Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Activation of Antibiotic-Resistant Mechanisms in the Absence of Major Drug Efflux Systems of Escherichia coli

Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. ABSTRACT Mutations are one of the common means by which bacteria acquire resistance to antibiotics. In an Escherichia coli mutant lacking major antibiotic efflux pumps AcrAB and AcrEF, mutations can activate alternative pathways that lead to increased antibiotic resistance. In this work, we isolated and characterized compensatory mutations of this nature mapping in four different regulatory genes, baeS, crp, hns, and rpoB. The gain-of-function mutations in baeS constitutively activated the BaeSR two-component regulatory system to increase the expression of the MdtABC efflux pump. Missense or insertion mutations in crp and hns caused derepression of an operon coding for the MdtEF efflux pump. Interestingly, despite the dependence of rpoB missense mutations on MdtABC for their antibiotic resistance phenotype, neither the expression of the mdtABCD-baeSR operon nor that of other known antibiotic efflux pumps went up. Instead, the transcriptome sequencing (RNA-seq) data revealed a gene expression profile resembling that of a “stringent” RNA polymerase where protein and DNA biosynthesis pathways were downregulated but pathways to combat various stresses were upregulated. Some of these activated stress pathways are also controlled by the general stress sigma factor RpoS. The data presented here also show that compensatory mutations can act synergistically to further increase antibiotic resistance to a level similar to the efflux pump-proficient parental strain. Together, the findings highlight a remarkable genetic ability of bacteria to circumvent antibiotic assault, even in the absence of a major intrinsic antibiotic resistance mechanism. IMPORTANCE Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. Here, we explored E. coli’s ability to amass mutations in a background devoid of a major constitutively expressed efflux pump and identified mutations in several regulatory genes that confer resistance by activating specific or pleiotropic mechanisms.
Habitat restoration weakens negative environmental effects on telomere dynamics

Habitat quality can have far‐reaching effects on organismal fitness, an issue of concern given the current scale of habitat degradation. Many temperate upland streams have reduced nutrient levels due to human activity. Nutrient restoration confers benefits in terms of invertebrate food availability and subsequent fish growth rates. Here we test whether these mitigation measures also affect the rate of cellular ageing of the fish, measured in terms of the telomeres that cap the ends of eukaryotic chromosomes. We equally distributed Atlantic salmon eggs from the same 30 focal families into 10 human‐impacted oligotrophic streams in northern Scotland. Nutrient levels in five of the streams were restored by simulating the deposition of a small number of adult Atlantic salmon Salmo salar carcasses at the end of the spawning period, while five reference streams were left as controls. Telomere lengths and expression of the telomerase reverse transcriptase (TERT) gene that may act to lengthen telomeres were then measured in the young fish when 15 months old. While TERT expression was unrelated to any of the measured variables, telomere lengths were shorter in salmon living at higher densities and in areas with a lower availability of the preferred substrate (cobbles and boulders). However, the adverse effects of these habitat features were much reduced in the streams receiving nutrients. These results suggest that adverse environmental pressures are weakened when nutrients are restored, presumably because the resulting increase in food supply reduces levels of both competition and stress.
Extrapolation and dosing recommendations for raxibacumab in children from birth to age <18 years

The US Food and Drug Administration's Animal Rule allows for the approval of drugs when human efficacy studies are not ethical. While the therapeutic doses of raxibacumab, a monoclonal antibody for the prophylaxis and treatment of inhalational anthrax, have been based on pharmacokinetic data from adult subjects, its disposition in children has not been investigated in clinical trials. Here we evaluate the effect of demographic covariates and maturation processes on the pharmacokinetics of raxibacumab and explore opportunities for the optimisation of paediatric doses.
Automated Generation of Personalized Shock Wave Lithotripsy Protocols: Treatment Planning Using Deep Learning

Background Though shock wave lithotripsy (SWL) has developed to be one of the most common treatment approaches for nephrolithiasis in recent decades, its treatment planning is often a trial-and-error process based on physicians’ subjective judgement. Physicians’ inexperience with this modality can lead to low-quality treatment and unnecessary risks to patients. Objective To improve the quality and consistency of shock wave lithotripsy treatment, we aimed to develop a deep learning model for generating the next treatment step by previous steps and preoperative patient characteristics and to produce personalized SWL treatment plans in a step-by-step protocol based on the deep learning model. Methods We developed a deep learning model to generate the optimal power level, shock rate, and number of shocks in the next step, given previous treatment steps encoded by long short-term memory neural networks and preoperative patient characteristics. We constructed a next-step data set (N=8583) from top practices of renal SWL treatments recorded in the International Stone Registry. Then, we trained the deep learning model and baseline models (linear regression, logistic regression, random forest, and support vector machine) with 90% of the samples and validated them with the remaining samples. Results The deep learning models for generating the next treatment steps outperformed the baseline models (accuracy = 98.8%, F1 = 98.0% for power levels; accuracy = 98.1%, F1 = 96.0% for shock rates; root mean squared error = 207, mean absolute error = 121 for numbers of shocks). The hypothesis testing showed no significant difference between steps generated by our model and the top practices (P=.480 for power levels; P=.782 for shock rates; P=.727 for numbers of shocks). Conclusions The high performance of our deep learning approach shows its treatment planning capability on par with top physicians. To the best of our knowledge, our framework is the first effort to implement automated planning of SWL treatment via deep learning. It is a promising technique in assisting treatment planning and physician training at low cost.
Differentially expressed microRNAs that target functional genes in mature soybean nodules

MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr. ], we identified high‐confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium‐inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA‐seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high‐affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole‐plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole‐plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi–nitrogen balance to promote SNF in nodules.
AGO2 promotes tumor progression in KRAS-driven mouse models of non–small cell lung cancer

Significance RAS proteins (HRAS, NRAS, and KRAS) integrate extracellular trophic signals to promote cell proliferation. Constitutively active KRAS drives tumor initiation and progression in nonsmall cell lung cancer (NSCLC). As RAS proteins are often refractory to direct pharmacological inhibition, RAS-interacting proteins are under investigation as potential drug targets. We previously found Argonaute 2 (AGO2) to bind RAS and positively regulate RAS-dependent signaling pathways. AGO2 knockdown blunted proliferation in NSCLC cells containing a KRAS-activating mutation. Here, we demonstrate that AGO2 promotes tumor progression in multiple mouse models of KRAS-driven NSCLC. In these animals, Ago2 knockout impairs tumor growth, lowers pathologic grade, and inhibits KRAS signaling. Targeting the AGO2-KRAS interaction may hold future therapeutic promise in NSCLC and other KRAS-driven malignancies. Lung cancer is the deadliest malignancy in the United States. Non–small cell lung cancer (NSCLC) accounts for 85% of cases and is frequently driven by activating mutations in the gene encoding the KRAS GTPase (e.g., KRASG12D). Our previous work demonstrated that Argonaute 2 (AGO2)—a component of the RNA-induced silencing complex (RISC)—physically interacts with RAS and promotes its downstream signaling. We therefore hypothesized that AGO2 could promote KRASG12D-dependent NSCLC in vivo. To test the hypothesis, we evaluated the impact of Ago2 knockout in the KPC (LSL-Kras G12D/+;p53f/f;Cre) mouse model of NSCLC. In KPC mice, intratracheal delivery of adenoviral Cre drives lung-specific expression of a stop-floxed KRASG12D allele and biallelic ablation of p53. Simultaneous biallelic ablation of floxed Ago2 inhibited KPC lung nodule growth while reducing proliferative index and improving pathological grade. We next applied the KPHetC model, in which the Clara cell–specific CCSP-driven Cre activates KRASG12D and ablates a single p53 allele. In these mice, Ago2 ablation also reduced tumor size and grade. In both models, Ago2 knockout inhibited ERK phosphorylation (pERK) in tumor cells, indicating impaired KRAS signaling. RNA sequencing (RNA-seq) of KPC nodules and nodule-derived organoids demonstrated impaired canonical KRAS signaling with Ago2 ablation. Strikingly, accumulation of pERK in KPC organoids depended on physical interaction of AGO2 and KRAS. Taken together, our data demonstrate a pathogenic role for AGO2 in KRAS-dependent NSCLC. Given the prevalence of this malignancy and current difficulties in therapeutically targeting KRAS signaling, our work may have future translational relevance.
Changing epidemiology of calcific aortic valve disease: 30-year trends of incidence, prevalence, and deaths across 204 countries and territories

Calcific aortic valve disease (CAVD) is associated with increased morbidity and mortality. We aimed to elucidate the 30-year epidemiology of CAVD globally. Global CAVD incidence, prevalence, and deaths increased 3.51-, 4.43-, and 1.38-fold from 1990 to 2019, respectively, without any decreasing trends, even after age standardization. In 2019, Slovenia had the highest age-standardized rate (ASR) of CAVD incidence (62.21/100,000 persons) and prevalence (1,080.06/100,000) whereas Cyprus had the highest ASR of deaths (8.20/100,000). Population aging was an important contributor to incidence. Compared with women, more men had CAVD and men had earlier peaks in disease prevalence. High systolic blood pressure, diet high in sodium, and lead exposure were the main risk factors for deaths owing to CAVD. The estimated annual percentage change, a measure to estimate the variation of ASR, was significantly associated with the ASR and sociodemographic index (SDI) in 2019 for incidence and prevalence across all 204 countries and territories (all p<0.0001). With increased lifespan and risk factors, the overall burden of CAVD is high and remains on the rise, with differences by sex, age, and SDI level. Our findings serve to sound the alarm for organizations, institutions, and resources whose primary purpose is to improve human health.
Neutrophil gelatinase-associated lipocalin as a biomarker for short-term outcomes among trauma patients: A single-center observational study

Background Urinary biomarkers for organ dysfunction could predict the outcomes of severe trauma patients. However, the use of neutrophil gelatinase-associated lipocalin (NGAL) as a biomarker of trauma is not well studied. Objectives To evaluate the association between the short-term prognosis of trauma patients and NGAL levels. Methods We conducted a single center study and compared predictive performances between NGAL levels and the trauma severity. Results A total of 104 patients were included in the study. Patients were divided into two groups based on ISS score of 16. There was no significant difference in patient characteristics based on trauma severity. However, the lactate level was significantly higher in the more severe group. There was a significant association between urinary NGAL levels and trauma severity indicators, such as intensive care unit stay (ICU) (p = 0.005) and emergency care unit (ECU) stay (p = 0.049). In addition, receiver operating curve analysis showed that as a predictor, NGAL could be used for detecting severity with moderate precision, especially for short-term outcomes (specificity 70.6 for ICU and 69.0 for ECU stay). Conclusion In this study, we revealed that the level of NGAL could predict the degree of invasiveness in trauma patients with moderate precision and estimate the duration of treatment during the acute phase. It is necessary to examine the validity of the findings of this study using a prospective, cohort, and multi-center collaborative study design.
Transfusion practices in a large cohort of hospitalized children

While previous studies have described the use of blood components in subsets of children, such as the critically ill, little is known about transfusion practices in hospitalized children across all departments and diagnostic categories. We sought to describe the utilization of red blood cell, platelet, plasma, and cryoprecipitate transfusions across hospital settings and diagnostic categories in a large cohort of hospitalized children.
Levels and Characteristics of mRNAs in Spores of Firmicute Species

Only ∼6% of mRNAs in spores of six firmicute species are at ≥1 molecule/spore, many abundant spore mRNAs encode proteins similar to B. subtilis spore proteins, and some abundant B. subtilis and C. difficile spore mRNAs were fragmented. Most of the abundant B. subtilis and other Bacillales spore mRNAs are transcribed under the control of the forespore-specific RNA polymerase σ factors, F or G, and these results may stimulate transcription analyses in developing spores of species other than B. subtilis. ABSTRACT Spores of firmicute species contain 100s of mRNAs, whose major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. To determine if this is a general phenomenon, RNA was isolated from spores of multiple firmicute species and relative mRNA levels determined by transcriptome sequencing (RNA-seq). Determination of RNA levels in single spores allowed calculation of RNA nucleotides/spore, and assuming mRNA is 3% of spore RNA indicated that only ∼6% of spore mRNAs were present at >1/spore. Bacillus subtilis, Bacillus atrophaeus, and Clostridioides difficile spores had 49, 42, and 51 mRNAs at >1/spore, and numbers of mRNAs at ≥1/spore were ∼10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores and ∼4-fold higher in Bacillus megaterium spores. In all species, some to many abundant spore mRNAs (i) were transcribed by RNA polymerase with forespore-specific σ factors, (ii) encoded proteins that were homologs of those encoded by abundant B. subtilis spore mRNAs and are proteins in dormant spores, and (iii) were likely transcribed in the mother cell compartment of the sporulating cell. Analysis of the coverage of RNA-seq reads on mRNAs from all species suggested that abundant spore mRNAs were fragmented, as was confirmed by reverse transcriptase quantitative PCR (RT-qPCR) analysis of abundant B. subtilis and C. difficile spore mRNAs. These data add to evidence indicating that the function of at least the great majority of mRNAs in all firmicute spores is to be degraded to generate ribonucleotides for new RNA synthesis when spores germinate. IMPORTANCE Only ∼6% of mRNAs in spores of six firmicute species are at ≥1 molecule/spore, many abundant spore mRNAs encode proteins similar to B. subtilis spore proteins, and some abundant B. subtilis and C. difficile spore mRNAs were fragmented. Most of the abundant B. subtilis and other Bacillales spore mRNAs are transcribed under the control of the forespore-specific RNA polymerase σ factors, F or G, and these results may stimulate transcription analyses in developing spores of species other than B. subtilis. These findings, plus the absence of key nucleotide biosynthetic enzymes in spores, suggest that firmicute spores’ abundant mRNAs are not translated when spores germinate but instead are degraded to generate ribonucleotides for new RNA synthesis by the germinated spore.
Disfluency clusters in typical and atypical finnish adult speech. A pilot study

ABSTRACT This study first aimed to investigate disfluency clusters in typical and atypical Finnish adult speakers. Secondly, it aimed to observe possible fluency strategies in speakers representing different fluency levels. In addition to individual disfluency types, we examined different characteristics of disfluency clusters produced by 23 speakers in a fluency continuum. Three adult speaker groups participated in this study: typical speakers with high disfluency frequencies (GA), typical and atypical speakers with very high disfluency frequencies (GB) and atypical speakers with the highest disfluency frequencies (GC). Data were based on a narrative speech task, and disfluency clusters were analysed with both traditional methods and alternative methods. Two statistically significant differences between the speaker groups were found: 1) the length of the clusters was highest in GC compared to other groups, and 2) speakers in GC formulated their utterances more than other groups. Other results, although nonsignificant, were that 3) speakers in GA revised utterances more often than interrupted them compared to GB and GC speakers, and 4) clusters using repetitive words and phrases to maintain fluency were found in GA and GB only. In this study, different fluency levels revealed different strategies in both the production of single disfluencies and in disfluency clusters. It seems that more fluent speakers formulate their messages differently than less fluent speakers, and repetitions can be used to maintain fluency and possibly prevent difficult clusters, as noted with more fluent speakers.
Soft soled footwear has limited impact on toddler gait

The development of walking in young toddlers is an important motor milestone. Walking patterns can differ widely amongst toddlers, and are characterised by unique biomechanical strategies. This makes comparisons between newly walking toddler’s and older children’s walking difficult. Little is currently understood regarding the effects of footwear on the gait in newly walking toddlers. A quasi-experimental pre-post study design was used to assess whether spatiotemporal parameters of gait, and in-shoe foot and lower limb kinematics, differed when walking barefoot and in soft-soled footwear in newly walking toddlers. There were 18 toddlers recruited, with 14 undergoing testing. The GAITRite system collected spatial and temporal data. The Vicon camera system collected kinematic data. The testing conditions included barefoot and footwear. Footwear tested was a commercially available soft soled shoe (Bobux XPLORER). Data was extracted directly from the GAITRite system and analysed. Walking in footwear did not change spatial or temporal data, however there were small but significant decreases in hip adduction/abduction range of motion (mean difference (MD) = 1.79°, 95% CI = -3.51 to -0.07, p = 0.04), knee flexion (MD = -7.63°, 95% CI = 2.70 to 12.55, p = 0.01), and knee flexion/extension range of movement (MD = 6.25°, 95% CI = -10.49 to -2.01, p = 0.01), and an increase in subtalar joint eversion (MD = 2.85°, 95% CI = 5.29 to -0.41, p = 0.03). Effect sizes were small for hip and ankle range, peak knee extension, and subtalar joint ranges (d<0.49), medium for knee flexion/extension range (d = 0.75) and large for peak knee flexion (d = 0.87). The magnitude of kinematic changes with soft-soled footwear were small thus the clinical importance of these findings is uncertain. Future longitudinal studies are needed to develop recommendations regarding footwear for newly walking toddlers.
Developing Global Health Diplomacy-related Skills Using a COVID-19-like Epidemic Simulation as a Learning Strategy

Abstract. Public health and global health practitioners need to develop global health diplomacy (GHD) skills to efficiently work within complex global health scenarios, such as the current coronavirus disease (COVID-19) pandemic. Problem-based learning was used as a framework to create a scenario-based activity designed to develop GHD-related skills. The application and effectiveness of this scenario-based activity to develop GHD-related skills were assessed. A mixed-methods approach involving a self-administered survey and one focus group discussion was used. The survey collected baseline participant characteristics as well as understanding and improvements in GHD-related skills using a 5-point Likert scale. The focus group was audio-recorded and thematically analyzed using both inductive and deductive codes. Data integration was achieved by connecting and weaving. Method and investigator triangulation techniques were used. Participants self-reported significantly better postscenario-based activity responses when asked about their understanding of diplomacy, negotiation, communication, and how to address public health emergencies (P < 0.01, Wilcoxon signed rank test). Most participants either agreed or strongly agreed that their GHD-related skills improved with participation in the scenario-based activity (diplomacy = 55.6%; negotiation = 66.5%; communication = 72.2%; addressing public health emergencies = 72.1%). Overall, qualitative data were consistent with results obtained using quantitative methods. The scenario-based activity was effective for improving the self-reported understanding of GHD-related skills. The scenario-based activity was also effective for developing the selected GHD-related skills (as self-reported). This scenario-based activity is likely to reduce cognitive load and avoid participant overload, thereby facilitating learning. Further research is required to elucidate its long-term impact on skills development.