Miracle-dz/UniFAR-FTUs huggingface dataset:
How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies

A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
The Social Utility and Health Benefits for Older Adults of Amenity Buildings in China’s Urban Parks: A Nanjing Case Study

As China’s population rapidly ages, research and discussion on how to better optimize public spaces for the elderly’s health and benefit continue to deepen. This study uses observational surveys and questionnaires to investigate the elderly visitors of Nanjing’s urban parks and explore the impact the parks’ amenity buildings (structures built to provide visitors with conveniences, e.g., shelters and pavilions) has on their health and associated socialization tendencies. Data were collected from ten amenity buildings in ten separate parks to compose a total dataset of 728 activity statistics and 270 valid questionnaires. The study’s results indicate that amenity buildings significantly increase opportunities for older adults to socialize and thereby can increase this demographic’s associated health benefits. The social activities formed around amenity buildings are found to improve social interactions and connectedness among older adults more compared to other age groups. Elderly participation in social activities is also found to positively correlate with environmental characteristics. High-quality landscapes ensure healthy development of social activities within amenity buildings and promote the occurrence and continuation of social interactions. In order of highest to lowest impact on elderly activities, the following factors were identified and scored: amenity building scale, lighting, comprehensive surrounding environment, surrounding amenities, water features, and vegetation. This research also reveals that among existing amenity buildings, there is insufficient support for certain activities and therefore, parks need to be improved to address this deficiency. Overall, this study indicates that under China’s current aging trends, amenity buildings have become an especially important infrastructure within urban public space, and their design trend is to incorporate the dual characteristics of “recreation + society”.
Psychometric properties of Meaningful Activity Participation Assessment (MAPA) in chronic stroke survivors

ABSTRACT Background Meaningful Activity Participation Assessment (MAPA) is an appropriate tool for assessing both objective and subjective aspects of participation. Objectives This study aimed to investigate the psychometric properties of MAPA in chronic stroke survivors. Methods Translation of MAPA was done according to the standard protocol of forward-backward translation. One hundred and seven chronic stroke survivors participated in this study. In addition to the MAPA, they were assessed by Satisfaction With Life Scale (SWLS), Center for Epidemiologic Studies of Depression Scale (CES-D), Life Satisfaction Index-Z (LSI-Z), Purpose in Life Test-Short Form (PIL-SF), and 36-Item Short-Form Survey (SF-36). To investigate the test-retest reliability, 37 participants were reassessed by MAPA after two weeks. Reliability, construct and known-groups validity were evaluated for MAPA. Results The results showed an acceptable internal consistency (Cronbach’s α = 0.79) and good test-retest reliability (ICC = 0.92) of MAPA. A significant moderate to high correlation was found between the MAPA and PIL-SF, CES-D, LSI-Z, SWLS, and different subscales of SF-36 (r = 0.32–0.65). MAPA showed good ability to differentiate between young adults (age≤ 65 years) and older adults (age> 65 years) with chronic stroke (P = .005) as well as between chronic stroke survivors with different levels of disability (P < .001). Conclusions The MAPA has appropriate reliability and validity in chronic stroke survivors and is suggested to be used in research and clinical settings.
Frailty of Māori, Pasifika, and non-Māori/non-Pasifika older people in New Zealand: a national population study of older people referred for home care services.

BACKGROUND Little is known about the prevalence of frailty in indigenous populations. We developed a frailty index for older New Zealand Māori and Pasifika who require publicly funded support services. METHODS A frailty index (FI) was developed for New Zealand adults aged ≥65 years who had an interRAI-Home Care assessment between 1 June 2012 and 30 October 2015. A frailty score for each participant was calculated by summing the number of deficits recorded and dividing by the total number of possible deficits. This created a FI with a potential range from 0 to 1. Linear regression models for FIs with ethnicity were adjusted for age and sex. Cox proportional hazards models were used to assess the association between the FI and mortality for Māori, Pasifika, and non-Māori/non-Pasifika. RESULTS Of 54,345 participants, 3,096 (5.7%) identified as Māori, 1,846 (3.4%) were Pasifika, and 49,415 (86.7%) identified as neither Māori nor Pasifika. New Zealand Europeans (48,178, 97.5%) constituted most of the latter group. Within each sex, the mean FIs for Māori and Pasifika were greater than the mean FIs for non-Māori and non-Pasifika, with the difference being more pronounced in females. The FI was associated with mortality (Māori SHR 2.53, 95% CI 1.63 to 3.95; Pasifika SHR 6.03, 95% CI 3.06 to 11.90; non-Māori and non-Pasifika SHR 2.86, 95% 2.53 to 3.25). CONCLUSIONS This study demonstrated differences in FI between the ethnicities in this select cohort. After adjustment for age and sex, increases in FI were associated with increased mortality. This suggests that FI is predictive of poor outcomes in these ethnic groups.
Relationships between perceived coach leadership and athletes’ affective states experienced during competition

ABSTRACT We examined whether coach leadership behaviours predicted the intensity and direction of positive and negative affects experiencing during competition controlling for affects experienced within two hours before competition. A total of 296 athletes (33% female and 67% male; Mage = 21.61; SD = 6.32) voluntarily participated in the study. A partial least square path modelling (PLS-PM) approach was used to examine the relationships between the study variables. The results showed that coach social support significantly positively predicted the direction of negative affects during competition controlling for pre-competitive negative affect direction. Besides, results revealed that coach democratic behaviour marginally and negatively predicted Negative Affects direction during competition whereas coach autocratic behaviour marginally and negatively predicted Positive Affects intensity. Thus, coach social support emerged as an adaptive coaching behaviour. The usefulness of a longitudinal approach might reveal the multivariate experience of affects states and the manner to handle them from a coach leadership perspective.
Osteomyelitis Due to Mycobacterium goodii in an Adolescent, United States

Osteomyelitis is a rare clinical manifestation of infection with nontuberculous mycobacteria (NTM). We report an adolescent with femoral osteomyelitis associated with prosthetic material due to an emerging pathogen, Mycobacterium goodii. Application of secA1 and 16S ribosomal RNA gene sequencing reliably determined the NTM species, enabling targeted antimicrobial therapy.
The Clinical Dose of Pretomanid: An Exposure-Response Perspective

Authors: 6 Jerry R. Nedelman – TB Alliance, New York, NY 7 8 David H. Salinger Certara Inc., Princeton, NJ; under contract with the Bill and 9 Melinda Gates Foundation 10 11 Vishak Subramoney Certara Strategic Consulting, Canada; under contract with 12 the Bill and Melinda Gates Foundation 13 14 Rob Woolson – Rho, Raleigh, NC 15 16 Karen Wade – Rho, Raleigh, NC 17 18 Mengchun Li – TB Alliance, New York, NY 19 20 Daniel Everitt – TB Alliance, New York, NY 21 22 Carl M. Mendel – TB Alliance, New York, NY 23 24 Mel Spigelman – TB Alliance, New York, NY 25 26 (corresponding author) Jerry R. Nedelman – TB Alliance# 27 Jerry.Nedelman@tballiance.org 28 AAC Accepted Manuscript Posted Online 19 October 2020 Antimicrob. Agents Chemother. doi:10.1128/AAC.01121-20 Copyright © 2020 Nedelman et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Body Fluid Biomarkers for Alzheimer’s Disease—An Up-To-Date Overview

Neurodegeneration is a highly complex process which is associated with a variety of molecular mechanisms related to ageing. Among neurodegenerative disorders, Alzheimer’s disease (AD) is the most common, affecting more than 45 million individuals. The underlying mechanisms involve amyloid plaques and neurofibrillary tangles (NFTs) deposition, which will subsequently lead to oxidative stress, chronic neuroinflammation, neuron dysfunction, and neurodegeneration. The current diagnosis methods are still limited in regard to the possibility of the accurate and early detection of the diseases. Therefore, research has shifted towards the identification of novel biomarkers and matrices as biomarker sources, beyond amyloid-β and tau protein levels within the cerebrospinal fluid (CSF), that could improve AD diagnosis. In this context, the aim of this paper is to provide an overview of both conventional and novel biomarkers for AD found within body fluids, including CSF, blood, saliva, urine, tears, and olfactory fluids.
A focus on high-lycopene tomato cultivars: horticultural performance and functional quality

Both transgenic and conventional breeding methods have been used to increase levels and diversify the profile of antioxidants in ripe tomato fruit. The high-pigment (hp) tomato mutants exemplify this approach, representing useful genetic resources to be introgressed into elite cultivars (high-lycopene cultivars) to simultaneously enhance the levels of different classes of antioxidants. Although several studies have been recently published on high-lycopene cultivars, information on their horticultural performance, processing attributes and functional quality is still scarce. In spite of the high content of lycopene, flavonoids and ascorbic acid, high-lycopene tomato cultivars are claimed to have poor horticultural performance, which limits their commercial acceptance. Therefore, the aim of this study was to review their agronomic and horticultural performance briefly as well as to review the functional quality of some recently developed high-lycopene tomato cultivars. Experiments conducted in the Mediterranean region showed that all the assayed high-lycopene tomato cultivars ('HLY02', 'HLY13', 'HLY18', 'Kalvert' and 'Lyco 2', including the latest developed lines 'HLT-F61' and 'HLT-F62') were vigorous, with an excellent dark-green foliage cover and characterized by dark-green immature fruits without morphological aberrations. Tomato yield ranged from 110 to 152 t ha-1, exceeding in some trials the yield of the elite industrial tomato cultivars ('Perfectpeel', 'Rio Grande' and 'Donald'). The average fruit weight ranged from 70 to 93 g, and soluble solids content was higher than 6 °Brix in some cases, associated with desirable titratable acidity values (0.381 for 'HLY18'). Regarding the phytochemical profiles, experiments under different geographical and environmental conditions confirmed that all tested high-lycopene cultivars were characterized by enhanced synthesis and accumulation of carotenoids, mainly lycopene and β-carotene (more than 280 and 20 mg kg-1 fw, respectively), as well as of other valuable health-promoting molecules such as phenolics, flavonoids and vitamins. Thus, the central role of high-lycopene tomato cultivars in enhancing fruit pigmentation and functional quality, summarized in this report, justifies extended efforts and breeding programs to decrease some initial adverse pleiotropic effects on their horticultural performance.
Understanding the Role of Perineuronal Nets in Developing Hippocampal Circuits in a Mouse Model of Fragile X Syndrome

Fragile X Syndrome (FXS) is a leading cause of intellectual disability and autism. It is caused by an expansion of CGG repeats that leads to hypermethylation and silencing of Fragile X Mental Retardation ( Fmr1 ) gene. Silencing of the Fmr1 gene results in the loss of Fragile X Mental retardation protein (FMRP), which can cause abnormal synaptic transmission. These deficits contribute to various FXS symptoms, including cognitive and learning impairments. However, the origins of these deficits remain unknown. Fmr1 KO mice were used in this study to understand the mechanisms of learning impairments in FXS. The FXS Fmr1 KO mouse model exhibits an excitatory-inhibitory (E/I) imbalance, which suggest abnormal synaptic functions in areas such as the hippocampus, area of the brain responsible for learning. Previous studies in Fmr1 KO mice have demonstrated an increase in levels of matrix metalloproteinase-9 (MMP-9), an extracellular enzyme that cleaves extracellular matrix (ECM), including perineuronal nets (PNNs) and can affect synaptic transmission. PNNs act as scaffolds around inhibitory neurons, such as parvalbumin (PV) positive cells, to regulate their activity. Based on this evidence, the goal of this study is to determine if there is abnormal development of PV positive cells and PNNs in the hippocampus of Fmr1 KO mice. We hypothesized that if MMP-9 levels are elevated with FXS, genetic reduction of MMP-9 may reverse the deficits. The results of this pilot study indicate reduced density of PV cells in the CA1 subfield of the hippocampus in the Fmr1 KO mice compared to the WT mice. The results of this study may provide new insight into E/I imbalance in autism spectrum disorders and into the mechanisms of abnormal hippocampal development that may lead to learning deficits in FXS. cell
Friend or Foe: Interbacterial Competition in the Nasal Cavity

Like other microbes that live on or in the human body, the bacteria that inhabit the upper respiratory tract, in particular the nasal cavity, have evolved to survive in an environment that presents a number of physical and chemical challenges; these microbes are constantly bombarded with nutritional fluctuations, changes in humidity, the presence of inhaled particulate matter (odorants and allergens), and competition with other microbes. Indeed, only a specialized set of species is able to colonize this niche and successfully contend with the host’s immune system and the constant threat from competitors. ABSTRACT Like other microbes that live on or in the human body, the bacteria that inhabit the upper respiratory tract, in particular the nasal cavity, have evolved to survive in an environment that presents a number of physical and chemical challenges; these microbes are constantly bombarded with nutritional fluctuations, changes in humidity, the presence of inhaled particulate matter (odorants and allergens), and competition with other microbes. Indeed, only a specialized set of species is able to colonize this niche and successfully contend with the host’s immune system and the constant threat from competitors. To this end, bacteria that live in the nasal cavity have evolved a variety of approaches to outcompete contenders for the limited nutrients and space; broadly speaking, these strategies may be considered a type of “bacterial warfare. ” A greater molecular understanding of bacterial warfare has the potential to reveal new approaches or molecules that can be developed as novel therapeutics. As such, there are many studies within the last decade that have sought to understand the complex polymicrobial interactions that occur in various environments. Here, we review what is currently known about the age-dependent structure and interbacterial relationships within the nasal microbiota and summarize the molecular mechanisms that are predicted to dictate bacterial warfare in this niche. Although the currently described interactions are complex, in reality, we have likely only scratched the surface in terms of a true understanding of the types of interbacterial competition and cooperation that are thought to take place in and on the human body.
Closing the Gap Between Deep Neural Network Modeling and Biomedical Decision-Making Metrics in Segmentation via Adaptive Loss Functions

Deep learning is becoming an indispensable tool for various tasks in science and engineering. A critical step in constructing a reliable deep learning model is the selection of a loss function, which measures the discrepancy between the network prediction and the ground truth. While a variety of loss functions have been proposed in the literature, a truly optimal loss function that maximally utilizes the capacity of neural networks for deep learning-based decision-making has yet to be established. Here, we devise a generalized loss function with functional parameters determined adaptively during model training to provide a versatile framework for optimal neural network-based decision-making in small target segmentation. The method is showcased by more accurate detection and segmentation of lung and liver cancer tumors as compared with the current state-of-the-art. The proposed formalism opens new opportunities for numerous practical applications such as disease diagnosis, treatment planning, and prognosis.
A Comparison of Stocking Methods for Pasture-Based Growing-Finishing Pig Production Systems

Simple Summary A sustainable pasture-based production system should provide benefits to the vegetation, soil and animals while providing means of economic support for the household that operates the system. If best management practices are implemented, this would allow the development of resilience for the pasture system and ameliorate the natural resources for present and future generations. Pasture-based pig production represents a production alternative for small scale or limited-resources farmers, offering them the possibility to brand their products. The implementation of best management practices would allow managers to reach productive and conservation goals. This study was conducted to compare the effects of continuous, rotational and strip-grazing stocking methods for growing-finishing pigs on tall fescue pastures. Stocking methods had effect on soil bulk density and some soil nutrients, vegetative ground cover, animal weight gain and feed use efficiency. The rotational and strip grazing stocking methods offer potential to improve the sustainability of pasture-based pig systems. Abstract Two alternative stocking methods (rotational and strip-grazing) were compared to continuous stocking at a stocking rate of 47 pigs ha−1 in tall fescue pastures. The research was conducted during two twelve-weeks grazing periods in North Carolina (USA). In total 144 (females and castrated males, 17.5 and 29.1 kg initial body weight) crossbred Yorkshire X Berkshire, Yorkshire/Landrace X Hampshire and Yorkshire/Landrace X Duroc pigs without nose rings were used. Greater soil bulk density and soil concentrations of NO3−, P, K, Mn, Zn and Cu were observed in paddocks managed continuously, while greater final ground cover (+22%) was recorded in paddocks managed with rotational and strip-grazing stocking methods. No differences were detected in botanical composition of the paddocks. Greater weight gains (+8.5%) were registered for rotationally managed pigs. Feed efficiency was better (+8%) for rotationally than for continuously stocked pigs, while strip-grazed pigs presented intermediate values. The results indicated the potential of both alternative stocking methods to be implemented in sustainable pasture-based pig production systems.
Streptococcus pneumoniae Serotype 12F-CC4846 and Invasive Pneumococcal Disease after Introduction of 13-Valent Pneumococcal Conjugate Vaccine, Japan, 2015–2017

To prevent invasive pneumococcal disease (IPD), pneumococcal conjugate vaccines (PCVs) have been implemented in many countries; however, many cases of IPD still occur and can be attributable to nonvaccine serotypes of Streptococcus pneumoniae. In Japan, the number of IPD cases attributable to serotype 12F increased from 4.4% in 2015 to 24.6% in 2017 after 13-valent PCV was introduced. To clarify the associated genetic characteristics, we conducted whole-genome sequencing of 75 serotype 12F isolates. We identified 2 sequence types (STs) among the isolates: ST4846, which was the major type, and ST6945. Bayesian analysis suggested that these types diverged in »1942. Among serotype 12F-ST4846, we identified a major cluster, PC-JP12F, whose time of most recent common ancestor was estimated to be »2012. A phylogeographic analysis demonstrated that PC-JP12F isolates spread from the Kanto region, the most populated region in Japan, to other local regions.
Evaluation of the Yeast Schizosaccharomyces japonicus for Use in Wine Production

Schizosaccharomyces japonicus UCD2489 was evaluated for potential use as a starter culture in wine-making. Laboratory-scale fermentations of Trebbiano grape juice were set up to compare fermentation kinetics of pure cultures of Sch. japonicus, immobilized Sch. japonicus cells, a commercial strain of Saccharomyces cerevisiae (EC1118), and mixed cultures of both species. The fermentation kinetics of the sequential and coinoculated fermentations were largely driven by the presence of S. cerevisiae. UCD2489 cell immobilization resulted in a significant reduction in ethanol levels in mixed fermentations compared with EC1118. Acetic acid levels similar to those of EC1118 in pure culture were produced when fermentations were coinoculated. The ability of UCD2489 to consume malic acid was adversely affected by EC1118, particularly in the coinoculated fermentation, suggesting that acid levels could be manipulated by adjusting the relative ratios of the two yeasts and the timing of inoculation with S. cerevisiae. Depending upon the inoculation conditions used, Sch. japonicus produced a quantity of glycerol ~2-fold higher than those released by S. cerevisiae. The analyses of volatile compounds showed increases in aroma-impacting compounds such as ethyl acetate in all Sch. japonicus wines, and acetaldehyde in the free-cell coinoculated fermentation that exceed reported sensory thresholds for these compounds, and for other important aroma compounds such as isoamyl acetate, hexyl acetate, phenyl ethyl acetate, ethyl isobutyrate, and ethyl butyrate. Polysaccharide release by UCD2489 was ~4.7-fold greater than that of S. cerevisiae alone. Reduction of induced wine protein haze was correlated with the concentration of polysaccharides. Our findings suggest that Sch. japonicus could be useful in wine production to reduce acidity and final ethanol levels and to increase glycerol, volatile compounds, and active polysaccharides with potential beneficial enhancement of protein stability.