Miracle-dz/UniFAR-FTUs huggingface dataset:
Asterisk

Labeling datasets is one of the most expensive bottlenecks in data preprocessing tasks in machine learning. Therefore, organizations, in many domains, are applying weak supervision to produce noisy labels. However, since weak supervision relies on cheaper sources, the quality of the generated labels is problematic. Therefore, in this article, we present Asterisk, an end-to-end framework to generate high-quality, large-scale labeled datasets. The system, first, automatically generates heuristics to assign initial labels. Then, the framework applies a novel data-driven active learning process to enhance the labeling quality. We present an algorithm that learns the selection policy by accommodating the modeled accuracies of the heuristics, along with the outcome of the generative model. Finally, the system employs the output of the active learning process to enhance the quality of the labels. To evaluate the proposed system, we report its performance against four state-of-the-art techniques. In collaboration with our industrial partner, IBM, we test the framework within a wide range of real-world applications. The experiments include 10 datasets of varying sizes with a maximum size of 11 million records. The results illustrate the effectiveness of the framework in producing high-quality labels and achieving high classification accuracy with minimal annotation efforts.
Mycobacterial infections in wild boars (Sus scrofa) from Southern Switzerland: Diagnostic improvements, epidemiological situation and zoonotic potential

Abstract The occurrence of mycobacterial infections in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. In addition to the well‐known pathogenic members of the Mycobacterium tuberculosis – complex (MTBC), over 180 non‐tuberculous mycobacteria (NTM) species have been described. Although the large majority of the NTM is assumed to be non‐pathogenic to most individuals, an increasing trend in NTM infections has been observed over the last decades. The reasons of such augmentation are probably more than one: improved laboratory diagnostics, an increasing number of immunocompromised patients and individuals with lung damage are some of the possible aspects. Mandibular lymph nodes of 176 hunted wild boars from the pre‐Alpine region of Canton Ticino, Switzerland, were collected. Following gross inspection, each lymph node was subjected to culture and to an IS6110 based real‐time PCR specific for MTBC members. Histology was performed of a selection of lymph nodes (n = 14) presenting gross visible lesions. Moreover, accuracy of matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) species identification was compared with sequence analysis of a combination of housekeeping genes. Mycobacteria of the MTBC were detected in 2.8% of the wild boars (n = 5; CI95% 1.2–6.5) and were all confirmed to be Mycobacterium microti by molecular methods. In addition, based on the examined lymph nodes, NTM were detected in 57.4% (n = 101; CI95% 50.0–64.5) of the wild boars originating from the study area. The 111 isolates belonged to 24 known species and three potentially undescribed Mycobacterium species. M. avium subsp. hominissuis thereby predominated (22.5%) and was found in lymph nodes with and without macroscopic changes. Overall, the present findings show that, with the exception of undescribed Mycobacterium species where identification was not possible (3.6%; 4/111), MALDI‐TOF MS had a high concordance rate (90.1%; 100/111 isolates) to the sequence‐based reference method.
Evolutionary Waves: Patterns in the Origins of Animal Phyla.

Concordant patterns of embryology, morphology and functional anatomy delimit grades of animal phyla, each of which contains a 'Major Phylum': PARACOELOMATA (nom.nov.) = acoelomates + pseudocoelomates, flexible hydrostatic skeleton, Nematoda; DEUTEROSTOMIA (including lophophorates) = enterocoelic coelom, rigid internal skeleton, Chordata; and PROTOSTOMIA with two subgrades, MONOMERIC P. = unsegmented, single coelom, molluscan blastular cross, partial rigid exoskeleton, Molluscs; and POLYMERIC P. = segmented, multiple coelom, annelid cross, rigid exoskeleton, Uniramia. Such groups are usually treated as arbitrary stages in mono- and limited-branch phylogenies, but recent studies show them to be real and significant because the only phylogenetic links are from each Paracoelomata and Protostomia Phylum to Turbellaria; and each Deuterostomia Phylum to Cnidaria-Ctenophora and/or enteropneust Hemichordata. Similar grades have often been explained by hypothetical common ancestors, which are unnecessary if the phyla arose during 'evolutionary waves'. These attribute the origin of each grade to the likelihood that its constituent phyla arose independently, about the same time, from the same ciliary powered ancestral stock which was preadapted to enabling a potential body cavity to be actualized while evolving a cylindrical, wholly muscle-powered, body with a hydrostatic skeleton. Because such a skeleton is functionally dependent upon other structural modifications, particularly of the body wall, it could appear only when these were also available. If the latter could be supplied in a number of ways, all opportunities would be exploited and a body cavity would appear several times. The morphology suggests that this did happen, so that a pseudocoelom and coelom evolved independently in each phylum where they occur. Because of evidence that Protostomia and Deuterostomia were never linked during evolution, the origin of the coeloms in the former are explained by the Gonocoelic Theory and in the latter by the Enterocoelic. This, with the recognition of the monomeric protostomes as a distinct group, establishes that segmentation arose at the same time as the coeloms, so that their origins are one problem and not two as usually thought. Finally, protistan data suggest that Turbellaria, and so Paracoelomata and Protostomia, arose from 'close mitosis' flagellates, as did Fungi; while Cnidaria, and so Deuterostomia, arose from 'open mitosis' flagellates. as did Plantae. Thus, the classic Animalia division into Protostomia and Deuterostomia may represent a Protista division such that the animal groups are closer to fungi and plants respectively than they are to each other.
Influence of the Ovine Genital Tract Microbiota on the Species Artificial Insemination Outcome. A Pilot Study in Commercial Sheep Farms

To date, there is a lack of research into the vaginal and sperm microbiome and its bearing on artificial insemination (AI) success in the ovine species. Using hypervariable regions V3–V4 of the 16S rRNA, we describe, for the first time, the combined effect of the ovine microbiome of both females (50 ewes belonging to five herds) and males (five AI rams from an AI center) on AI outcome. Differences in microbiota abundance between pregnant and non-pregnant ewes and between ewes carrying progesterone-releasing intravaginal devices (PRID) with or without antibiotic were tested at different taxonomic levels. The antibiotic treatment applied with the PRID only altered Streptobacillus genus abundance, which was significantly lower in ewes carrying PRID with antibiotic. Mageebacillus, Histophilus, Actinobacilllus and Sneathia genera were significantly less abundant in pregnant ewes. In addition, these genera were more abundant in two farms with higher AI failure. Species of these genera such as Actinobacillus seminis and Histophilus somni have been associated with reproductive disorders in the ovine species. These genera were not present in the sperm samples of AI rams, but were found in the foreskin samples of rams belonging to herd 2 (with high AI failure rate) indicating that their presence in ewes’ vagina could be due to prior transmission by natural mating with rams reared in the herd.
Polydrug Use and Dating Violence Among Emerging Adults

We examined sociodemographic and psychosocial risk factors that moderate the (poly) substance use and dating violence victimization and perpetration relationship among emerging adults. Using an ethnically diverse sample (N = 698), we used latent class analyses to identify mutually exclusive groups based on monthly and past-year substance use. We then examined these groups as they relate to dating violence victimization and perpetration and the moderating effect of various risk factors. Five classes were identified based on substance use patterns: (a) Regular Alcohol use, (b) Polysubstance use, (c) Heavy Alcohol and Marijuana use, (d) Mild Alcohol use, and (e) Occasional Alcohol and Marijuana use classes. Participants in the Polysubstance use class were the most likely to perpetrate dating violence followed by Heavy Alcohol and Marijuana use, Occasional Alcohol and Marijuana use, Regular Alcohol, and Mild Alcohol use classes. Similarly, participants in the Polysubstance use class were the most likely to be victims of dating violence followed by Occasional Alcohol and Marijuana, Heavy Alcohol and Marijuana, Regular Alcohol, and Mild Alcohol use classes. Depending on substance use class, gender, ethnicity, socioeconomic status, history of dating violence, and trauma symptoms differentially influenced dating violence perpetration and victimization at 1-year follow-up. Our findings support the need to comprehensively address dating violence among emerging adults. Intimate partner violence prevention and intervention programs may benefit from targeting emerging adults who misuse substances and incorporating substance use interventions into dating violence prevention efforts.
EFFECT OF LIGHT INTENSITY ON ACTIVITY PATTERNS OF PATAGONIAN LEAF-EARED MICE, PHYLLOTIS XANTHOPYGUS

Abstract The effect of light intensity on activity was investigated in a study of captive leaf-eared mice, Phyllotis xanthopygus. This nocturnal mouse lives in rocky outcrops but forages in open areas with little vegetative cover. Primary predators are raptors and canids, all of which are expected to have increased hunting success under higher levels of moonlight. Because of this correlation between light intensity and predation risk, we predicted that increased light intensity during the dark period would result in decreased nocturnal activity. Data were collected continuously for 3 days under varying light intensities and were analyzed using cosinor analysis to estimate parameters describing the activity rhythm (mesor, amplitude, and acrophase). Number of diurnal activity bouts increased after exposure to light intensities similar to full moonlight (3.0 lux). Total activity of mice in middle (1.5 lux) and high (3.0 lux) light treatments was depressed as evinced by significantly lower mesor and amplitude estimates compared with those of mice in control conditions (0.0 lux). The acrophase also was significantly different between the control and the 2 treatment groups.
FORAGING HABITAT OF THE INDIANA BAT (MYOTIS SODALIS) AT AN URBAN–RURAL INTERFACE

Abstract We captured 11 Myotis sodalis and radiotracked them to foraging areas near Indianapolis International Airport during summer 2002. A series (3–7) of multiazimuth triangulations was used to obtain an estimate of the location of each bat throughout the night. Compositional analysis was used to compare habitat that bats used to available habitat at 2 spatial scales. At both spatial scales, bats preferentially used woodlands over other available habitats (especially developed habitats). These findings suggest that suburban development may negatively impact M. sodalis by limiting foraging options. Many conservation plans aimed at protecting bats exclusively target roosting sites. Although roost conservation should continue to be central in efforts to protect bats, available foraging habitat also should be considered.
Mitigating the Effects of Oxidative Sperm DNA Damage

Sperm DNA damage is correlated with reduced embryo development and increased miscarriage risk, reducing successful conception. Given its links with oxidative stress, antioxidants have been investigated as a potential treatment, yet results are conflicting. Importantly, individual antioxidants are not identical in composition, and some compounds may be more effective than others. We investigated the use of the polyphenol-rich, high-antioxidant-capacity fruit acai as a treatment for elevated sperm DNA fragmentation (>16%), measured by terminal deoxynucleotidyl transferase dUTP nick end labelling (TUNEL). Following ≥ 74 days of treatment, we observed a significant decrease in sperm DNA fragmentation (−17.0% ± 2.5%) to 11.9 ± 1.7% (0–37%), with a 68.6% success rate (defined as post-treatment TUNEL < 16%). Post-treatment decreases in DNA fragmentation and success rates were not significantly impacted by low motility and/or concentration, or exceptionally high (> 25%) TUNEL. Treatment significantly reduced concentration in men with normal semen parameters, but 88% remained normal. Overall, successful treatment was not associated with age, semen parameters or TUNEL result at baseline. However, body mass index was significantly higher in nonresponders at baseline. This study provides evidence of a low-cost, effective treatment for elevated sperm DNA damage using acai.
Evaluation of the mechanical properties and clinical efficacy of biphasic calcium phosphate-added collagen membrane in ridge preservation

Purpose This study aimed to evaluate the biocompatibility and the mechanical properties of ultraviolet (UV) cross-linked and biphasic calcium phosphate (BCP)-added collagen membranes and to compare the clinical results of ridge preservation to those obtained using chemically cross-linked collagen membranes. Methods The study comprised an in vitro test and a clinical trial for membrane evaluation. BCP-added collagen membranes with UV cross-linking were prepared. In the in vitro test, scanning electron microscopy, a collagenase assay, and a tensile strength test were performed. The clinical trial involved 14 patients undergoing a ridge preservation procedure. All participants were randomly divided into the test group, which received UV cross-linked membranes (n=7), and the control group, which received chemically cross-linked membranes (n=7). BCP bone substitutes were used for both the test group and the control group. Cone-beam computed tomography (CBCT) scans were performed and alginate impressions were taken 1 week and 3 months after surgery. The casts were scanned via an optical scanner to measure the volumetric changes. The results were analyzed using the nonparametric Mann-Whitney U test. Results The fastest degradation rate was found in the collagen membranes without the addition of BCP. The highest enzyme resistance and the highest tensile strength were found when the collagen-to-BCP ratio was 1:1. There was no significant difference in dimensional changes in the 3-dimensional modeling or CBCT scans between the test and control groups in the clinical trial (P>0.05). Conclusions The addition of BCP and UV cross-linking improved the biocompatibility and the mechanical strength of the membranes. Within the limits of the clinical trial, the sites grafted using BCP in combination with UV cross-linked and BCP-added collagen membranes (test group) did not show any statistically significant difference in terms of dimensional change compared with the control group.
Designing Lentiviral Gene Vectors

Gene therapy relies on the delivery of therapeutic genes into patients’ cells. The microdevices used to reach the cells and to transfer the gene payload are called gene vectors. Viral packaging machinery is often utilized to generate the particles transporting the cargo genes. Lentiviruses, a subgroup of retroviruses, are highly suitable for remodeling into gene transfer vectors because they offer the stability of transgene expression, the ability to reach the nuclei of the therapeutically important non-dividing cells and are known to have a low immunogenic profile. Well studied members of the lentiviruses include human immunodeficiency viruses 1 and 2 (HIV-1 and HIV-2), feline immunodeficiency virus (FIV) and equine infectious anemia virus (EIAV). It is important not to confuse “gene delivery vectors” and “gene cloning vectors”. While the former are microparticles delivering genes, the latter are replicating vehicles for the amplification of nucleic acid sequences. “Gene delivery vectors” and “gene cloning vectors” coincide when the naked DNA of replicating bacterial plasmids or replication competent viruses is used for gene delivery into cells. Viral gene delivery vectors are normally nonreplicating and should correctly be referred to as “viral vectors”, not “viruses”. Particles of viral vectors can be referred to as “virions” or “transducing particles”, because viral gene transfer is traditionally described as “transduction”. Replication deficient viral gene vector particles are similar to “defective interfering particles”, that is, faulty non-self-viable virions arising during natural viral infections and competing with non-defective virions, which were described in virology literature many years ago. Native lentiviral envelope proteins, which determine the cell range of viral infectivity (tropism) and mediate the fusion of viral and cellular membranes, are always composed from two non-covalently attached subunits, one of which (e.g. gp41 glycoprotein in HIV-1) is membrane-embedded and the other is an external subunit (e.g. gp120 glycoprotein in HIV-1). This arrangement makes lentiviruses notoriously unstable because of their tendency to shed the external subunit of the envelope protein. As the virion’s stability is a pre-requisite for the effective purification and concentration of viral vector preparations, in
Duration of SARS‐CoV‐2 RNA shedding and factors associated with prolonged viral shedding in patients with COVID‐19

To investigate the factors associated with the duration of severe acute respiratory syndrome coronavirus 2 RNA shedding in patients with coronavirus disease 2019 (COVID‐19). A retrospective cohort of COVID‐19 patients admitted to a designated hospital in Beijing was analyzed to study the factors affecting the duration of viral shedding. The median duration of viral shedding was 11 days (IQR, 8‐14.3 days) as measured from illness onset. Univariate regression analysis showed that disease severity, corticosteroid therapy, fever (temperature>38.5°C), and time from onset to hospitalization were associated with prolonged duration of viral shedding (P < .05). Multivariate regression analysis showed that fever (temperature>38.5°C) (OR, 5.1, 95%CI: 1.5‐18.1), corticosteroid therapy (OR, 6.3, 95%CI: 1.5‐27.8), and time from onset to hospitalization (OR, 1.8, 95%CI: 1.19‐2.7) were associated with increased odds of prolonged duration of viral shedding. Corticosteroid treatment, fever (temperature>38.5°C), and longer time from onset to hospitalization were associated with prolonged viral shedding in COVID‐19 patients.
Copigmentation and UPLC-ESI-MS/MS of anthocyanin in Ipomoea nil as potential source of food colorant

Abstract Anthocyanins are good alternative to synthetic dyes for food, pharmaceutical and nutraceutical industries. Owing to their wide occurrence in plant kingdom, an UPLC-ESI-MS/MS method was used to identify and quantify the constituents in flowers of Ipomoea nil. The qualitative evaluation of I. nil results in the characterisation of acylated and non-acylated anthocyanins. Besides characterisation, the total phenolic contents in different fractions of I. nil were found to be 49.69 ± 1.74 and 331.54 ± 1.14 mg GAE/g, respectively. The total anthocyanins content was also determined by spectrophotometer and found to be 5.89 mg/100g of cyanidin-3-O-glucoside equivalent. The antioxidant activity of different fraction of I. nil was evaluated by different assays (DPPH●, ABTS●+ and FRAP). In the direction of natural colour stability, we had studied different stabilising agents/copigments and were found to provide stability up to 140 °C. The extracted anthocyanins were evaluated for acute oral toxicity studies and observed to be non-toxic and may direct the use of I. nil for human consumption. Graphical Abstract
Transcriptomic Modifications in Developmental Cardiopulmonary Adaptations to Chronic Hypoxia Using a Murine Model of Simulated High Altitude Exposure.

Mechanisms driving adaptive developmental responses to chronic high altitude (HA) exposure are incompletely known. We developed a novel rat model mimicking the human condition of cardiopulmonary adaptation to HA starting at conception and spanning the in utero and post-natal timeframe. We assessed lung growth and cardiopulmonary structure and function, and performed transcriptome analyses to identify mechanisms facilitating developmental adaptations to chronic hypoxia. To generate the model, breeding pairs of Sprague-Dawley rats were exposed to hypobaric hypoxia (equivalent to 9,000 feet elevation). Mating, pregnancy and delivery occurred in hypoxic conditions. Six weeks postpartum, structural and functional data were collected in the offspring. RNAseq was performed on right ventricle (RV) and lung tissue. Age-matched breeding pairs and offspring under room air (RA) conditions served as controls. Hypoxic rats exhibited significantly lower body weights and higher hematocrit levels, alveolar volumes, pulmonary diffusion capacities, RV mass, RV systolic pressure as well as increased pulmonary artery remodeling. RNAseq analyses revealed multiple differentially expressed genes in lungs and RVs from hypoxic rats. While there was considerable similarity between hypoxic lungs and RVs compared to RA controls, several upstream regulators unique to lung or RV were identified. We noted a pattern of immune down-regulation and regulation patterns of immune and hormonal mediators similar to the genome from patients with pulmonary arterial hypertension. In summary, we developed a novel murine model of chronic hypoxia exposure that demonstrates functional and structural phenotypes similar to human adaptation. We identified transcriptomic alterations that suggest potential mechanisms for adaptation to chronic HA.
Using trauma registry data to predict prolonged mechanical ventilation in patients with traumatic brain injury: Machine learning approach

Objectives We aimed to build a machine learning predictive model to predict the risk of prolonged mechanical ventilation (PMV) for patients with Traumatic Brain Injury (TBI). Methods This study included TBI patients who were hospitalized in a level 1 trauma center between January 2014 and February 2019. Data were analyzed for all adult patients who received mechanical ventilation following TBI with abbreviated injury severity (AIS) score for the head region of ≥ 3. This study designed three sets of machine learning models: set A defined PMV to be greater than 7 days, set B (PMV > 10 days) and set C (PMV >14 days) to determine the optimal model for deployment. Patients’ demographics, injury characteristics and CT findings were used as predictors. Logistic regression (LR), Artificial neural networks (ANN) Support vector machines (SVM), Random Forest (RF) and C.5 Decision Tree (C.5 DT) were used to predict the PMV. Results The number of eligible patients that were included in the study were 674, 643 and 622 patients in sets A, B and C respectively. In set A, LR achieved the optimal performance with accuracy 0.75 and Area under the curve (AUC) 0.83. SVM achieved the optimal performance among other models in sets B with accuracy/AUC of 0.79/0.84 respectively. ANNs achieved the optimal performance in set C with accuracy/AUC of 0.76/0.72 respectively. Machine learning models in set B demonstrated more stable performance with higher prediction success and discrimination power. Conclusion This study not only provides evidence that machine learning methods outperform the traditional multivariate analytical methods, but also provides a perspective to reach a consensual definition of PMV.