Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Transcriptomic Regulation in Sweet Orange Fruit (Citrus sinensis L. Osbeck) Following Dehydration and Rehydration Conditions Leading to Peel Damage

Water stress is the most important environmental agent that contributes to the crop productivity and quality losses globally. In citrus, water stress is the main driver of the fruit peel disorders that impact the quality and market ability. An increasingly present post-harvest peel disorder is non-chilling peel pitting (NCPP). Non-chilling peel pitting is manifested as collapsed areas of flavedo randomly scattered on the fruit and its incidence increases due to abrupt increases in the environmental relative humidity (RH) during post-harvest fruit manipulation. In this study, we have used a custom-made cDNA microarray containing 44k unigenes from Citrus sinensis (L. Osbeck), covering for the first time the whole genome from this species, to study transcriptomic responses of mature citrus fruit to water stress. In the study, the global gene expression profiles of flavedo from Navelate oranges subjected to severe water stress are compared with those fruits subjected to rehydration stress provoked by changes in the RH during post-harvest, which enhances the development of NCPP. The study results show that NCPP is a complex physiological process that shares molecular responses with those from prolonged dehydration in fruit, but the damage associated with NCPP may be explained by unique features of rehydration stress at the molecular level, such as membrane disorganization, cell wall modification, and proteolysis.
Increasing Establishment of Non-native Fish Species in the Seine River Basin: Insights From Medium- and Long-Term Approaches

The spread of non-native species is nowadays recognized as a major threat to the biodiversity of freshwater ecosystems. However, for a very long time the introduction and acclimatization of new species has been perceived mainly as a source of wealth for human societies. Here, we examined the establishment of non-native fish species in the Seine River basin from a historical perspective by adopting a twofold approach. In a first step, at the whole basin scale, considering various written and archeological sources, we traced the chronology, over the last millennium, of the establishments of non-native species. In a second step, by analyzing fish monitoring from several hundred sites covering the diversity of rivers and streams, we examined the changes in numbers and abundance of non-native species in local fish communities over the last three decades. The first documented species introduction dates back to the 13th century but it is from the middle of the 19th century that the introduction attempts accelerated. Today, these introductions have reached an unprecedented level and 46% of the species recorded in the basin are non-native. During the last three decades, non-native species have continued to increase within fish communities both in terms of number of species and abundance of individuals. The most pronounced increases are noted on large rivers and sites where anthropic pressures are strong. Waterways connecting European basins, globalization of trade, and ongoing climate change provide a general background suggesting that the increase in the proportion of non-native species in the fish communities of the Seine River basin is likely to continue for several decades.
Acute Impacts of Different Types of Exercise on Circulating α-Klotho Protein Levels

Introduction: Elevated plasma α-klotho (αKl) protects against several ageing phenotypes and has been proposed as a biomarker of a good prognosis for different diseases. The beneficial health effects of elevated plasma levels of soluble αKl (SαKl) have been likened to the positive effects of exercise on ageing and chronic disease progression. It has also been established that molecular responses and adaptations differ according to exercise dose. The aim of this study is to compare the acute SαKl response to different exercise interventions, cardiorespiratory, and strength exercise in healthy, physically active men and to examine the behavior of SαKl 72h after acute strength exercise. Methods: In this quasi-experimental study, plasma SαKl was measured before and after a cardiorespiratory exercise session (CR) in 43 men, and strength exercise session (ST) in 39 men. The behavior of SαKl was also examined 24, 48, and 72h after ST. Results: Significant differences (time×group) were detected in SαKl levels (p=0.001; d=0.86) between CR and ST. After the ST intervention, SαKl behavior varied significantly (p=0.009; d=0.663) in that levels dropped between pre- and post-exercises (p=0.025; d=0.756) and were also significantly higher compared to pre ST values at 24h (p=0.033; d=0.717) and at 48h (p=0.015; d=0.827). Conclusions: SαKl levels increased in response to a single bout of cardiorespiratory exercise; while they decreased immediately after strength exercise, levels were elevated after 24h indicating different klotho protein responses to different forms of exercise.
Presence of Meaning in Life in Older Men and Women: The Role of Dimensions of Frailty and Social Support

Presence of meaning in life is an important component of eudemonic wellbeing while aging. While subjective health and interpersonal relationships are among important sources of meaning for older adults, less research has explored the gender differences in the potential contribution of these sources to the presence of meaning in late life. The current study aims to examine the associations of frailty dimensions (daily activities, health problems, and psychosocial functioning) and social support with the presence of meaning in late life, and whether these associations differ for older men and women. The study employs the data from the 65+ and Safe Study – a cross-sectional survey of residents of senior apartments. The data were collected in 2019 in a mid-sized Swedish municipality (N=618; age range from 64 to 106years, 60.5% female). Results showed significant associations of health problems, psychosocial functioning, and social support with the presence of meaning in life. Further, the results demonstrated no statistically significant gender differences in the associations between frailty dimensions, social support, and presence of meaning. However, since the interaction between health problems and gender approached statistical significance, this association was further explored indicating a more detrimental role of health problems in relation to the presence of meaning in life among older men than among older women. Overall, the study highlights the importance of physical and psychosocial health and social support for the presence of meaning in life among older adults and warrants further research on possible gender differences in the relation between health problems and meaning in late life.
Editorial: Humans in an Animal's World—How Non-human Animals Perceive and Interact With Humans

Whilst humans undisputedly shape and transform most of earth’s habitats, the number of animals (captive and wild) living on this planet far outnumbers that of humans. Humans, therefore, inevitably interact with different animals in a variety of contexts: we keep them for companionship, farm them for their products, use them for biomedical research, house them in zoos and sanctuaries, and interact with animals in the wild. How humans engage in these interactions has been extensively debated in areas such as ethics, sociology, and psychology. Given the rise of animal welfare concerns over the last decades, but also our growing interest in understanding the minds of non-human animals, there is now a strong demand to shift from a rather traditional anthropocentric view and focus on how animals themselves perceive and interact with humans in this variety of contexts. Over a range of fields, such as psychology, ethology and animal welfare science, questions on how non-human animals acquire knowledge about humans, how this knowledge is generalised and how it can spread socially are of increasing relevance to mediating conflicts arising from human-animal interactions across different settings (Bensky et al., 2013; Nawroth et al., 2019). This is the focus of this Frontiers Research Topic. This Research Topic comprises 18 articles, including state-of-the-art empirical work as well as review articles concerning the role of humans in the sensory and cognitive world of non-human animals, either in captivity or in the wild. It provides discussions on the applied implementation of these findings (e.g., for conservation attempts or farmed animal husbandry management) and considerations of future interdisciplinary approaches and applications.
Convergent Loss of the Necroptosis Pathway in Disparate Mammalian Lineages Shapes Viruses Countermeasures

Programmed cell death is a vital process in the life cycle of an organism. Necroptosis, an evolutionary restricted form of programmed necrosis, contributes to the innate immune response by killing pathogen-infected cells. This virus-host interaction pathway is organized around two key components: the receptor-interacting protein kinase 3 (RIPK3), which recruits and phosphorylates the mixed lineage kinase-like protein (MLKL), thus inducing cellular plasma membrane rupture and cell death. Critically, the presence of necroptotic inhibitors in viral genomes validates necroptosis as an important host defense mechanism. Here, we show, counterintuitively, that in different mammalian lineages of mammalian, central components of the necroptotic pathway, such as RIPK3 and MLKL genes, are deleted or display inactivating mutations. Frameshifts or premature stop codons are observed in all the studied species of cetaceans and leporids. In carnivores’ genomes, the MLKL gene is deleted, while in a small number of species from afrotheria and rodentia premature stop codons are observed in RIPK3 and/or MLKL. Interestingly, we also found a strong correlation between the disruption of necroptosis in leporids and cetaceans and the absence of the C-terminal domain of E3-like homologs (responsible for necroptosis inhibition) in their naturally infecting poxviruses. Overall, our study provides the first comprehensive picture of the molecular evolution of necroptosis in mammals. The loss of necroptosis multiple times during mammalian evolution highlights the importance of gene/pathway loss for species adaptation and suggests that necroptosis is not required for normal mammalian development. Moreover, this study highlights a co-evolutionary relationship between poxviruses and their hosts, emphasizing the role of host adaptation in shaping virus evolution.
Distribution Patterns of Ciliate Diversity in the South China Sea

Ciliates are abundant microplankton that are widely distributed in the ocean. In this paper, the distribution patterns of ciliate diversity in the South China Sea (SCS) were analyzed by compiling community data from previous publications. Based on morphological identification, a total of 592 ciliate species have been recorded in the SCS. The ciliate communities in intertidal, neritic and oceanic water areas were compared in terms of taxonomy, motility and feeding habit composition, respectively. Significant community variation was revealed among the three areas, but the difference between the intertidal area and the other two areas was more significant than that between neritic and oceanic areas. The distributions of ciliates within each of the three areas were also analyzed. In the intertidal water, the community was not significantly different among sites but did differ among habitat types. In neritic and oceanic areas, the spatial variation of communities among different sites was clearly observed. Comparison of communities by taxonomic and ecological traits (motility and feeding habit) indicated that these traits similarly revealed the geographical pattern of ciliates on a large scale in the SCS, but to distinguish the community variation on a local scale, taxonomic traits has higher resolution than ecological traits. In addition, we assessed the relative influences of environmental and spatial factors on assembly of ciliate communities in the SCS and found that environmental selection is the major process structuring the taxonomic composition in intertidal water, while spatial processes played significant roles in influencing the taxonomic composition in neritic and oceanic water. Among ecological traits, environmental selection had the most important impact on distributions.
Metabolic Switch and Cytotoxic Effect of Metformin on Burkitt Lymphoma

Altered cellular energetic metabolism has recently emerged as important feature of neoplastic cells. Indeed, interfering with cancer cell metabolism might represent a suitable therapeutic strategy. In this study, we aimed to assess glucose metabolism activation in human lymphomas and evaluate how metformin can exert its action on lymphoma cells. We studied a large series of human lymphomas (N = 252) and an in vitro model of Burkitt lymphoma (BL) cells. We combined molecular biology techniques, including global gene expression profiling (GEP) analysis, quantitative PCR (qPCR) and Western blotting, and biochemical assays, aimed to assess pentose phosphate pathway, tricarboxylic acid (TCA) cycle, and aerobic glycolysis rates. We found that glucose metabolism is overall enhanced in most lymphoma subtypes, based on gene expression profiling (GEP), with general shift to aerobic glycolysis. By contrast, normal B cells only showed an overall increase in glucose usage during germinal center transition. Interestingly, not only highly proliferating aggressive lymphomas but also indolent ones, like marginal zone lymphomas, showed the phenomenon. Consistently, genes involved in glycolysis were confirmed to be overexpressed in BL cells by qPCR. Biochemical assays showed that while aerobic glycolysis is increased, TCA cycle is reduced. Finally, we showed that metformin can induce cell death in BL cells by stressing cellular metabolism through the induction of GLUT1, PKM2, and LDHA. In conclusion, we unveiled glucose metabolism abnormalities in human lymphomas and characterized the mechanism of action of metformin in Burkitt lymphoma model.
Social Network Analysis Reveals the Subtle Impacts of Tourist Provisioning on the Social Behavior of a Generalist Marine Apex Predator

Shark dive ecotourism is a lucrative industry in many regions around the globe. In some cases, sharks are provisioned using bait, prompting increased research on how baited dives influence shark behavior and yielding mixed results. Effects on patterns of habitat use and movement seemly vary across species and locations. It is unknown, however, whether wide-ranging, marine apex predators respond to provisioning by changing their patterns of grouping or social behavior. We applied a tiered analytical approach (aggregation-gregariousness-social preferences) examining the impact of provisioning on the putative social behavior of tiger sharks (Galeocerdo cuvier) at a dive tourism location in The Bahamas. Using network inference on three years of acoustic tracking data from 48 sharks, we tested for non-random social structure between non-provisioned and provisioned monitoring sites resulting in 12 distinct networks. Generally considered a solitary nomadic predator, we found evidence of sociality in tiger sharks, which varied spatiotemporally. We documented periods of both random (n = 7 networks) and non-random aggregation (n = 5 networks). Three of five non-random aggregations were at locations unimpacted by provisioning regardless of season, one occurred at an active provisioning site during the dry season and one at the same receivers during the wet season when provision activity is less prevalent. Aggregations lasted longer and occurred more frequently at provisioning sites, where gregariousness was also more variable. While differences in gregariousness among individuals was generally predictive of non-random network structure, individual site preferences, size and sex were not. Within five social preference networks, constructed using generalized affiliation indices, network density was lower at provisioning sites, indicating lower connectivity at these locations. We found no evidence of size assortment on preferences. Our data suggest that sociality may occur naturally within the Tiger Beach area, perhaps due to the unusually high density of individuals there. This study demonstrates the existence of periodic social behavior, but also considerable variation in association between tiger sharks, which we argue may help to mitigate any long-term impacts of provisioning on this population. Finally, we illustrate the utility of combining telemetry and social network approaches for assessing the impact of human disturbance on wildlife behavior.
Goldilocks Principle: Preference for Change in Breast Size in Breast Cancer Reconstruction Patients

Patients’ preferences regarding changing or maintaining their breast size after mastectomy and reconstruction are important but understudied determinants of post-surgical satisfaction and quality of life. The goal of this study was to identify factors associated with preferences for changing or maintaining breast size for women undergoing breast reconstruction at The University of Texas MD Anderson Cancer Center in the United States from 2011 to 2014. The average age of participants was 45.7 ± 9.1 years. At baseline, mean average breast volumes were 755.7 ± 328.4 mL for all women (n = 48), 492.3 mL ± 209.3 for 13 women who preferred to be “bigger than now,” 799.2 mL ± 320.9 for 25 women who preferred to remain “about the same,” and 989.3 mL ± 253.1 for 10 women who preferred “smaller than now. ” Among the 23 women who preferred to change their breast size, 19 desired to shift toward the mean. Women with the smallest and largest 20% of baseline breast size were more likely to desire a change toward the mean (p = 0.006). Multinomial logistic regression models found average breast volume and satisfaction with breast size to be the most important factors associated with preferences for changing or maintaining breast size for women undergoing breast reconstruction. This study provides preliminary evidence for a “Goldilocks principle” in women’s preferences for breast size change in the context of breast reconstruction, and identifies hypotheses for future studies of the associations among preference for change in breast size, preference achievement, and post-reconstruction body image.
Identifying Silver Linings During the Pandemic Through Natural Language Processing

COVID-19 has presented an unprecedented challenge to human welfare. Indeed, we have witnessed people experiencing a rise of depression, acute stress disorder, and worsening levels of subclinical psychological distress. Finding ways to support individuals' mental health has been particularly difficult during this pandemic. An opportunity for intervention to protect individuals' health & well-being is to identify the existing sources of consolation and hope that have helped people persevere through the early days of the pandemic. In this paper, we identified positive aspects, or “silver linings,” that people experienced during the COVID-19 crisis using computational natural language processing methods and qualitative thematic content analysis. These silver linings revealed sources of strength that included finding a sense of community, closeness, gratitude, and a belief that the pandemic may spur positive social change. People's abilities to engage in benefit-finding and leverage protective factors can be bolstered and reinforced by public health policy to improve society's resilience to the distress of this pandemic and potential future health crises.
Crystal Structure of Mycobacterium tuberculosis Elongation Factor G1

Mycobacterium tuberculosis (Mtb) caused an estimated 10 million cases of tuberculosis and 1.2 million deaths in 2019 globally. The increasing emergence of multidrug-resistant and extensively drug-resistant Mtb is becoming a public health threat worldwide and makes the identification of anti-Mtb drug targets urgent. Elongation factor G (EF-G) is involved in tRNA translocation on ribosomes during protein translation. Therefore, EF-G is a major focus of structural analysis and a valuable drug target of antibiotics. However, the crystal structure of Mtb EF-G1 is not yet available, and this has limited the design of inhibitors. Here, we report the crystal structure of Mtb EF-G1 in complex with GDP. The unique crystal form of the Mtb EF-G1-GDP complex provides an excellent platform for fragment-based screening using a crystallographic approach. Our findings provide a structure-based explanation for GDP recognition, and facilitate the identification of EF-G1 inhibitors with potential interest in the context of drug discovery.
Comparison of Behavior-Related Features in the MMSE Sentence in Behavioral Variant Frontotemporal Dementia and Alzheimer’s Disease

Background: Despite the ubiquity of cognitive assessments using the MMSE, there has been little investigation of currently unscored features of the MMSE sentence item relevant to behavior and language in patients with behavioral variant Frontotemporal Dementia (bvFTD) and Alzheimer’s disease (AD). Objective: To describe and compare the unscored content and grammar elements of the MMSE sentence item in patients with bvFTD and AD. Methods: Categorization of predefined content and grammar elements of the MMSE sentence was performed by two blinded raters in patients with bvFTD (n = 74) and AD (n = 84). Chi-square and ANCOVAs were conducted to identify differences between the diagnostic groups. A multinomial logistic regression analysis was conducted to determine whether these features aid in the prediction of diagnosis of bvFTD or AD. Results: A higher proportion of patients with bvFTD wrote sentences addressed to the examiner (22.7% vs. 4.7%, X2 = 11.272, p = 0.001) and about interpersonal relationships (35.3% vs. 16.0%, X2 = 10.139, p = 0.017) in comparison to those with AD. The number of words written was lower in patients with AD and was positively correlated with lower total MMSE scores in AD but not in bvFTD (AD: r = 0.370, p < 0.001; FTD: r = 0.209, p = 0.07). Assessment of the MMSE sentence content and grammar variables did not add to the prediction bvFTD or AD diagnosis beyond the variance explained by age and total MoCA score. Conclusions: Patients with bvFTD and AD showed differences in aspects of the content of the written MMSE sentence item, though these differences did not aid in the diagnosis prediction.