Miracle-dz/UniFAR-FTUs huggingface dataset:
Xylocopa caerulea and Xylocopa auripennis harbor a homologous gut microbiome related to that of eusocial bees

Background Eusocial bees, such as bumblebees and honey bees, harbor host-specific gut microbiota through their social behaviors. Conversely, the gut microbiota of solitary bees is erratic owing to their lack of eusocial activities. Carpenter bees (genus Xylocopa) are long-lived bees that do not exhibit advanced eusociality like honey bees. However, they often compete for nests to reproduce. Xylocopa caerulea and Xylocopa auripennis are important pollinators of wild plants on Hainan Island. Whether they have host-specific bacteria in their guts similar to eusocial bees remains unknown. Methods We targeted the bacterial 16S rRNA V3-V4 region to investigate the diversity of bacterial symbionts in the fore-midgut and hindgut of two carpenter bees, X. caerulea and X. auripennis. Results A maximum of 4,429 unique amplicon sequence variants (ASVs) were detected from all samples, belonging to 10 different phyla. X. caerulea and X. auripennis shared similar bacterial community profiles, with Lactobacillaceae, Bifidobacteriaceae, and Orbaceae being dominant in their entire guts. X. caerulea and X. auripennis harbor a highly conserved core set of bacteria, including the genera Candidatus Schmidhempelia and Bombiscardovia. These two bacterial taxa from carpenter bees are closely related to those isolated from bumblebees. The LEfSe analysis showed that Lactobacillaceae, Bifidobacteriaceae, and the genus Bombilactobacillus were significantly enriched in the hindguts of both carpenter bees. Functional prediction suggested that the most enriched pathways were involved in carbohydrate and lipid metabolism. Conclusions Our results revealed the structure of the gut microbiota in two carpenter bees and confirmed the presence of some core bacterial taxa that were previously only found in the guts of social bees.
DCIR suppresses osteoclastic proliferation and resorption by downregulating M-CSF and RANKL signaling

Dendritic cell immunoreceptor (DCIR) is an inhibitory C-type lectin receptor that acts as a negative regulator in the immune system and bone metabolism. We previously revealed that DCIR deficiency enhanced osteoclastogenesis and antigen presentation of dendritic cells, and that asialo-biantennary N-glycan (NA2) functions as a ligand for DCIR. NA2 binding to DCIR suppressed murine and human osteoclastogenesis that occurs in the presence of M-CSF and RANKL. The DCIR-NA2 axis, therefore, plays an important role in regulating osteoclastogenesis in both mice and humans, although the underlying mechanisms remain unclear. Here we found that Dcir −/− bone marrow–derived macrophages (BMMs) exhibited greater proliferative and differentiation responses to M-CSF and RANKL, respectively, than wild-type (WT) BMMs. Moreover, Dcir −/− osteoclasts (OCs) increased resorptive activity and cell fusion more significantly than WT OCs. DCIR deficiency affects gene expression patterns in OCs, and we found that the expression of neuraminidase 4 was increased in Dcir −/− OCs. Furthermore, DCIR-NA2 interaction in WT BMMs, but not Dcir −/− BMMs, decreased Akt phosphorylation in response to M-CSF and RANKL. These data suggest that DCIR regulates osteoclastogenesis by downregulating M-CSF and RANKL signaling, and that DCIR-mediated signaling may contribute to the terminal modification of oligosaccharides by controlling the expression of glycosylation enzymes.
Oncoplastic surgery for Paget’s disease of the breast

Introduction Paget’s disease of the breast (PDB) is a rare nipple entity associated with multifocality. Due to its location, resection of the entire nipple-areolar complex is necessary. Historically central quadrantectomy and mastectomy have the surgical treatments of choice. The feasibility of oncoplastic breast surgery (OBS) for PDB is unknown. Methods This was a retrospective study performed in a Brazilian oncological hospital. We evaluated the factors related to the performance of OBS in PDB. In addition, the impact of OBS on local recurrence and survival was analysed. Comparisons were made between groups using the chi-square test, Mann−Whitney U test, and Kaplan–Meier method. To assess the impact factor of the variables on the performance of OBS, logistic regression was performed. Results Eighty-five patients were evaluated. OBS was performed in 69.4% (n=59), and of these, 16 (27.2%) were symmetrized with contralateral surgery. Mastectomy without reconstruction was performed in 28.3% of the patients. The primary procedure performed was mastectomy with reconstruction (n=38; 44.7%), and the preferential technique for immediate reconstruction was skin-sparing mastectomy with prosthesis; for late reconstruction, the preferred technique was using the latissimus dorsi. Breast conserving-surgery was performed in 27.0% (n=23), primarily using the plug-flap technique (OBS). Age was associated with the use of OBS; as patients aged 40-49 exhibited a higher rate of OBS (p = 0.002; odds ratio 3.22). OBS did not influence local recurrence (p=1.000), overall survival (p=0.185), or cancer-specific survival (p=0.418). Conclusion OBS improves options related to surgical treatment in PDB without affecting local recurrence or survival rates.
Exploring the role of gut microbiota dysbiosis in gout pathogenesis: a systematic review

Objectives Gut dysbiosis is believed to be one of the several mechanisms that are involved in the pathogenesis of gout. This systematic review aimed to summarize the role of gut dysbiosis in gout disease and uncover the underlying mechanisms. Methods A comprehensive search was conducted on PubMed, Web of Science, and Scopus databases up to October 2021. Animal studies and human observational studies, including case-control, cross-sectional, and cohort studies assessing the association between gut microbiota composition and gout were included. The quality of included studies has been evaluated using the Newcastle–Ottawa Quality Assessment scale (NOS) and the SYRCLE's risk of bias tool. Results Initially, we found 274 studies among which 15 studies were included in this systematic review. Of them, 10 studies were conducted on humans and 5 studies were conducted on animals. Increased abundance of Alistipes and decreased abundance of Enterobacteriaceae alters purine metabolism, thereby aggravating gout condition. Moreover, a higher abundance of Phascolarctobacterium and Bacteroides in gout modulates enzymatic activity in purine metabolism. Butyrate-producing bacteria such as Faecalibacterium, prausnitzii, Oscillibacter, Butyricicoccus, and Bifidobacterium have higher abundance in healthy controls compared to gout patients, suggesting the anti-inflammatory and anti-microbial role of short-chain fatty acids (SCFAs). Lipopolysaccharides (LPS)-releasing bacteria, such as Enterobacteriaceae, Prevotella, and Bacteroides, are also involved in the pathogenesis of gout disease by stimulating the innate immune system. Conclusion Exploring the role of gut dysbiosis in gout and the underlying mechanisms can help develop microbiota-modulating therapies for gout.
Crossmodal interactions in human learning and memory

Most studies of memory and perceptual learning in humans have employed unisensory settings to simplify the study paradigm. However, in daily life we are often surrounded by complex and cluttered scenes made up of many objects and sources of sensory stimulation. Our experiences are, therefore, highly multisensory both when passively observing the world and when acting and navigating. We argue that human learning and memory systems are evolved to operate under these multisensory and dynamic conditions. The nervous system exploits the rich array of sensory inputs in this process, is sensitive to the relationship between the sensory inputs, and continuously updates sensory representations, and encodes memory traces based on the relationship between the senses. We review some recent findings that demonstrate a range of human learning and memory phenomena in which the interactions between visual and auditory modalities play an important role, and suggest possible neural mechanisms that can underlie some surprising recent findings. We outline open questions as well as directions of future research to unravel human perceptual learning and memory.
COAMPS Real-Time Dust Storm Forecasting during Operation Iraqi Freedom

Abstract Dust storms are a significant weather phenomenon in the Iraq region in winter and spring. Real-time dust forecasting using the U.S. Navy’s Coupled Ocean–Atmospheric Mesoscale Prediction System (COAMPS) with an in-line dust aerosol model was conducted for Operation Iraqi Freedom (OIF) in March and April 2003. Daily forecasts of dust mass concentration, visibility, and optical depth were produced out to 72 h on nested grids of 9-, 27-, and 81-km resolution in two-way nest interaction. In this paper, the model is described, as are examples of its application during OIF. The model performance is evaluated using ground weather reports, visibility observations, and enhanced satellite retrievals. The comparison of the model forecasts with observations for the severe dust storms of OIF shows that COAMPS predicted the arrival and retreat of the major dust events within 2 h. In most cases, COAMPS predicted the intensity (reduction in visibility) of storms with an error of less than 1 km. The forecasts of t.
Selection on female reproductive schedules in the marula fly, Ceratitis cosyra (Diptera: Tephritidae) affects dietary optima for female reproductive traits but not lifespan

Introduction A changing environment can select on life-history traits and trade-offs in a myriad of ways. For example, global warming may shift phenology and thus the availability of host-plants. This may alter selection on survival and fertility schedules in herbivorous insects. If selection on life-histories changes, this may in turn select for altered nutrient intake, because the blend of nutrients organisms consume helps determine the expression of life-history traits. However, we lack empirical work testing whether shifts in the timing of oviposition alter nutrient intake and life-history strategies. Methods We tested in the marula fruit fly, Ceratitis cosyra, how upward-selection on the age of female oviposition, in comparison with laboratory adapted control flies, affects the sex-specific relationship between protein and carbohydrate intake and life-history traits including lifespan, female lifetime egg production and daily egg production. We then determined the macronutrient ratio consumed when flies from each selection line and sex were allowed to self-regulate their intake. Results Lifespan, lifetime egg production and daily egg production were optimised at similar protein to carbohydrate (P:C) ratios in flies from both selection lines. Likewise, females and males of both lines actively defended similar nutrient intake ratios (control =1:3.6 P:C; upward-selected = 1:3.2 P:C). Discussion Our results are comparable to those in non-selected C. cosyra, where the optima for each trait and the self-selected protein to carbohydrate ratio observed were nearly identical. The nutrient blend that needs to be ingested for optimal expression of a given trait appeared to be well conserved across laboratory adapted and experimentally selected populations. These results suggest that in C. cosyra, nutritional requirements do not respond to a temporal change in oviposition substrate availability.
Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data

When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies.
Influence of the casing layer on the specific volatile compounds and microorganisms by Agaricus bisporus

One of the major variables affecting yield of the mushroom Agaricus bisporus is the casing layer, which directly affects the productivity and mass. Here, volatile organic compounds were extracted by headspace solid-phase microextraction and high-throughput sequencing was used to analyze the microbial community diversity. The relationship between mushroom yield at different cropping stages and the contents of volatile organic compounds and microorganisms in three different casing layers: peat, peat + soil and soil were systematically evaluated. The result shows that Benzaldehyde and (E)-2-octenal which stimulate yield, obviously increased as mushrooms grew, while 3-octanone, which inhibits yield, decreased over time in all three casing layers. However, there was not a strong correlation between the concentration of volatile compounds and yield. In addition, more than 3,000 bacterial operational taxonomic units (OTUs) by performing high throughput sequencing of the microbes were obtained in the three casing layers. Interestingly, the microbial community compositions were very similar between the three casing layers at a later cropping stage, but the community richness varied significantly in different casing layers and at different cropping stages. At the phylum level, the communities had similar structures but were quantitively very different, and this was even more obvious at the genus level. Principal component analysis revealed significant alterations in microbial community structure in different casing layers. Sphingomonas, Dongia and Achromobacter were the dominant genera at cropping stage 1, and the stage 3 were abundant in Saccharibacteria_norank, Pseudomonas, Flavobacterium and Brevundimonas, which was positively correlated with yield, while the abundance of Pseudomonas at stage 1 and Lactococcus and Bacillus at stage 3 was negatively correlated with yield. These results provide a guide for the development and agricultural application of microbial agents for yield improvement in the production of A. bisporus.
How the rise of academic families across cohorts influences sons’ and daughters’ tertiary education in West Germany?

In this article, we examine how the rising proportion of academic families across cohorts affects sons’ and daughters’ tertiary educational attainment in the process of educational expansion. Using data from the National Educational Panel Study (NEPS), we focus on West Germany and examine whether the upgrading of the educational composition of families across cohorts has particularly contributed to daughters catching up with and even overtaking sons in tertiary educational attainment over time, or whether daughters and sons have benefited equally. In particular, we ask whether the rise of academic families, who are assumed to have stronger gender-egalitarian attitudes toward their children, has contributed to daughters faster increase in tertiary education compared to sons. Our empirical analysis shows that the long-term upgrading of families’ education across cohorts has in a similar manner increased tertiary educational attainment of both sons and daughters. Thus, women’s educational catch-up process cannot be explained by the greater gender-egalitarian focus of academic parents. Rather all origin families, independent of their educational level, are following the same secular trend toward more gender egalitarianism. We also examine to which extent highly qualified mothers serve as role models for their daughters. We find that academic mothers do not serve as particular role models for their daughters. Rather mother’s education is equally important for both sons’ and daughters’ success in higher education. Finally, we show that the rising proportion of academic families across cohorts is connected to a rising proportion of downward mobility for both sons and daughters. However, the share of upward mobile daughters from non-academic families is converging with that of sons.
Size regulation of the lateral organ initiation zone and its role in determining cotyledon number in conifers

Introduction Unlike monocots and dicots, many conifers, particularly Pinaceae, form three or more cotyledons. These are arranged in a whorl, or ring, at a particular distance from the embryo tip, with cotyledons evenly spaced within the ring. The number of cotyledons, nc , varies substantially within species, both in clonal cultures and in seed embryos. nc variability reflects embryo size variability, with larger diameter embryos having higher nc . Correcting for growth during embryo development, we extract values for the whorl radius at each nc . This radius, corresponding to the spatial pattern of cotyledon differentiation factors, varies over three-fold for the naturally observed range of nc . The current work focuses on factors in the patterning mechanism that could produce such a broad variability in whorl radius. Molecularly, work in Arabidopsis has shown that the initiation zone for leaf primordia occurs at a minimum between inhibitor zones of HD-ZIP III at the shoot apical meristem (SAM) tip and KANADI (KAN) encircling this farther from the tip. PIN1-auxin dynamics within this uninhibited ring form auxin maxima, specifying primordia initiation sites. A similar mechanism is indicated in conifer embryos by effects on cotyledon formation with overexpression of HD-ZIP III inhibitors and by interference with PIN1-auxin patterning. Methods We develop a mathematical model for HD-ZIP III/KAN spatial localization and use this to characterize the molecular regulation that could generate (a) the three-fold whorl radius variation (and associated nc variability) observed in conifer cotyledon development, and (b) the HD-ZIP III and KAN shifts induced experimentally in conifer embryos and in Arabidopsis. Results This quantitative framework indicates the sensitivity of mechanism components for positioning lateral organs closer to or farther from the tip. Positional shifting is most readily driven by changes to the extent of upstream (meristematic) patterning and changes in HD-ZIP III/KAN mutual inhibition, and less efficiently driven by changes in upstream dosage or the activation of HD-ZIP III. Sharper expression boundaries can also be more resistant to shifting than shallower expression boundaries. Discussion The strong variability seen in conifer nc (commonly from 2 to 10) may reflect a freer variation in regulatory interactions, whereas monocot (nc = 1) and dicot (nc = 2) development may require tighter control of such variation. These results provide direction for future quantitative experiments on the positional control of lateral organ initiation, and consequently on plant phyllotaxy and architecture.
AGE-RAGE axis culminates into multiple pathogenic processes: a central road to neurodegeneration

Advanced glycation end-products (AGEs; e.g., glyoxal, methylglyoxal or carboxymethyl-lysine) are heterogenous group of toxic compounds synthesized in the body through both exogenous and endogenous pathways. AGEs are known to covalently modify proteins bringing about loss of functional alteration in the proteins. AGEs also interact with their receptor, receptor for AGE (RAGE) and such interactions influence different biological processes including oxidative stress and apoptosis. Previously, AGE-RAGE axis has long been considered to be the maligning factor for various human diseases including, diabetes, obesity, cardiovascular, aging, etc. Recent developments have revealed the involvement of AGE-RAGE axis in different pathological consequences associated with the onset of neurodegeneration including, disruption of blood brain barrier, neuroinflammation, remodeling of extracellular matrix, dysregulation of polyol pathway and antioxidant enzymes, etc. In the present article, we attempted to describe a new avenue that AGE-RAGE axis culminates to different pathological consequences in brain and therefore, is a central instigating component to several neurodegenerative diseases (NGDs). We also invoke that specific inhibitors of TIR domains of TLR or RAGE receptors are crucial molecules for the therapeutic intervention of NGDs. Clinical perspectives have also been appropriately discussed.
Signaling – transcription interactions in mouse retinal ganglion cells early axon pathfinding –a literature review

Sending an axon out of the eye and into the target brain nuclei is the defining feature of retinal ganglion cells (RGCs). The literature on RGC axon pathfinding is vast, but it focuses mostly on decision making events such as midline crossing at the optic chiasm or retinotopic mapping at the target nuclei. In comparison, the exit of RGC axons out of the eye is much less explored. The first checkpoint on the RGC axons’ path is the optic cup - optic stalk junction (OC-OS). OC-OS development and the exit of the RGC pioneer axons out of the eye are coordinated spatially and temporally. By the time the optic nerve head domain is specified, the optic fissure margins are in contact and the fusion process is ongoing, the first RGCs are born in its proximity and send pioneer axons in the optic stalk. RGC differentiation continues in centrifugal waves. Later born RGC axons fasciculate with the more mature axons. Growth cones at the end of the axons respond to guidance cues to adopt a centripetal direction, maintain nerve fiber layer restriction and to leave the optic cup. Although there is extensive information on OC-OS development, we still have important unanswered questions regarding its contribution to the exit of the RGC axons out of the eye. We are still to distinguish the morphogens of the OC-OS from the axon guidance molecules which are expressed in the same place at the same time. The early RGC transcription programs responsible for axon emergence and pathfinding are also unknown. This review summarizes the molecular mechanisms for early RGC axon guidance by contextualizing mouse knock-out studies on OC-OS development with the recent transcriptomic studies on developing RGCs in an attempt to contribute to the understanding of human optic nerve developmental anomalies. The published data summarized here suggests that the developing optic nerve head provides a physical channel (the closing optic fissure) as well as molecular guidance cues for the pioneer RGC axons to exit the eye.