Miracle-dz/UniFAR-FTUs huggingface dataset:
Running throughout Middle-Age Keeps Old Adult-Born Neurons Wired

Abstract Exercise may prevent or delay aging-related memory loss and neurodegeneration. In rodents, running increases the number of adult-born neurons in the dentate gyrus (DG) of the hippocampus, in association with improved synaptic plasticity and memory function. However, it is unclear whether adult-born neurons remain fully integrated into the hippocampal network during aging and whether long-term running affects their connectivity. To address this issue, we labeled proliferating DG neural progenitor cells with retrovirus expressing the avian TVA receptor in two-month-old sedentary and running male C57Bl/6 mice. More than six months later, we injected EnvA-pseudotyped rabies virus into the DG as a monosynaptic retrograde tracer, to selectively infect TVA expressing “old” new neurons. We identified and quantified the direct afferent inputs to these adult-born neurons within the hippocampus and (sub)cortical areas. Here, we show that long-term running substantially modifies the network of the neurons generated in young adult mice, upon middle-age. Exercise increases input from hippocampal interneurons onto “old” adult-born neurons, which may play a role in reducing aging-related hippocampal hyperexcitability. In addition, running prevents the loss of adult-born neuron innervation from perirhinal cortex, and increases input from subiculum and entorhinal cortex, brain areas that are essential for contextual and spatial memory. Thus, long-term running maintains the wiring of “old” new neurons, born during early adulthood, within a network that is important for memory function during aging.
Gas chromatography–mass spectrometric determination of bisphenol residues by dispersive solid phase extraction followed by activated carbon spheres cleanup from fish feed samples

Bisphenols are known endocrine disruptors commonly utilized in food packaging and storage materials, which frequently come into touch with multiple food products packed in them. The bisphenols in fish feed and other feed materials for aquatic organisms are harmful. The consumption of such marine foods is hazardous. Hence, the feed of aquatic products needs to be verified for the presence of bisphenols. The present study was focused on developing and validating a rapid, selective, and sensitive method to quantify 11 bisphenols from the fish feed with dispersive solid-phase extraction, which was cleaned by an optimized amount of activated carbon spheres and silylated by N,O-bis(trimethylsilyl)trifluoro acetamide and analyzed by gas chromatography–mass spectrometry. The new method was rigorously tested and verified after carefully tuning various parameters affecting analyte recovery. Limit of detection (LOD) were set at 0.5–5 ng/g and limit of quantification (LOQ) at 1–10 ng/g, respectively, resulting in 95–114% recoveries. Interday and intraday precisions in terms of relative standard deviation were found to be less than 11%. The proposed approach was effectively applied in floating and sinking fish feeds. The obtained results showed that higher concentration of bisphenol A, followed by bisphenol TMC, and bisphenol M at a concentration of 256.10, 159.01, and 168.82 ng/g in floating feed and 88.04, 200.79, and 98.03 ng/g in sinking feed samples, respectively.
Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation

Antibiotic resistance is a persistent problem in health care and a factor that may help maintain bacterial diversity in natural environments. Bacteriophages (“phages”) are viruses that specifically infect bacteria. ABSTRACT Bacteriophages have received recent attention for their therapeutic potential to treat antibiotic-resistant bacterial infections. One particular idea in phage therapy is to use phages that not only directly kill their bacterial hosts but also rely on particular bacterial receptors, such as proteins involved in virulence or antibiotic resistance. In such cases, the evolution of phage resistance would correspond to the loss of those receptors, an approach termed evolutionary steering. We previously found that during experimental evolution, phage U136B can exert selection pressure on Escherichia coli to lose or modify its receptor, the antibiotic efflux protein TolC, often resulting in reduced antibiotic resistance. However, for TolC-reliant phages like U136B to be used therapeutically, we also need to study their own evolutionary potential. Understanding phage evolution is critical for the development of improved phage therapies as well as the tracking of phage populations during infection. Here, we characterized phage U136B evolution in 10 replicate experimental populations. We quantified phage dynamics that resulted in five surviving phage populations at the end of the 10-day experiment. We found that phages from all five surviving populations had evolved higher rates of adsorption on either ancestral or coevolved E. coli hosts. Using whole-genome and whole-population sequencing, we established that these higher rates of adsorption were associated with parallel molecular evolution in phage tail protein genes. These findings will be useful in future studies to predict how key phage genotypes and phenotypes influence phage efficacy and survival despite the evolution of host resistance. IMPORTANCE Antibiotic resistance is a persistent problem in health care and a factor that may help maintain bacterial diversity in natural environments. Bacteriophages (“phages”) are viruses that specifically infect bacteria. We previously discovered and characterized a phage called U136B, which infects bacteria through TolC. TolC is an antibiotic resistance protein that helps bacteria pump antibiotics out of the cell. Over short timescales, phage U136B can be used to evolutionarily “steer” bacterial populations to lose or modify the TolC protein, sometimes reducing antibiotic resistance. In this study, we investigate whether U136B itself evolves to better infect bacterial cells. We discovered that the phage can readily evolve specific mutations that increase its infection rate. This work will be useful for understanding how phages can be used to treat bacterial infections.
Therapeutic potential of phytochemicals for cystic fibrosis

The aim of this review was to review and discuss various phytochemicals that exhibit beneficial effects on mutated membrane channels, and hence, improve transmembrane conductance. These therapeutic phytochemicals may have the potential to decrease mortality and morbidity of CF patients. Four databases were searched using keywords. Relevant studies were identified, and related articles were separated. Google Scholar, as well as gray literature (i.e., information that is not produced by commercial publishers), were also checked for related articles to locate/identify additional studies. The relevant databases were searched a second time to ensure that recent studies were included. In conclusion, while curcumin, genistein, and resveratrol have demonstrated effectiveness in this regard, it should be emphasized that coumarins, quercetin, and other herbal medicines also have beneficial effects on transporter function, transmembrane conductivity, and overall channel activity. Additional in vitro and in vivo studies should be conducted on mutant CFTR to unequivocally define the mechanism by which phytochemicals alter transmembrane channel function/activity, since the results of the studies evaluated in this review have a high degree of heterogenicity and discrepancy. Finally, continued research be undertaken to clearly define the mechanism(s) of action and the therapeutic effects that therapeutic phytochemicals have on the symptoms observed in CF patients in an effort to reduce mortality and morbidity.
Investigation on the Prestage of a Water Hydraulic Jet Pipe Servo Valve Based on CFD

In a water hydraulic jet pipe servo valve, the overall performance of the valve is directly influenced by the structure dimension of the receiver and the prestage— jet pipe amplifier. This paper deals with the influence rules of the structure dimension parameters and performance parameters on the buildup pressure in the two receiving holes, including the vertical clearance between the nozzle and the receiver, the diameter of the nozzle hole, the diameter of the receiving orifice, and the nozzle offset distance. The best combination of structure size is finally obtained by using numerical simulation, computer emulation and experiment analysis methods. Then build up the finite volume analysis models about the pressure field and the speed field of the jet pipe amplifier. Through analyzing the characteristics of the flow field, a mathematics relation between the jet nozzle offset and the pressure ratio inside the two receiver holes is established, which reveals the energy distribution and conversion mechanism. The conclusion could be an important reference for the design and research of jet pipe servo valve.
Estimation of Left Ventricular Stroke Work for Rotary Left Ventricular Assist Devices

Continuous monitoring of left ventricular stroke work (LVSW) may improve the medical management of patients with rotary left ventricular assist devices (LVAD). However, implantable pressure–volume sensors are limited by measurement drift and hemocompatibility. Instead, estimator algorithms derived from rotary LVAD signals may be a suitable alternative. An LVSW estimator algorithm was developed and evaluated in a range of in vitro and ex vivo cardiovascular conditions during full assist (closed aortic valve [AoV]) and partial assist (opening AoV) mode. For full assist, the LVSW estimator algorithm was based on LVAD flow, speed, and pump pressure head, whereas for partial assist, the LVSW estimator combined the full assist algorithm with an estimate of AoV flow. During full assist, the LVSW estimator demonstrated a good fit in vitro and ex vivo (R2: 0.97 and 0.86, respectively) with errors of ± 0.07 J. However, LVSW estimator performance was reduced during partial assist, with in vitro: R2: 0.88 and an error of ± 0.16 J and ex vivo: R2: 0.48 with errors of ± 0.11 J. Further investigations are required to improve the LVSW estimate with partial assist; however, this study demonstrated promising results for a continuous estimate of LVSW for rotary LVADs.
Periodic Traffic Prediction Algorithm of Markov Based on Normal Smooth Sequence

In order to improve the accuracy of network traffic prediction,a new traffic prediction algorithm of Markov model is proposed.The actual network traffic is decomposed into periodic sequences and normal smooth sequence,and a Markov model is established to predict the normal smooth sequence,then the prediction of the actual network traffic can be obtained by the synthesis of predictive results and periodic sequences.As shown in a set of experiments,the algorithm is of higher accuracy in comparision with the traditional prediction algorithms of ? short range dependence models.
Deriving the number of salience maps an observer has from the number and quality of concurrent centroid judgments

Significance In order to determine what in the visual field to process first, Koch and Ullman proposed the brain uses a topographical map that combines a wide range of inputs to record at each spatial location just one value—salience (likely importance). The location with the highest salience is processed first. Here, we demonstrate that the same or a similar salience map is used for centroid judgments, the judged center of a cloud of items. Following a brief flash of five different item types, all our observers were able to make five accurate concurrent centroid judgments. This indicates that our observers each have at least five concurrently available salience maps, an unexpected visual information processing capacity of the brain.
Left Behind: Medicaid Immigrant Exclusions and Access to Maternal Health Care Across the Reproductive-Perinatal Continuum

Noncitizen immigrants are often excluded from accessing critical safety-net programs, such as Medicaid. Access to health care plays a central role in current policy debates on maternal health. Yet, immigrant exclusions are rarely considered in maternal health policy research. Through open-ended interviews with 31 policymakers, researchers, and program administrators, we examined state variations in approaches to providing care for pregnant, post, and intrapartum immigrant women. We found four themes: (a) a patchwork safety-net exists that provides some access to immigrants ineligible for Medicaid; (b) patchwork coverage leads to patchwork care, which can contribute to maternal health inequities; (c) immigrant Medicaid policy is assembled along a hierarchy of deservingness based on documentation status; (d) Trump-era public charge rules and political climate may have a substantial chilling effect on benefit uptake regardless of eligibility. We discuss implications for efforts to expand Medicaid postpartum and address the maternal health crisis.
Anemia and periprocedural complications determine contrast‐associated acute kidney injury after recanalization of chronic coronary occlusions in chronic kidney disease

Contrast‐associated acute kidney injury (CA‐AKI) is a potential risk associated with the percutaneous coronary interventions (PCI) for chronic total coronary occlusions (CTO) particularly with pre‐existing chronic kidney disease (CKD). The determinants of CA‐AKI in patients with pre‐existing CKD in an era of advanced strategies of CTO recanalization techniques need to be considered for a risk evaluation of the procedure.
Microbiota and pathogens in an invasive bee: Megachile sculpturalis from native and invaded regions

The present study aimed to characterise the bacterial, fungal and parasite gut community of the invasive bee Megachile sculpturalis sampled from native (Japan) and invaded (USA and France) regions via 16S rRNA and ITS2 amplicon sequencing and PCR detection of bee microparasites. The bacterial and fungal gut microbiota communities in bees from invaded regions were highly similar and differed strongly from those obtained in Japan. Core amplicon sequence variants (ASVs) within each population represented environmental micro‐organisms commonly present in bee‐associated niches that likely provide beneficial functions to their host. Although the overall bacterial and fungal communities of the invasive M. sculpturalis in France and the co‐foraging native bees Anthidium florentinum and Halictus scabiosae, were significantly different, five out of eight core ASVs were shared suggesting common environmental sources and potential transmission. None of the 46 M. sculpturalis bees analysed harboured known bee pathogens, while microparasite infections were common in A. florentinum, and rare in H. scabiosae. A common shift in the gut microbiota of M. sculpturalis in invaded regions as a response to changed environmental conditions, or a founder effect coupled to population re‐establishment in the invaded regions may explain the observed microbial community profiles and the absence of parasites. While the role of pathogen pressure in shaping biological invasions is still debated, the absence of natural enemies may contribute to the invasion success of M. sculpturalis.
Rapamycin treatment increases survival, autophagy biomarkers and expression of the anti‐aging klotho protein in elderly mice

Previous investigations have demonstrated that treatment of animals with rapamycin increases levels of autophagy, which is a process by which cells degrade intracellular detritus, thus suppressing the emergence of senescent cells, whose pro‐inflammatory properties, are primary drivers of age‐associated physical decline. A hypothesis is tested here that rapamycin treatment of mice approaching the end of their normal lifespan exhibits increased survival, enhanced expression of autophagic proteins; and klotho protein—a biomarker of aging that affects whole organism senescence, and systemic suppression of inflammatory mediator production. Test groups of 24‐month‐old C57BL mice were injected intraperitoneally with either 1.5 mg/kg/week rapamycin or vehicle. All mice administered rapamycin survived the 12‐week course, whereas 43% of the controls died. Relative to controls, rapamycin‐treated mice experienced minor but significant weight loss; moreover, nonsignificant trends toward decreased levels of leptin, IL‐6, IL‐1β, TNF‐α, IL‐1α, and IGF‐1, along with slight elevations in VEGF, MCP‐1 were observed in the blood serum of rapamycin‐treated mice. Rapamycin‐treated mice exhibited significantly enhanced autophagy and elevated expression of klotho protein, particularly in the kidney. Rapamycin treatment also increased cardiomyocyte Ca2+‐sensitivity and enhanced the rate constant of force re‐development, which may also contribute to the enhanced survival rate in elderly mice.
Multiplexed single-cell transcriptome analysis reveals molecular characteristics of monkey pluripotent stem cell lines

Efforts have been made to establish various human pluripotent stem cell lines. However, such methods have not yet been duplicated in non-human primate cells. Here, we introduce a multiplexed single-cell sequencing technique to profile the molecular features of monkey pluripotent stem cells in published culture conditions. The results demonstrate suboptimized maintenance of pluripotency and show that the selected signaling pathways for resetting human stem cells can also be interpreted for establishing monkey cell lines. Overall, this work legitimates the translation of novel human cell line culture conditions to monkey cells and provides guidance for exploring chemical cocktails for monkey stem cell line derivation.
The health and environmental risks and rewards of modernity that shape scientific optimism

Individuals in high-income countries increasingly express less scientific optimism than in lower-income societies. In this article, we utilize risk society theory to understand the complicated relationship between individual- and country-level factors, and optimism toward the role of science in society in “reflexively modern” societies. We use multilevel modeling with 16 high-income countries to determine the individual-level and country-level factors that shape scientific optimism. Next, we look at the individual characteristics that affect scientific optimism in each country individually. At the individual level, we find that older people, the more highly educated and higher earning, those farther to the Right on the political spectrum, and those with more materialist (rather than postmaterialist) attitudes have higher scientific optimism, while more religious people have lower optimism regarding science. At the country level, we make a corollary argument about materialism: societies that have higher measles immunization rates, generate more electricity from fossil fuels, and have a greater percentage of mobile phone subscriptions, have populaces that are more optimistic toward science.
Identification of Salmonella Pullorum Factors Affecting Immune Reaction in Macrophages from the Avian Host

Salmonella Pullorum is host specific to avian species, where it causes life-threatening infection in young birds. It is unknown why it is host restricted and causes systemic disease, rather than gastroenteritis normally seen with Salmonella. ABSTRACT The host-specific Salmonella serovar S. Pullorum (SP) modulates the chicken immune response to a Th2-biased response associated with persistent infection. This is different from the Th1-biased immune response induced by the genetically close serovar, S. Enteritidis (SE). Based on core genome differences between SP and SE, we used three complementary bioinformatics approaches to identify SP genes, which may be important for stimulation of the immune response. Defined mutants were constructed in selected genes, and the infection potential and ability of mutants to stimulate cytokine production in avian derived HD11 macrophages were determined. Deletion of large genomic regions unique to SP did not change infection potential nor immune stimulation significantly. Mutants in genes with conserved single nucleotide polymorphisms (SNPs) between the two serovars in the region 100 bp upstream of the start codon (conserved upstream SNPs [CuSNPs]) such as sseE, osmB, tolQ, a putative immune antigen, and a putative persistent infection factor, exhibited differences in induction of inflammatory cytokines compared to wild-type SP, suggesting a possible role of these CuSNPs in immune regulation. Single nucleotide SP mutants correcting for the CuSNP difference were constructed in the upstream region of sifA and pipA. The SNP corrected pipA mutant expressed pipA at a higher level than the wild-type SP strain, and the mutant differentially caused upregulation of proinflammatory cytokines. It suggests that this CuSNP is important for the suppression of proinflammatory responses. In conclusion, this study has identified putative immune stimulating factors of relevance to the difference in infection dynamics between SP and SE in avian macrophages. IMPORTANCE Salmonella Pullorum is host specific to avian species, where it causes life-threatening infection in young birds. It is unknown why it is host restricted and causes systemic disease, rather than gastroenteritis normally seen with Salmonella. In the present study, we identified genes and single nucleotide polymorphisms (SNPs; relative to the broad-host-range type Salmonella Enteritidis), which affected survival and immune induction in macrophages from hens suggesting a role in development of the host specific infection. Further studies of such genes may enable understanding of which genetic factors determine the development of host specific infection by S. Pullorum. In this study, we developed an in silico approach to predict candidate genes and SNPs for development of the host-specific infection and the specific induction of immunity associated with this infection. This study flow can be used in similar studies in other clades of bacteria.
Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides

ABSTRACT Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.