Miracle-dz/UniFAR-FTUs huggingface dataset:
Low levels of tissue inhibitor of metalloproteinase-2 at birth may be associated with subsequent development of bronchopulmonary dysplasia in preterm infants

Purpose Bronchopulmonary dysplasia (BPD) is characterized by inflammation with proteolytic damage to the lung extracellular matrix. The results from previous studies are inconsistent regarding the role of proteinases and antiproteinases in the development of BPD. The aim of the present study was to investigate whether matrix metalloproteinase (MMP)-8, MMP-9, tissue inhibitor of metalloproteinase (TIMP)-2, and TIMP-1 levels in the serum of preterm infants at birth are related to the development of BPD. Methods Serum was collected from 62 preterm infants at birth and analyzed for MMP-8, MMP-9, TIMP-2, and TIMP-1 by using enzyme-linked immunosorbent assay. MMPs and TIMPs were compared in BPD (n=24) and no BPD groups (n=38). Clinical predictors of BPD (sex, birth weight, gestational age, etc.) were assessed for both groups. The association between predictors and outcome, BPD, was assessed by using multivariate logistic regression. Results Sex, birth weight, and mean gestational age were similar between the groups. BPD preterm infants had significantly lower TIMP-2 levels at birth compared with no BPD preterm infants (138.1±23.0 ng/mL vs. 171.8±44.1 ng/mL, P=0.027). No significant difference was observed in MMP-8, MMP-9, and TIMP-1 levels between the two groups. Multivariate logistic regression analysis indicated that the TIMP-2 levels were predictive of BPD after adjusting for sex, birth weight, gestational age, proteinuric preeclampsia, and intraventricular hemorrhage (β=-0.063, P=0.041). Conclusion Low TIMP-2 serum levels at birth may be associated with the subsequent development of BPD in preterm infants.
Adaptive Viterbi decoding of convolutional codes over memoryless channels

In this paper, an adaptive decoding algorithm for convolutional codes, which is a modification of the Viterbi algorithm (VA) is presented. For a given code, the proposed algorithm yields nearly the same error performance as the VA while requiring a substantially smaller average number of computations. Unlike most of the other suboptimum algorithms, this algorithm is self-synchronizing. If the transmitted path is discarded, the adaptive Viterbi algorithm (AVA) can recover the state corresponding to the transmitted path after a few trellis depths. Using computer simulations over hard and soft 3-bit quantized additive white Gaussian noise channels, it is shown that codes with a constraint length K up to 11 can be used to improve the bit-error performance over the VA with K=7 while maintaining a similar average number of computations. Although a small variability of the computational effort is present with our algorithm, this variability is exponentially distributed, leading to a modest size of the input buffer and, hence, a small probability of overflow.
Hierarchical Abstraction in Reinforcement Learning Based on Feature Discovery

— Hierarchical reinforcement learning (HRL) is one of the approaches taken in dealing with the curse of dimensionality in learning problems with large state and action spaces. Although previous work on HLR has shown positive results, there exists a reliance on the predefined structure of the core Markov decision processes (MDPs). This paper presents a new approach to automatically construct HRL based on the discovery of relevant environmental features. We investigate the formulation of HRL based on the theory of Semi-Markov decision processes (SMDPs). We develop new concurrent algorithms that estimate the contribution of the combination of state features whose relevance can be quantified with respect to a set of related learning tasks. Through the mining of online learning experience, the learning task is decomposed into sub-tasks which can be solved as SMDPs. We explain and demonstrate our methods using the taxi domain. We compare the proposed algorithms under three different conditions, including flat reinforcement learning, relevant feature learning and hierarchical task learning. Our validation results show that using the concurrent learning method, we can efficiently detect relevant features from the environment on sequential tasks. Using these discovered state features and action features, a hierarchical structure of the learning task can be generated automatically which can significantly improve the learning speed both on the current task and other tasks with related semantics structure.
Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids

Numerous initiatives have been undertaken to circumvent the problem of antibiotic resistance, including the development of new antibiotics, the use of narrow spectrum antibiotics, and the reduction of inappropriate antibiotic use. We propose an alternative but complimentary approach to reduce antibiotic resistant bacteria (ARB) by implementing more stringent technologies for treating municipal wastewater, which is known to contain large quantities of ARB and antibiotic resistance genes (ARGs). In this study, we investigated the ability of conventional aerobic digestion to reduce the quantity of ARGs in untreated wastewater solids. A bench-scale aerobic digester was fed untreated wastewater solids collected from a full-scale municipal wastewater treatment facility. The reactor was operated under semi-continuous flow conditions for more than 200 days at a residence time of approximately 40 days. During this time, the quantities of tet(A), tet(W), and erm(B) decreased by more than 90%. In contrast, intI1 did not decrease, and tet(X) increased in quantity by 5-fold. Following operation in semi-continuous flow mode, the aerobic digester was converted to batch mode to determine the first-order decay coefficients, with half-lives ranging from as short as 2.8 days for tet(W) to as long as 6.3 days for intI1. These results demonstrated that aerobic digestion can be used to reduce the quantity of ARGs in untreated wastewater solids, but that rates can vary substantially depending on the reactor design (i.e., batch vs. continuous-flow) and the specific ARG.
Involvement of Nuclear Import and Export Factors in U8 Box C/D snoRNP Biogenesis

ABSTRACT Box C/D snoRNPs, factors essential for ribosome biogenesis, are proposed to be assembled in the nucleoplasm before localizing to the nucleolus. However, recent work demonstrated the involvement of nuclear export factors in this process, suggesting that export may take place. Here we show that there are distinct distributions of U8 pre-snoRNAs and pre-snoRNP complexes in HeLa cell nuclear and cytoplasmic extracts. We observed differential association of nuclear export (PHAX, CRM1, and Ran) factors with complexes in the two extracts, consistent with nucleocytoplasmic transport. Furthermore, we show that the U8 pre-snoRNA in one of the cytoplasmic complexes contains an m3G cap and is associated with the nuclear import factor Snurportin1. Using RNA interference, we show that loss of either PHAX or Snurportin1 results in the incorrect localization of the U8 snoRNA. Our data therefore show that nuclear export and import factors are directly involved in U8 box C/D snoRNP biogenesis. The distinct distribution of U8 pre-snoRNP complexes between the two cellular compartments together with the association of both nuclear import and export factors with the precursor complex suggests that the mammalian U8 snoRNP is exported during biogenesis.
Intensity of the cosmic X-ray backgound from HEAO1/A2 experiment

We reanalyze data of HEAO1/A2 – the Cosmic X-ray Experiment – in order to repeat the measurements of the cosmic X-ray background (CXB) intensity and accurately compare this value with other measurements of the CXB. We used the data of MED, HED1, and HED3 detectors in scan mode, which allowed us to measure effective solid angles and effective areas of detectors self consistently, in the same mode as the CXB intensity was measured. We found that the average value of the CXB intensity is 1.96 ± 0.10 × 10 −11 erg s −1 cm −2 deg −2 in the energy band 2−10 keV, or 9.7 ± 0.5 phot s −1 cm −2 at 1 keV assuming the power law spectral shape with photon index Γ= 1.4 in this energy band. We compare the obtained measurements with those obtained by different instruments over the past few decades.
New evidence for a linear colour-magnitude relation and a single Schechter function for red galaxies in a nearby cluster of galaxies down to M ∗ + 8

The colour and luminosity distributions of red galaxies in the cluster Abell 1185 (z = 0.0325) were studied down to M ∗ + 8 in the B, V and R bands. The colour‐magnitude (CM) relation is linear without evidence for significant bending down to absolute magnitudes that are seldom probed in the literature (MR =− 12.5 mag). The CM relation is thin (±0.04 mag) and its thickness is quite independent of the magnitude. The luminosity function (LF) of red galaxies in Abell 1185 is adequately described by a Schechter function, with a characteristic magnitude and a faint end slope that also well describe the LF of red galaxies in other clusters. There is no passband dependence of the LF shape other than an obvious M ∗ shift due to the colour of the considered population. Finally, we conclude that, based on colours and luminosity, red galaxies form a homogeneous population over four decades in stellar mass, providing a second piece of evidence against faint red galaxies being a recent cluster population.
Review and Perspective for Distance-Based Clustering of Vehicle Trajectories

In this paper, we tackle the issue of clustering trajectories of geolocalized observations based on the distance between trajectories. We first provide a comprehensive review of the different distances used in the literature to compare trajectories. Then, based on the limitations of these methods, we introduce a new distance: symmetrized segment-path distance (SSPD). We compare this new distance to the others according to their corresponding clustering results obtained using both the hierarchical clustering and affinity propagation methods. We finally present a python package: trajectory distance, which contains the methods for calculating the SSPD distance, and the other distances reviewed in this paper.
ORIGIN OF SPATIAL VARIATIONS OF SCATTERING POLARIZATION IN THE WINGS OF THE Ca i 4227 Å line

Polarization that is produced by coherent scattering can be modified by magnetic fields via the Hanle effect. This has opened a window to explorations of solar magnetism in parameter domains not accessible to the Zeeman effect. According to standard theory the Hanle effect should only be operating in the Doppler core of spectral lines but not in the wings. In contrast, our observations of the scattering polarization in the Ca i 4227 Å line reveal the existence of spatial variations of the scattering polarization throughout the far line wings. This raises the question whether the observed spatial variations in wing polarization have a magnetic or nonmagnetic origin. A magnetic origin may be possible if elastic collisions are able to cause sufficient frequency redistribution to make the Hanle effect effective in the wings without causing excessive collisional depolarization, as suggested by recent theories for partial frequency redistribution (PRD) with coherent scattering in magnetic fields. To model the wing polarization we bypass the problem of solving the full polarized radiative transfer equations and instead apply an extended version of the technique based on the “last scattering approximation. ” It assumes that the polarization of the emergent radiation is determined by the anisotropy of the incident radiation field at the last scattering event. We determine this anisotropy from the observed limb darkening as a function of wavelength throughout the spectral line. The empirical anisotropy profile is used together with the single-scattering redistribution matrix, which contains all the PRD, collisional, and magnetic field effects. The model further contains a continuum opacity parameter, which increasingly dilutes the polarized line photons as we move away from the line center, and a continuum polarization parameter that represents the observed polarization level far from the line. This model is highly successful in reproducing the observed Stokes Q/I polarization (linear polarization parallel to the nearest solar limb), including the location of the wing polarization maxima and the minima around the Doppler core, but it fails to reproduce the observed spatial variations of the wing polarization in terms of magnetic field effects with frequency redistribution. This null result points in the direction of a nonmagnetic origin in terms of local inhomogeneities (varying collisional depolarization, radiation-field anisotropies, and deviations from a plane-parallel atmospheric stratification).
Antibacterial class is not obviously important in outpatient pneumonia: a meta-analysis

The aim of the present study was to systematically compare outcomes between antibiotic classes in treating outpatient community-acquired pneumonia, with regard to antibacterials active against atypical organisms, as well as between various antibacterial classes with similar atypical coverage. A meta-analysis was performed on randomised controlled trials of antibacterials for community-acquired pneumonia in outpatients aged ≥18 yrs. The studies were independently reviewed by two reviewers. Clinical success and mortality were compared between different oral antibiotic classes, and antibacterials with atypical coverage (macrolides and fluoroquinolones) were specifically compared with other antibacterials. In total, 13 eligible studies involving a total of 4,314 patients were included. The quality of the studies was variable. Five studied macrolides and fluoroquinolones, three macrolides and β-lactams, three fluoroquinolones and β-lactams and two cephalosporins versus β-lactams/ β-lactamase inhibitors. No significant difference was detected regarding clinical success or mortality, regardless of atypical coverage or between antibacterial classes with similar atypical coverage. It was not possible to demonstrate any advantage of specific antibacterials for mild community-acquired pneumonia in relatively healthy outpatients. The need for coverage of atypical pathogens in this setting was not apparent. In mild-to-moderate cases of outpatient-treated community-acquired pneumonia, it might be most appropriate to select antibacterials according to side-effects, patient preferences, availability and cost.
Intrinsic Structure of Visual Exemplar and Category Representations in Macaque Brain

One of the most remarkable properties of the visual system is the ability to identify and categorize a wide variety of objects effortlessly. However, the underlying neural mechanisms remain elusive. Specifically, the question of how individual object information is represented and intrinsically organized is still poorly understood. To address this question, we presented images of isolated real-world objects spanning a wide range of categories to awake monkeys using a rapid event-related functional magnetic resonance imaging (fMRI) design and analyzed the responses of multiple areas involved in object processing. We found that the multivoxel response patterns to individual exemplars in the inferior temporal (IT) cortex, especially area TE, encoded the animate-inanimate categorical division, with a subordinate cluster of faces within the animate category. In contrast, the individual exemplar representations in V4, the amygdala, and prefrontal cortex showed either no categorical structure, or a categorical structure different from that in IT cortex. Moreover, in the IT face-selective regions (“face patches”), especially the anterior face patches, (1) the multivoxel response patterns to individual exemplars showed a categorical distinction between faces and nonface objects (i.e., body parts and inanimate objects), and (2) the regionally averaged activations to individual exemplars showed face-selectivity and within-face exemplar-selectivity. Our findings demonstrate that, at both the single-exemplar and the population level, intrinsic object representation and categorization are organized hierarchically as one moves anteriorly along the ventral pathway, reflecting both modular and distributed processing.
Magnesium in Prevention and Therapy

Magnesium is the fourth most abundant mineral in the body. It has been recognized as a cofactor for more than 300 enzymatic reactions, where it is crucial for adenosine triphosphate (ATP) metabolism. Magnesium is required for DNA and RNA synthesis, reproduction, and protein synthesis. Moreover, magnesium is essential for the regulation of muscular contraction, blood pressure, insulin metabolism, cardiac excitability, vasomotor tone, nerve transmission and neuromuscular conduction. Imbalances in magnesium status—primarily hypomagnesemia as it is seen more common than hypermagnesemia—might result in unwanted neuromuscular, cardiac or nervous disorders. Based on magnesium’s many functions within the human body, it plays an important role in prevention and treatment of many diseases. Low levels of magnesium have been associated with a number of chronic diseases, such as Alzheimer’s disease, insulin resistance and type-2 diabetes mellitus, hypertension, cardiovascular disease (e.g., stroke), migraine headaches, and attention deficit hyperactivity disorder (ADHD).
Sequences of Abstract Nonbiological Stimuli Share Ventral Premotor Cortex with Action Observation and Imagery

Activation triggered by either observed or imagined actions suggests that the ventral premotor cortex (PMv) provides an action vocabulary that allows us to detect and anticipate basically invariant perceptual states in observed actions. In the present study, we tested the hypothesis that the same PMv region is also recruited by nonbiological (abstract) stimulus sequences as long as the temporal order of stimuli has to be processed. Using functional magnetic resonance imaging, we instructed participants to assess expected outcomes in observed actions [external biological cues (EB)], motor imagery [internal biological cues (IB)], or geometrical figure sequences [external nonbiological cues (EN)]. As hypothesized, we found that each condition elicited significant activation within PMv [left hemisphere, Brodman Area (BA) 6], in contrast to a sequential target detection control task. In addition, cue-specific activations were identified in areas that were only engaged for biologically (action) cued (EB, IB) and nonbiologically cued (EN) tasks. Biologically cued tasks elicited activations within inferior frontal gyri adjacent to PMv (BA 44/45), in the frontomedian wall, the extrastriate body area, posterior superior temporal sulci, somatosensory cortices, and the amygdala-hippocampal-area, whereas the nonbiologically cued task engaged presupplementary motor area, middle frontal gyri, intraparietal sulci, and caudate nuclei of the basal ganglia. In sum, findings point to a basic premotor contribution to the representation or processing of sequentially structured events, supplemented by different sets of areas in the context of either biological or nonbiological cues.
SURGE: Surface Regularized Geometry Estimation from a Single Image

This paper introduces an approach to regularize 2.5D surface normal and depth predictions at each pixel given a single input image. The approach infers and reasons about the underlying 3D planar surfaces depicted in the image to snap predicted normals and depths to inferred planar surfaces, all while maintaining fine detail within objects. Our approach comprises two components: (i) a four-stream convolutional neural network (CNN) where depths, surface normals, and likelihoods of planar region and planar boundary are predicted at each pixel, followed by (ii) a dense conditional random field (DCRF) that integrates the four predictions such that the normals and depths are compatible with each other and regularized by the planar region and planar boundary information. The DCRF is formulated such that gradients can be passed to the surface normal and depth CNNs via backpropagation. In addition, we propose new planar-wise metrics to evaluate geometry consistency within planar surfaces, which are more tightly related to dependent 3D editing applications. We show that our regularization yields a 30% relative improvement in planar consistency on the NYU v2 dataset [24].
Examining the Efficacy of a Multitiered Intervention for At-Risk Readers in Grade 1

This study reports the results of a cluster RCT evaluating the impact of Enhanced Core Reading Instruction on reading achievement of grade 1 at-risk readers. Forty-four elementary schools, blocked by district, were randomly assigned to condition. In both conditions, at-risk readers received 90 minutes of whole-group instruction (Tier 1) plus an additional 30 minutes of daily, small-group intervention (Tier 2). In the treatment condition, Tier 1 instruction included enhancements to the core program and Tier 2 intervention was highly aligned with the core program. In the comparison condition, Tier 1 instruction used the same core program as treatment schools in the district and Tier 2 intervention followed standard district protocol. Significant treatment effects were found on measures of phonemic decoding and oral reading fluency from fall to winter and word reading from fall to spring. Student- and classroom-level variables predicted student response to instruction differentially by condition.
Investigation of Dysregulation of Several MicroRNAs in Peripheral Blood of Schizophrenia Patients

Objective The prevalence of schizophrenia is 1%, and it is a debilitating disorder that often results in a shortened lifespan. Peripheral blood samples are good candidates to investigate because they can be easily drawn, and they are widely studied in psychiatric disorders. MicroRNAs are small non-coding RNA transcripts. They regulate the expression of genes by binding to the 3′-untranslated region (UTR) of mRNAs and pointing them to degrade. In this study, we aimed to investigate the expression of miR-9-5p, miR-29a-3p, miR-106-5p, miR-106b-5p, miR-107, miR-125a-3p, and miR-125b-3p in schizophrenia patients and healthy controls. Methods We collected blood samples from 16 patients with schizophrenia and 16 healthy controls. MicroRNAs were measured with reverse transcriptase polymerase chain reaction. Results Schizophrenia patients showed statistically significant upregulation of five microRNAs: miR9-5p (p=0.002), miR29a-3p (p<0.001), miR106b-5p (p=0.002), miR125a-3p (p<0.001), and miR125b-3p (p=0.018). Conclusion Our results increased the value of the miR106 and miR29 families as potentially and consistently dysregulated in psychiatric disorders. Our results should be considered preliminary, and they need confirmation in future studies with larger sample sizes.
Sleeping Our Way to Weight Normalization and Stable Learning

The functions of sleep have been an enduring mystery. Tononi and Cirelli (2003) hypothesized that one of the functions of slow-wave sleep is to scale down synapses in the cortex that have strengthened during awake learning. We create a computational model to test the functionality of this idea and examine some of its implications. We show that synaptic scaling during slow-wave sleep is capable of keeping Hebbian learning in check and that it enables stable development. We also show theoretically how it implements classical weight normalization, which has been in common use in neural models for decades. Finally, a significant computational limitation of this form of synaptic scaling is revealed through computer simulations.