behaviors (p = 0.02), after controlling for student- and school-level covariates. Conclusions: This study demonstrates that prior experience with SWITCH–MS may not be a prominent factor for implementation and effectiveness, although greater experience is associated with favorable behavioral tracking when the intervention is first launched.
ADAR-deficiency perturbs the global splicing landscape in mouse tissues

Adenosine-to-inosine RNA editing and pre-mRNA splicing largely occur cotranscriptionally and influence each other. Here, we use mice deficient in either one of the two editing enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of RNA editing on splicing across different tissues. We find that ADAR has a 100× higher impact on splicing than ADARB1, although both enzymes target a similar number of substrates with a large common overlap. Consistently, differentially spliced regions frequently harbor ADAR editing sites. Moreover, catalytically dead ADAR also impacts splicing, demonstrating that RNA binding of ADAR affects splicing. In contrast, ADARB1 editing sites are found enriched 5′ of differentially spliced regions. Several of these ADARB1-mediated editing events change splice consensus sequences, therefore strongly influencing splicing of some mRNAs. A significant overlap between differentially edited and differentially spliced sites suggests evolutionary selection toward splicing being regulated by editing in a tissue-specific manner.
A Thermosensitive, Phase-Variable Epigenetic Switch: pap Revisited

It has been more than a decade since the last comprehensive review of the phase-variable uropathogen-associated pyelonephritis-associated pilus (pap) genetic switch. Since then, important data have come to light, including additional factors that regulate pap expression, better characterization of H-NS regulation, the structure of the Lrp octamer in complex with pap regulatory DNA, the temperature-insensitive phenotype of a mutant lacking the acetyltransferase RimJ, evidence that key components of the regulatory machinery are acetylated, and new insights into the role of DNA binding by key regulators in shaping both the physical structure and regulatory state of the papI and papBA promoters. SUMMARY It has been more than a decade since the last comprehensive review of the phase-variable uropathogen-associated pyelonephritis-associated pilus (pap) genetic switch. Since then, important data have come to light, including additional factors that regulate pap expression, better characterization of H-NS regulation, the structure of the Lrp octamer in complex with pap regulatory DNA, the temperature-insensitive phenotype of a mutant lacking the acetyltransferase RimJ, evidence that key components of the regulatory machinery are acetylated, and new insights into the role of DNA binding by key regulators in shaping both the physical structure and regulatory state of the papI and papBA promoters. This review revisits pap, integrating these newer observations with older ones to produce a new model for the concerted behavior of this virulence-regulatory region.
Wasserstein generative adversarial networks for motion artifact removal in dental CT imaging

In dental computed tomography (CT) scanning, high-quality images are crucial for oral disease diagnosis and treatment. However, many artifacts, such as metal artifacts, downsampling artifacts and motion artifacts, can degrade the image quality in practice. The main purpose of this article is to reduce motion artifacts. Motion artifacts are caused by the movement of patients during data acquisition during the dental CT scanning process. To remove motion artifacts, the goal of this study was to develop a dental CT motion artifact-correction algorithm based on a deep learning approach. We used dental CT data with motion artifacts reconstructed by conventional filtered back-projection (FBP) as inputs to a deep neural network and used the corresponding high-quality CT data as labeled data during training. We proposed training a generative adversarial network (GAN) with Wasserstein distance and mean squared error (MSE) loss to remove motion artifacts and to obtain high-quality CT dental images. In our network, to improve the generator structure, the generator used a cascaded CNN-Net style network with residual blocks. To the best of our knowledge, this work describes the first deep learning architecture method used with a commercial cone-beam dental CT scanner. We compared the performance of a general GAN and the m-WGAN. The experimental results confirmed that the proposed algorithm effectively removes motion artifacts from dental CT scans. The proposed m-WGAN method resulted in a higher peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) and a lower root-mean-squared error (RMSE) than the general GAN method.
Effect of a Lactobacillus Spp-Based Probiotic Culture Product on Broiler Chicks Performance under Commercial Conditions

Concern about antimicrobial resistance has led to increased attention to alternatives for controlling infections and increasing performance in animal production. Probiotics and organic acids have gained attention as options in poultry industry. Our laboratory has been working in the selection of lactic acid bacteria, mainly from the genus Lactobacillus, as potential probiotic candidates. Previous data indicates that these selected probiotic bacteria are able to reduce Salmonella infection and improve performance in broiler and turkey under experimental and commercial trials in the USA. The selected probiotic organisms were used in field trials to evaluate their efficacy in commercial conditions in Mexico. In the present report, the probiotic culture significantly reduced mortality (p<0.01) compared to the control houses. Also, a consistent improvement of body weight (2.06%) and reduction of FCR (3.5%) was observed in the treated flocks. The results of this report suggest that this Lactobacillus-based probiotic culture could be useful to reduc e mortality in commercial poultry farms.
Lysine-specific histone demethylase 1B (LSD2/KDM1B) represses p53 expression to promote proliferation and inhibit apoptosis in colorectal cancer through LSD2-mediated H3K4me2 demethylation

Epigenetic alterations have been reported to play critical roles in the development of colorectal cancer (CRC). However, the biological function of the lysine-specific histone demethylase 1B (LSD2/KDM1B) in CRC is not well understood. Therefore, we investigated the characteristics of LSD2 in CRC. We observed significant upregulation of LSD2 in CRC tissue compared to that in normal colorectal tissue. LSD2 promotes CRC cell proliferation and inhibits cell apoptosis through cell cycle regulation, promoting CRC progression both in vitro and in vivo. We found that LSD2 performs these functions by inhibiting the p53-p21-Rb pathway. Finally, we found that LSD2 directly binds to p53 and represses p53 expression via H3K4me2 demethylation at the p53 promoter. Our results revealed that LSD2 acts as an oncogene by binding and inhibiting p53 activity in CRC. Thus, LSD2 may be a new molecular target for CRC treatment.
Effects of temperature and volume of water on the growth and development of tadpoles of Pleurodema diplolister and Rhinella granulosa (Amphibia: Anura)

The capacity of tadpoles to reduce their metamorphosis time and body size in response to fluctuations in environmental variables of temporary ponds has been recorded in field and laboratory studies. The main alterations in this habitat are related to the decrease of the water level and increase in temperature. However, few studies tried to dissociate the effect of these two variables. The aim of the present study was to analyze simultaneously the effects of water volume reduction and temperature on the development and growth in tadpoles of Pleurodema diplolister (Peters, 1870) and Rhinella granulosa (Spix, 1824) - species that use temporary ponds for reproduction. The tadpoles of these two species were subject to four treatments: (1) constant volume of water of 2000 ml and constant temperature of 26oC; (2) gradually decreasing water volume from 2000 ml to 200 ml or 150 ml and constant temperature of 26 oC; (3) Constant water volume as in (1) and constant temperature of 30 oC or 33 oC and (4) Decreasing water volume (as above) and constant temperature as in the treatment (3). There was no interaction between both tested variables on the growth and development of tadpoles of both species. Tadpoles of P. diplolister and R. granulosa responded to high temperature by decreasing development time. Tadpoles responded to decreasing volume of water by metamorphosing into smaller size. Tadpoles of P. diplolister maintained at 30oC showed growth reduction. Tadpoles of R. granulosa increased their body size when subject to the treatment at 30oC.
ANALYSIS OF THE SPATIAL DISTRIBUTION OF FOLIAGE BY TWO‐DIMENSIONAL POINT QUADRATS

Summary ‘Relative frequency’, yielded by point quadrat analysis of vegetation, is a measure of the area of the foliage in vertical projection. Because this projected area varies according to the foliage angle (i.e. the angle between foliage and horizontal), values of relative frequency fluctuate as attitudes change with environmental variation; also, misleading estimates are obtained when comparisons are made between species of different habit. By using horizontal as well as vertical point quadrats it is possible to estimate the foliage angle and the foliage denseness (i.e. total area of foliage per unit volume of space). If the frequencies of contacts with foliage per unit length of point quadrat are F90 and F0 for vertical and horizontal quadrats respectively, foliage angle (α) is given by tan α/2(F0/F90) and foliage denseness (F) by F=F90 sec α. The vegetation is analysed within horizontal layers. An apparatus is described which can give the required data, and which avoids the errors inherent in point quadrat methods that use needles of appreciable thickness. The total area of foliage per unit area of ground can be obtained by summation of F for all layers. Trials show that the method is practicable in the field, and that it gives values of α and F which reflect the character of the vegetation. Values of F obtained by this method agreed with direct estimates for the same vegetation within 2.5%. Some assumptions made by the method are discussed; provided that certain precautions are taken, the errors resulting from these are small or none.
Anti-Thyroid Peroxidase and Anti-Thyroglobulin Autoantibodies in the Cerebrospinal Fluid of Patients with Unipolar Depression

Introduction: The risk of developing depression is increased in patients with autoimmune thyroiditis. Autoimmune Hashimoto thyroiditis is diagnosed using the serum markers anti-thyroid peroxidase (TPO) and anti-thyroglobulin (TG) antibodies. In rare cases, patients with autoimmune thyroiditis can also suffer from the heterogeneous and ill-defined syndrome of Hashimoto encephalopathy. Biomarkers for Hashimoto encephalopathy or for any brain involvement of autoimmune thyroiditis are currently lacking. The aim of the present descriptive study was therefore to determine whether a subgroup of seropositive patients shows intrathecal anti-thyroid antibody synthesis in the cerebrospinal fluid (CSF). Participants and methods: Paired serum and CSF samples from 100 patients with unipolar depression were examined for anti-TPO and anti-TG antibodies using enzyme-linked immunosorbent assays. Antibody-specific indices (ASIs) were calculated for seropositive samples. These ASIs allow the differentiation between the brain-derived fraction of antibodies and antibodies which are passively diffused from the serum. ASIs >1.4 were assessed as positive for brain-derived antibodies. Additionally, for explorative evaluations, a stricter ASI limit of >2 was applied. Results: Anti-TPO antibodies were increased in the serum of 16 patients (16%); increased anti-TPO ASIs (>1.4) were detected in 11 of these patients (69%). Anti-TG antibodies in the serum were detected in three patients (3%), with two of them (67%) showing increased ASIs (>1.4). Overall, the authors found increased anti-thyroid antibodies in 17 of 100 patients (17%), with 13 out of 17 patients showing increased ASIs (76%; range 1.4–4.1). Choosing ASI levels of >2 led to positive findings in six out of 16 patients (38%) with anti-TPO antibodies in their serum but no increase in ASIs in three patients (0%) who were seropositive for anti-TG antibodies. The patients with elevated ASIs (N = 13) were younger than the ASI-negative patients (N = 87; p = 0.009); no differences were noted in the frequency of CSF, electroencephalography, and/or magnetic resonance imaging alterations. Discussion: A subgroup of seropositive patients showed intrathecal synthesis of anti-TPO and, more rarely, of anti-TG antibodies, which might be an indication of central autoimmunity in a subgroup of patients with unipolar depression. The confirmation of elevated ASIs as a biomarker for Hashimoto encephalopathy must await further studies. The relevance of the findings is limited by the study’s retrospective and uncontrolled design.
De Novo Transcriptome Assembly and Gene Expression Profiling of the Copepod Calanus helgolandicus Feeding on the PUA-Producing Diatom Skeletonema marinoi

Diatoms are the dominant component of the marine phytoplankton. Several diatoms produce secondary metabolites, namely oxylipins, with teratogenic effects on their main predators, crustacean copepods. Our study reports the de novo assembled transcriptome of the calanoid copepod Calanus helgolandicus feeding on the oxylipin-producing diatom Skeletonema marinoi. Differential expression analysis was also performed between copepod females exposed to the diatom and the control flagellate Prorocentrum minimum, which does not produce oxylipins. Our results showed that transcripts involved in carbohydrate, amino acid, folate and methionine metabolism, embryogenesis, and response to stimulus were differentially expressed in the two conditions. Expression of 27 selected genes belonging to these functional categories was also analyzed by RT-qPCR in C. helgolandicus females exposed to a mixed solution of the oxylipins heptadienal and octadienal at the concentration of 10 µM, 15 µM, and 20 µM. The results confirmed differential expression analysis, with up-regulation of genes involved in stress response and down-regulation of genes associated with folate and methionine metabolism, embryogenesis, and signaling. Overall, we offer new insights on the mechanism of action of oxylipins on maternally-induced embryo abnormality. Our results may also help identify biomarker genes associated with diatom-related reproductive failure in the natural copepod population at sea.
Linking text readability and learner proficiency using linguistic complexity feature vector distance

Abstract How can we identify authentic reading material that matches the learner's proficiency and fosters their language development? Traditionally, this involves assigning a one-dimensional label to the text that identifies the grade or proficiency level of the learners that the text is intended for. Such an approach is inadequate given that both the text complexity and proficiency constructs are multi-dimensional in nature. We propose to instead link readers and texts through multidimensional vectors characterizing the linguistic complexity of the reading material and that of texts written by the learners as proxy of their proficiency level. We first validate the approach using a leveled reading corpus by showing that vector distances computed on the complexity representations can serve the function of the traditional labels. We then highlight the advantage of the multi-dimensional approach using data from a continuation writing task, showing that it makes it possible to study individual complexity dimensions and to explore different degrees of challenge for different dimensions. Our approach essentially makes it possible to empirically investigate the +1 of Krashen's i+1, the challenge that best fosters development given the learner's interlanguage. On the practical side, we discuss an ICALL system demonstrating the viabilityof the approach in real-life.
Nut and Peanut Butter Consumption and the Risk of Total Cancer: A Prospective Cohort Study

Background: Nut intake has been associated with reduced cancer-related mortality, but there is very limited evidence on total cancer risk. We investigated the associations of nut and peanut butter intake with the risk of total cancer and smoking- and alcohol-related cancer subgroups. Methods: In the prospective Netherlands Cohort Study, 120,852 men and women aged 55 to 69 years provided information on lifestyle and dietary habits at baseline in 1986. After 20.3 years of follow-up, 19,255 total cancer cases and 3,499 subcohort members were included in multivariable-adjusted Cox regression analyses, using a case–cohort approach. Results: No significant associations were found between total nut, tree nut, peanut, and peanut butter intake and total cancer risk in men and women. There were also no significant associations with smoking-(un)related and alcohol-(un)related cancers in both sexes. Conclusions: Our findings suggest that nut and peanut butter intake are not associated with a reduced risk of total cancer in men or women. Impact: Nut and peanut butter consumption are not related to the risk of total cancer.
Crosses between frog populations reveal genetic divergence in larval life history at short geographical distance

A number of studies have documented interpopulation divergence in amphibian larval life-history traits across latitudes. Because many frogs are philopatric and have a patchy habitat distribution, genetic divergence could also exist on a much smaller geographical scale, revealed by recent estimates of population divergence using molecular markers. Whether this divergence is reflected in phenotypic traits is virtually unknown. Using artificial fertilization, individuals of the common frog, Rana temporaria, were crossed from two populations situated 130 km apart and differing in population size. The pattern of size at metamorphosis showed evidence of non-additive effects, as demonstrated by a significant interaction between male and female population of origin. Outbreeding resulted in an increase in metamorph size when eggs from the small population were fertilized with sperm from the large population. In the reciprocal cross, however, the pattern was in the opposite direction, with no significant effect of male population of origin. Genetic divergence of populations separated by a relatively short geographical distance may be more common in frogs than previously acknowledged, with potential implications for conservation of declining amphibian species. (Less)
Identifying and Predicting Intentional Self-Harm in Electronic Health Record Clinical Notes: Deep Learning Approach

Background Suicide is an important public health concern in the United States and around the world. There has been significant work examining machine learning approaches to identify and predict intentional self-harm and suicide using existing data sets. With recent advances in computing, deep learning applications in health care are gaining momentum. Objective This study aimed to leverage the information in clinical notes using deep neural networks (DNNs) to (1) improve the identification of patients treated for intentional self-harm and (2) predict future self-harm events. Methods We extracted clinical text notes from electronic health records (EHRs) of 835 patients with International Classification of Diseases (ICD) codes for intentional self-harm and 1670 matched controls who never had any intentional self-harm ICD codes. The data were divided into training and holdout test sets. We tested a number of algorithms on clinical notes associated with the intentional self-harm codes using the training set, including several traditional bag-of-words–based models and 2 DNN models: a convolutional neural network (CNN) and a long short-term memory model. We also evaluated the predictive performance of the DNNs on a subset of patients who had clinical notes 1 to 6 months before the first intentional self-harm event. Finally, we evaluated the impact of a pretrained model using Word2vec (W2V) on performance. Results The area under the receiver operating characteristic curve (AUC) for the CNN on the phenotyping task, that is, the detection of intentional self-harm in clinical notes concurrent with the events was 0.999, with an F1 score of 0.985. In the predictive task, the CNN achieved the highest performance with an AUC of 0.882 and an F1 score of 0.769. Although pretraining with W2V shortened the DNN training time, it did not improve performance. Conclusions The strong performance on the first task, namely, phenotyping based on clinical notes, suggests that such models could be used effectively for surveillance of intentional self-harm in clinical text in an EHR. The modest performance on the predictive task notwithstanding, the results using DNN models on clinical text alone are competitive with other reports in the literature using risk factors from structured EHR data.