Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of Rotational Motions Caused by Multiple Mining Blasts Recorded by Different Types of Rotational Seismometers

Digging two vertical shafts with the multiple blasts technique gave the opportunity to measure the induced angular motions in a horizontal plane with well-defined positions of sources. Three kinds of rotation rate sensors, sharing an underground location, were used. Two of them—a Fiber-Optic System for Rotational Events & phenomena Monitoring (FOSREM) and a prototypical seismometer housing the liquid-filled torus—sensed the rotation, while a microarray of two double-pendulum seismometers sensed both the rotation and symmetric strain. The FOSREM was sampled at 656.168 Hz, while all the others were only sampled at 100 Hz. There were considerable differences within the results gathered from the mining blasts, which should be attributed to two causes. The first one is the difference in principles of the operation and sampling rates of the devices used, while the other is the complex and spatially variable character of the studied wave fields. Additionally, we established that the liquid-filled sensor, due to its relatively low sensitivity, proved to be viable only during a registration of strong ground motions. Overall, a comparative study of three different rotational seismometers was performed during mining-induced strong ground motions with well-localized sources.
Bilateral Permanent Childhood Hearing Loss and Health-Related Quality of Life in Adolescence

Little is known about the impact of bilateral permanent childhood hearing loss (PCHL) on health-related quality of life (HRQoL). The objective of this study was to describe preference-based and non-preference based HRQoL outcomes in adolescence, from both self and proxy perspectives, amongst participants of the Hearing Outcomes Project. The Health Utilities Index Marks II (HUI2) and III (HUI3) and the PedsQLTM Version 4.0 Generic Core Scales were used to measure HRQoL based on self and parent proxy reports in 114 adolescents aged 13–19 years, 76 with bilateral PCHL and 38 with normal hearing, recruited from a population sample that was followed up from birth to adolescence. Descriptive statistics and multivariable analyses were used to estimate the relationship between severity of PCHL and HRQoL outcomes. PCHL was associated with decrements in mean multi-attribute utility score that varied between 0.078 and 0.148 for the HUI2 (p = 0.001) and between 0.205 and 0.315 for the HUI3 (p < 0.001), dependent upon the national tariff set applied and respondent group. Multivariable analyses revealed that, after controlling for clinical and sociodemographic covariates, mean HUI3 multi-attribute utility scores were significantly lower in adolescents with moderately severe, severe and profound hearing loss than in adolescents with normal hearing. Significant differences in physical functioning, social functioning, psychosocial functioning and total PedsQLTM scores were only observed when assessments by parents were relied upon, but these dissipated in the multivariable analyses. Bilateral PCHL is associated with poorer HRQoL outcomes in adolescence. Further studies conducted are needed to understand the trajectory and underpinning mechanisms of HRQoL outcomes following PCHL.
The Characteristics of 206 Long-Term Survivors with Peritoneal Metastases from Colorectal Cancer Treated with Curative Intent Surgery: A Multi-Center Cohort from PSOGI

Simple Summary Cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy improves survival in selected patients with peritoneal metastases from colorectal cancer (CRC). However, the characteristics of long-term survivors are not well documented. This study set out to investigate the patient characteristics associated with the long-term survival of peritoneal metastases from CRC. We retrospectively analyzed 206 long-term survivors who underwent CRS for peritoneal metastases from CRC. We found that most long-term survivors showed low peritoneal cancer index (PCI), low PCI of small bowel subsets, and complete cytoreduction (CC-0), while some exhibited characteristics considered associated with poor prognosis. Abstract Background: We conducted this study to review the patient characteristics associated with long-term survival in patients with peritoneal metastases from colorectal cancer who underwent cytoreductive surgery (CRS). Methods: We retrospectively investigated patients with peritoneal metastases from CRC treated with curative intent surgery with or without hyperthermic intraperitoneal chemotherapy at 13 institutions worldwide between January 1985 and April 2015 and survived longer than five years after the first CRS for peritoneal metastases. Clinical and oncological features and therapeutic parameters were described and analyzed. Results: Two hundred six long-term survivors were available for study. The median peritoneal cancer index (PCI) of this cohort was 4 (interquartile range (IQR), 2–7), and the median score of the small bowel regions of the PCI (SB-PCI) was 0 (IQR, 0–2). Complete cytoreduction (CC-0) was achieved in 180 (87.4%) patients. Recurrence was observed in 122 (59.2%) patients at a median of 1.8 (IQR, 1.2–2.6) years. Conclusions: While most long-term survivors showed low PCI/SB-PCI and CCR-0, some had characteristics considered associated with poor prognosis. Curative intent treatments may be considered in well-informed and fit patients showing negative factors affecting survival outcome.
Alendronate Sodium Intercalation in Layered Double Hydroxide/Poly (ε-caprolactone): Application in Osteoporosis Treatment

Background: Osteoporosis is a bone disease alters the amount and variety of proteins in bone tissue and increases the potential of bone fracture. Antiresorptive therapy is one of the most popular treatment methods for osteoporosis. To reduce side effects and enhance the bioavailability of drug agents, the controlled delivery of drug is commonly utilized. Objectives: We investigated the controlled release of Alendronate in different composites of layered double hydroxide (LDH) using poly (ε-caprolactone) (PCL) as a matrix. Materials and Methods: We prepared different microsphere composites of ALD intercalated in various amounts of LDH, using PCL as a matrix. The controlled release of ALD from these composites is subsequently investigated. Samples are characterized and in vitro cell cytotoxicity, attachment, osteogenic activity including alkaline phosphatase activity and mineralization are examined using MG-63 human osteosarcoma cells. Results: The results showed that the release of ALD is more desirable and controlled in the samples having a higher amount of LDH incorporated into the PCL matrix. MG63 cells show a significant increase in viability, attachment, and mineralization while alkaline phosphatase activity remains almost at a constant level after 3 weeks. Conclusions: Overall, the findings showed that by incorporation of 15 wt% of LDH, the composite microsphere is capable of holding the antiresorptive drug longer and release it in a more controlled manner. This is an advantageous and promising characteristic for a carrier that could be used as a potential candidate for osteoporosis treatment.
Biological Functions of Type II Toxin-Antitoxin Systems in Bacteria

After the first discovery in the 1980s in F-plasmids as a plasmid maintenance system, a myriad of toxin-antitoxin (TA) systems has been identified in bacterial chromosomes and mobile genetic elements (MGEs), including plasmids and bacteriophages. TA systems are small genetic modules that encode a toxin and its antidote and can be divided into seven types based on the nature of the antitoxin molecules and their mechanism of action to neutralise toxins. Among them, type II TA systems are widely distributed in chromosomes and plasmids and the best studied so far. Maintaining genetic material may be the major function of type II TA systems associated with MGEs, but the chromosomal TA systems contribute largely to functions associated with bacterial physiology, including the management of different stresses, virulence and pathogenesis. Due to growing interest in TA research, extensive work has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules. However, there are still controversies about some of the functions associated with different TA systems. This review will discuss the most current findings and the bona fide functions of bacterial type II TA systems.
An Extended Correlation Dimension of Complex Networks

Fractal and self-similarity are important characteristics of complex networks. The correlation dimension is one of the measures implemented to characterize the fractal nature of unweighted structures, but it has not been extended to weighted networks. In this paper, the correlation dimension is extended to the weighted networks. The proposed method uses edge-weights accumulation to obtain scale distances. It can be used not only for weighted networks but also for unweighted networks. We selected six weighted networks, including two synthetic fractal networks and four real-world networks, to validate it. The results show that the proposed method was effective for the fractal scaling analysis of weighted complex networks. Meanwhile, this method was used to analyze the fractal properties of the Newman–Watts (NW) unweighted small-world networks. Compared with other fractal dimensions, the correlation dimension is more suitable for the quantitative analysis of small-world effects.
Residue–Residue Interaction Prediction via Stacked Meta-Learning

Protein–protein interactions (PPIs) are the basis of most biological functions determined by residue–residue interactions (RRIs). Predicting residue pairs responsible for the interaction is crucial for understanding the cause of a disease and drug design. Computational approaches that considered inexpensive and faster solutions for RRI prediction have been widely used to predict protein interfaces for further analysis. This study presents RRI-Meta, an ensemble meta-learning-based method for RRI prediction. Its hierarchical learning structure comprises four base classifiers and one meta-classifier to integrate predictive strengths from different classifiers. It considers multiple feature types, including sequence-, structure-, and neighbor-based features, for characterizing other properties of a residue interaction environment to better distinguish between noninteracting and interacting residues. We conducted the same experiments using the same data as previously reported in the literature to demonstrate RRI-Meta’s performance. Experimental results show that RRI-Meta is superior to several current prediction tools. Additionally, to analyze the factors that affect the performance of RRI-Meta, we conducted a comparative case study using different protein complexes.
Enhanced Antibacterial Activity of Echinacea angustifolia Extract against Multidrug-Resistant Klebsiella pneumoniae through Niosome Encapsulation

With the increased occurrence of antibiotic-resistant bacteria, alternatives to classical antibiotics are urgently needed for treatment of various infectious diseases. Medicinal plant extracts are among the promising candidates due to their bioactive components. The aim of this study was to prepare niosome-encapsulated Echinacea angustifolia extract and study its efficacy against multidrug-resistant Klebsiella pneumoniae strains. Encapsulation was first optimized by Design of Experiments, followed by the empirical study. The obtained niosomes were further characterized for the size and morphology using dynamic light scattering (DLS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). Spherical niosomes had a diameter of 142.3 ± 5.1 nm, as measured by DLS. The entrapment efficiency (EE%) of E. angustifolia extract reached up to 77.1% ± 0.3%. The prepared niosomes showed a controlled drug release within the tested 72 h and a storage stability of at least 2 months at both 4 and 25 °C. The encapsulated E. angustifolia displayed up to 16-fold higher antibacterial activity against multidrug-resistant K. pneumoniae strains, compared to the free extract. Additionally, the niosome exhibited negligible cytotoxicity against human foreskin fibroblasts. We anticipate that the results presented herein could contribute to the preparation of other plant extracts with improved stability and antibacterial activity, and will help reduce the overuse of antibiotics by controlled release of natural-derived drugs.
Vitamin D Supplementation and Disease-Free Survival in Stage II Melanoma: A Randomized Placebo Controlled Trial

Patients with newly resected stage II melanoma (n = 104) were randomized to receive adjuvant vitamin D3 (100,000 IU every 50 days) or placebo for 3 years to investigate vitamin D3 protective effects on developing a recurrent disease. Median age at diagnosis was 50 years, and 43% of the patients were female. Median serum 25-hydroxy vitamin D (25OHD) level at baseline was 18 ng/mL, interquartile range (IQ) was 13–24 ng/mL, and 80% of the patients had insufficient vitamin D levels. We observed pronounced increases in 25OHD levels after 4 months in the active arm (median 32.9 ng/mL; IQ range 25.9–38.4) against placebo (median 19.05 ng/mL; IQ range 13.0–25.9), constantly rising during treatment. Remarkably, patients with low Breslow score (<3 mm) had a double increase in 25OHD levels from baseline, whereas patients with Breslow score ≥3 mm had a significantly lower increase over time. After 12 months, subjects with low 25OHD levels and Breslow score ≥3 mm had shorter disease-free survival (p = 0.02) compared to those with Breslow score <3 mm and/or high levels of 25OHD. Adjusting for age and treatment arm, the hazard ratio for relapse was 4.81 (95% CI: 1.44–16.09, p = 0.011). Despite the evidence of a role of 25OHD in melanoma prognosis, larger trials with vitamin D supplementation involving subjects with melanoma are needed.
Saccharomyces cerevisiae Promoter Engineering before and during the Synthetic Biology Era

Simple Summary Promoters are DNA sequences where the process of transcription starts. They can work constitutively or be controlled by environmental signals of different types. The quantity of proteins and RNA present in yeast genetic circuits highly depends on promoter strength. Hence, they have been deeply studied and modified over, at least, the last forty years, especially since the year 2000 when Synthetic Biology was born. Here, we present how promoter engineering changed over these four decades and discuss its possible future directions due to novel computational methods and technology. Abstract Synthetic gene circuits are made of DNA sequences, referred to as transcription units, that communicate by exchanging proteins or RNA molecules. Proteins are, mostly, transcription factors that bind promoter sequences to modulate the expression of other molecules. Promoters are, therefore, key components in genetic circuits. In this review, we focus our attention on the construction of artificial promoters for the yeast S. cerevisiae, a popular chassis for gene circuits. We describe the initial techniques and achievements in promoter engineering that predated the start of the Synthetic Biology epoch of about 20 years. We present the main applications of synthetic promoters built via different methods and discuss the latest innovations in the wet-lab engineering of novel promoter sequences.
Mental health and the COVID-19 pandemic: a study of medical residency training over the years

OBJECTIVES: This study aims to assess the symptoms of burnout, depression, and anxiety in Brazilian medical residents during the COVID-19 pandemic and to compare residents' beliefs and clinical practices related to COVID-19 patients among all six years of medical residency training in Brazil. METHODS: A quantitative study was conducted in April 2020 with a convenience sample of medical resident volunteers from an anonymous online survey. This investigation collected sociodemographic information and used the Oldenburg Burnout Inventory (OLBI) to measure burnout, the Patient Health Questionnaire (PHQ-9) to measure depression, and the General Anxiety Disorders (GAD-7) to measure generalized anxiety disorder. This study also developed a COVID-19 Impact Questionnaire (CIQ-19) to assess the residents' beliefs and clinical practices related to COVID-19 patients. RESULTS: Our sample comprised 3071 respondents. Depressive symptoms were the most common among second-year residents (70.5%), followed by anxiety symptoms (56.0%) and burnout (55.2%) among fourth-year residents. We also observed burnout symptoms (55.1%) among second-year residents. CONCLUSION: The COVID-19 pandemic increased the risk of mental illnesses in some years of residency. Our study could not conclude the reasons why the incidence varies among levels of physician training. Final year medical residents have avoided seeing COVID-19 patients.
Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1

The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.
Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer

Simple Summary Standard treatment of locally advanced rectal cancer (LARC) consists of chemotherapy, radiotherapy, and surgery. Identification of radio-resistant (RR) and radio-sensitive (RS) LARC has been a major hurdle for patient-specific treatment. The development of biomarkers that can discriminate radio-responsiveness before surgery could improve standard treatment and minimize unwanted side effects. Abstract LARC patients were sorted according to their radio-responsiveness and patient-derived organoids were established from the respective cancer tissues. Expression profiles for each group were obtained using RNA-seq. Biological and bioinformatic analysis approaches were used in deciphering genes and pathways that participate in the radio-resistance of LARC. Thirty candidate genes encoding proteins involved in radio-responsiveness–related pathways, including the immune system, DNA repair and cell-cycle control, were identified. Interestingly, one of the candidate genes, cathepsin E (CTSE), exhibited differential methylation at the promoter region that was inversely correlated with the radio-resistance of patient-derived organoids, suggesting that methylation status could contribute to radio-responsiveness. On the basis of these results, we plan to pursue development of a gene chip for diagnosing the radio-responsiveness of LARC patients, with the hope that our efforts will ultimately improve the prognosis of LARC patients.
The Design of Alapropoginine, a Novel Conjugated Ultrashort Antimicrobial Peptide with Potent Synergistic Antimicrobial Activity in Combination with Conventional Antibiotics

(1) Background: Antimicrobial resistance represents an urgent health dilemma facing the global human population. The development of novel antimicrobial agents is needed to face the rising number of resistant bacteria. Ultrashort antimicrobial peptides (USAMPs) are considered promising antimicrobial agents that meet the required criteria of novel antimicrobial drug development. (2) Methods: Alapropoginine was rationally designed by incorporating arginine (R), biphenylalanine (B), and naproxen to create an ultrashort hexapeptide. The antimicrobial activity of alapropoginine was evaluated against different strains of bacteria. The hemolytic activity of alapropoginine was also investigated against human erythrocytes. Finally, synergistic studies with antibiotics were performed using the checkerboard technique and the determination of the fractional inhibitory index. (3) Results: Alapropoginine displayed potent antimicrobial activities against reference and multi-drug-resistant bacteria with MIC values of as low as 28.6 µg/mL against methicillin-resistant S. aureus. Alapropoginine caused negligible toxicity toward human red blood cells. Moreover, the synergistic studies showed improved activities for the combined conventional antibiotics with a huge reduction in their antimicrobial concentrations. (4) Conclusions: The present study indicates that alapropoginine exhibits promising antimicrobial activity against reference and resistant strains of bacteria with negligible hemolytic activity. Additionally, the peptide displays synergistic or additive effects when combined with several antibiotics.
Low Effectiveness of Prosulfocarb and Mesosulfuron-Methyl + Iodosulfuron-Methyl against Vulpia myuros

Due to natural tolerance to most widely used herbicides for grass weed control, prosulfocarb as pre-emergence or early post-emergence herbicide and mesosulfuron + iodosulfuron as post-emergence herbicide are the mainstays of any chemical control program for Vulpia myuros in Denmark. However, farmers often report variable efficacy of these herbicides on V. myuros compared to other grass weeds. Dose–response experiments were conducted to evaluate the performance of prosulfocarb and mesosulfuron + iodosulfuron on V. myuros. Prosulfocarb was sprayed at different plant growth stages to study the influence of plant growth stage on the performance of prosulfocarb on V. myuros in comparison with the more susceptible grass weed species Apera spica-venti. Doses causing 50% reduction in response variable (ED50) were estimated from the dose–response analysis. The ED50 values revealed a higher tolerance of V. myuros to prosulfocarb and mesosulfuron + iodosulfuron than A. spica-venti. The relative difference in the effectiveness of prosulfocarb between V. myuros and A. spica-venti was constant among plant growth stages studied. The highest levels of V. myuros control were achieved when prosulfocarb was sprayed pre-emergence (BBCH 00), while the control substantially declined at later growth stages. The results from the current study document the tolerance of V. myuros to prosulfocarb and mesosulfuron + iodosulfuron and highlight the importance of optimization of prosulfocarb spray timing for achieving maximum control of V. myuros.