Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Wave Approach of Thermodynamics and some Problems of Non-Linear Theories

This paper is concerned with the analysis of the theoretical and experimental circumstances of the linear, quasi-linear, strictly non-linear and wave phenomena of purely dissipative transport processes. The most fundamental relations of local equilibrium thermodynamics are treated in a general form. The quasi-linear approach of the Onsager-theory of purely dissipative transport processes is given together with the supplementary relations of the Onsagerian and Maxwellian symmetries, basically important in the exact quasi-linear theory. Two different representations between them are discussed. A new type of constitutive equations for continuous media with kinetic energy is obtained as a direct consequence of the original Onsager-Casimir-Machlup theory developed only for discontinuous systems. By means of these new constitutive equations two complete sets of the equations of motion for continua with kinetic energy are attained, adequate reduced forms of which represent two complete sets of thermodynamical wave equations. It is evident from the theory that the Cattaneo-Vernotte constitutive equation is an extremely special and ad hoc form of the exact equation given within the framework of Onsagerian thermodynamics. Finally, some explicit forms of the theory are analysed with respect to thermal, electromagnetic and diffusional waves. Introduction • In 1970 Meixner made the following remarks on the theory of heat conduction in solids [1]: a) There seems to be experimental evidence that Fourier's law of heat conduction does not give a reasonably accurate description of this phenomenon. 1 Dedicated to Professor Dr. Ilya Prigogine on the occasion of his 60 birthday. J. Non-Equilib. Thermodyn. , Vol. 2, 1977, No. 4
Bringing Tegenaria boitanii stat. rev. back to life with a review of the Tegenaria percuriosa-complex (Araneae: Agelenidae), description of a new species and insight into their phylogenetic relationships and evolutionary history

The funnel web spiders (Agelenidae) are a diverse and taxonomically challenging worldwide distributed family. The genus Tegenaria Latreille, 1804, includes more than 100 valid species, mostly circumscribed to Europe and western Asia, although some species may have been subsequently introduced to other regions by anthropogenic action. Here we revise and investigate phylogenetic relationships of a group of morphologically similar species from the south-western Black Sea region and Anatolia. We remove the species Tegenaria boitanii Brignoli, 1978 stat. rev. and Tegenaria bithyniae Brignoli, 1978 from synonymy of Tegenaria percuriosa Brignoli, 1972. Tegenaria boitanii stat. rev. is restored as a valid species, re-described and re-diagnosed, and T. bithyniae syn. nov. is placed as its junior synonym. We also provide an updated diagnosis for T. percuriosa, describe a new species, Tegenaria euxinica Dimitrov sp. nov. from the mesophilic beech forests (Fagus orientalis) in Bulgaria, and review the members of T. percuriosa complex. We provide new photographs for selected species, and a map of the updated distribution ranges of all the species in the complex. The phylogenetic position and internal structure of T. percuriosa species-complex is investigated by combining available morphological and molecular (target sequencing) data with new data from the species of interest. Finally, we propose to test in future studies the hypothesis that major climatic changes during the Miocene drove diversification of the group and imprinted its biogeography. http://zoobank.org/urn:lsid:zoobank.org:pub:08A77B59-ACFE-4C16-BBCB-BC45BE981360
Effect of oral administration of Limosilactobacillus reuteri on intestinal barrier function and mucosal immunity of suckling piglets

Abstract The aim of present study was to evaluate the effect of Limosilactobacillus reuteri (L. reuteri) on the intestinal barrier function and mucosal immunity of piglets at different suckling phase. In this study, fifty-four neonatal piglets (Rongchang × Yorkshire) were orally administered with 1.0 × 1010 CFU L. reuteri I5007 (dissolved in 2 ml 0.1% peptone) or 2 ml 0.1% peptone by gavage every day. The experiment had lasted for 20 days from the birth. Six piglets from each group were slaughtered at 10- and 20-day-old, respectively. Intestinal samples were collected for the evaluation of target genes by real-time PCR and western blot. The results showed that L. reuteri I5007 significantly increased the average daily gain, decreased the diarrhoea incidence, and improved the intestinal morphology of piglets (p < .05). Oral administration of L. reuteri I5007 also elevated the mRNA and protein level of jejunal and ileal Zonula Occludens-1, Claudin-1, and Occludin to enhance the intestinal mucosal barrier function. Additionally, L. reuteri I5007 treatment modulated toll-like receptors (TLRs) and porcine host defense peptides (HDPs) expression, such as increased the mRNA levels of ileal TLR9 and PBD2 at 10-day-old, jejunal TLR9 and ileal PG1-5 at 20-day-old, the protein level of ileal TLR2 at 20-day-old, and influenced the protein and mRNA level of ileal TLR4. These findings indicated that oral administration of L. reuteri I5007 could improve the intestinal mucosal barrier and enhance the intestinal innate immunity of piglets during suckling period. Highlights L. reuteri increased the average daily gain and decreased the diarrhoea incidence of piglets. L. reuteri increased the expression of Zonula Occludens-1, Claudin-1, and Occludin in jejunal and ileal mucosal. L. reuteri influenced the expression of toll-like receptors and porcine host defense peptides.
Efficacy of Rumex nervosus leaves or Cinnamomum verum bark as natural growth promoters on the growth performance, immune responsiveness, and serum biochemical profile of broiler chickens

Abstract This study was conducted to evaluate the potential growth and health promotion of Rumex nervosus leaves (RNL) and Cinnamomum verum bark (CVB) supplementation as phytogenic growth promoters on broilers. For 34 days, 540 day-old broiler chicks were randomly assigned to nine groups. Birds were fed the basal diet supplemented with 1, 3, or 5 g/kg RNL, 2, 4, or 6 g/kg CVB. In addition, birds were fed the basal diet complemented with antibiotic (AGP), or basal diet without feed additive as controls. All bird vaccinated for IBV, IBDV, and NDV except negative control (NC). The selected indicators were measured and analysed. Broilers given 1 g RNL were numerically heavier at 34 days and gained more to a degree comparable to the AGP group (p = .053). The addition of CVB at 2 g resulted in the best-feed conversion up to 21 d (p = .04). Throughout the study, dietary treatments had no impact on feed intake. Except for ALT, none of the immune-related parameters or serum biochemical profile differed statistically between treatments when compared to vaccinated control group. When comparing the non-vaccinated un-treated group on day 34, vaccination increased significantly antibody titres to NDV and IBDV. In conclusion, dietary RNL and CVB, especially at low doses, attempted to maximise the performance without compromising health in broiler chickens under typical conditions. Further research into the use of natural herbs under challenging conditions is required to maximise performance, maintain animal productivity, and achieve the ultimate goal of reducing antibiotic use in the poultry industry. Highlights Cinnamomum verum bark at a dose of 2 g/kg diet improved feed conversion ratio during the starter period. However, both selected herbs result unsatisfactory improvements in broiler performance at overall period under the ideal hygienic conditions. If broilers are exposed to bacterial challenges, phytogenic feed additives or even antibiotics may manifest their activity in promoting animal health and, as a result, growth performance. Low levels of hepatic enzymes at day 34 of age showed that birds’ health was good. Cinnamon powder improves kidney function at day 21 by lowering serum creatinine levels with increasing dose (p < .05). Rumex nervosus leaves or Cinnamomum verum bark have hypoglycaemia activity on day 31 by lowering serum glucose levels as the dose is reduced.
Growth performance and gut response of broiler chickens fed diets supplemented with grape (Vitis vinifera L.) seed extract

Abstract To evaluate the effects of the dietary supplementation with a grape seeds extract (GSE) on growth performance, gut morphology and immune response, and meat quality, 800 chickens (8 pens/group) were fed a control diet or the same diet added with 0.1%, 0.2%, or 0.4% GSE from hatching to 42 d of age. Growth performance did not differ among dietary treatments: final live weight averaged at 3,179 g, which corresponded to a daily growth rate of 76.1 g/d; feed intake averaged 113 g/d, for a feed conversion ratio at 1.49. On average of samplings at 14 d and 28 d of age, the density of CD45+ cells in the jejunal mucosa was higher (2,497 vs. 1,931 cells/10,000 μm2; p < .001) in chickens fed diet 0.2% GSE compared to chickens fed the other diets; jejunum villi height tended to be lower in chickens fed diet 0.2% GSE compared to those fed the other diets (965 μm vs. 1,054 μm; p = .07). Slaughter results and carcase traits, occurrence of myopathies at breast and meat quality after 24 h or 11 d of refrigerated storage were not affected by GSE inclusion or level. Under the conditions of the present study, no relevant effect of the dietary inclusion of GSE was observed on performance and health, but a pro-inflammatory immune response at the level of jejunum, based on which a positive response of chickens fed GSE can be expected under challenging conditions. Highlights Dietary supplementation with grape seed extract from 0.1% to 0.2% and 0.4% were tested in broiler chickens. Growth performance, meat oxidation and myopathy occurrence were not affected. A pro-inflammatory immune response at the level of jejunum was recorded with 0.2% inclusion level.
A mismatch between morphological and molecular data in lineages of Enteromius (Cypriniformes: Cyprinidae) from the Lowa basin (East Democratic Republic of the Congo: DRC) with the description of a new species

Six populations of morphologically similar Enteromius specimens with a weakly thickened and serrated dorsal spine from the Lowa basin were investigated using an integrative approach including qualitative characters, multivariate morphometrics, and DNA analyses (mtCOI and ncMyh6). These populations are nested within the COI lineage of the E. miolepis species-complex, but differ from all known Enteromius species from the Congo basin, by their dorsal spine morphology, colour pattern, and scale pattern at the dorsal-fin base. In addition, they represent two distinct COI lineages (genetic distance: 5.6–6.1%), with four populations forming a single well-supported lineage described as a new species, Enteromius radari sp. nov. The two remaining populations are sister to the E. miolepis lineage from the Itimbiri. The incongruent position of these two populations in the COI tree may point to past introgressive hybridization events, incomplete lineage sorting, or recent speciation. Analysis of a ncDNA marker (Myh6) did not provide more information due to its slow mutation rate. These results are indicative for introgression or mtDNA capture and provide the first report for such an evolutionary event in Enteromius from the Congo basin. http://zoobank.org/urn:lsid:zoobank.org:pub:D2263E5B-D403-404C-B66C-852215ED100C
Is Short Sleep Bad for the Brain? Brain Structure and Cognitive Function in Short Sleepers

Many sleep less than recommended without experiencing daytime sleepiness. According to prevailing views, short sleep increases risk of lower brain health and cognitive function. Chronic mild sleep deprivation could cause undetected sleep debt, negatively affecting cognitive function and brain health. However, it is possible that some have less sleep need and are more resistant to negative effects of sleep loss. We investigated this using a cross-sectional and longitudinal sample of 47,029 participants of both sexes (20–89 years) from the Lifebrain consortium, Human Connectome project (HCP) and UK Biobank (UKB), with measures of self-reported sleep, including 51,295 MRIs of the brain and cognitive tests. A total of 740 participants who reported to sleep <6 h did not experience daytime sleepiness or sleep problems/disturbances interfering with falling or staying asleep. These short sleepers showed significantly larger regional brain volumes than both short sleepers with daytime sleepiness and sleep problems (n = 1742) and participants sleeping the recommended 7–8 h (n = 3886). However, both groups of short sleepers showed slightly lower general cognitive function (GCA), 0.16 and 0.19 SDs, respectively. Analyses using accelerometer-estimated sleep duration confirmed the findings, and the associations remained after controlling for body mass index, depression symptoms, income, and education. The results suggest that some people can cope with less sleep without obvious negative associations with brain morphometry and that sleepiness and sleep problems may be more related to brain structural differences than duration. However, the slightly lower performance on tests of general cognitive abilities warrants closer examination in natural settings. SIGNIFICANCE STATEMENT Short habitual sleep is prevalent, with unknown consequences for brain health and cognitive performance. Here, we show that daytime sleepiness and sleep problems are more strongly related to regional brain volumes than sleep duration. However, participants sleeping ≤6 h had slightly lower scores on tests of general cognitive function (GCA). This indicates that sleep need is individual and that sleep duration per se is very weakly if at all related brain health, while daytime sleepiness and sleep problems may show somewhat stronger associations. The association between habitual short sleep and lower scores on tests of general cognitive abilities must be further scrutinized in natural settings.
Structural Basis of Prostaglandin Efflux by MRP4

MRP4 is unique among the C family of ATP-binding cassette transporters for its role in translocating prostanoids, an important group of signaling molecules derived from unsaturated fatty acids. Using a reconstituted system, we report that a pair of prostaglandins (PGs) and the sulfonated-sterol DHEA-S preferentially enhance the ATPase activity of MRP4 over other previously proposed physiological substrates such as cyclic nucleotides or leukotrienes. We determined the cryo-EM structures of nanodisc embedded bovine MRP4 in (i) a nucleotide- and substrate-free state, (ii) in complex with PGE1, (iii) PGE2, and (iv) DHEA-S, and (v) a catalytically dead mutant E1202Q bound to ATP-Mg2+. The substrate-bound structures suggest unique features of the MRP4 binding site that distinguish its specificity for prostanoids from that of the related leukotriene transporter MRP1. The ATP-bound structure is in an outward-occluded conformation, revealing a novel state in the proposed alternate-access mechanism of MRP transport. Our study provides insights into the endogenous function of this versatile efflux transporter.
The Beta secretase BACE1 drives fibroblasts activation in Systemic Sclerosis through the APP/β-catenin/Notch signalling axis

The beta-amyloid precursor protein cleaving enzyme 1 (BACE1) is well known for its role in the development of Alzheimer’s disease. Recent publications, including our own, have demonstrated a role for this enzyme in other chronic diseases. The aim of this study was to investigate the role of BACE1 in the autoimmune disease systemic sclerosis (SSc). BACE1 protein levels were elevated in SSc patient skin. Inhibition of BACE1 with small molecule inhibitors or siRNA blocked SSc and fibrotic stimuli mediated fibroblast activation. Furthermore, we show that BACE1 regulation of dermal fibroblast activation is dependent on β-catenin and Notch signalling. The Neurotropic factor BDNF negatively regulates BACE1 expression and activity in dermal fibroblasts. Finally, sera from SSc patients show higher Aβ and lower BDNF levels compared to healthy controls. The ability of BACE1 to regulate SSc fibroblast activation reveals a new therapeutic target in SSc. Several BACE1 inhibitors have been shown to be safe in clinical trials for Alzheimer’s disease and could be repurposed to ameliorate fibrosis progression.
Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

Cell state (phenotypic) plasticity is a carefully regulated feature of adult epithelial cells that enables adaptive responses to injury, inflammation, and other forms of stress. Aberrant expansion of the normally restricted capability for cell state plasticity to escape terminal differentiation is a critical aspect of neoplasia. The nongenetic factors and specific programs that mediate aberrant cell state plasticity and impaired differentiation require deeper characterization to understand this elusive aspect of cancer pathogenesis. Using genetically engineered and carcinogen-induced murine models of intestinal neoplasia, we demonstrate that impaired differentiation is a conserved event preceding cancer development. Single cell RNA-sequencing (scRNA-seq) of neoplastic intestinal lesions from both mouse models and a patient with familial adenomatous polyposis revealed that cancer initiates by adopting an aberrant transcriptional state characterized by nonoverlapping expression of a regenerative pathway, marked by Ly6a (Sca-1), and a fetal intestinal program, positive for Tacstd2 (Trop2). Genetic inactivation of Sox9 prevented adenoma formation in ApcKO mice, obstructed emergence of aberrant regenerative and fetal intestinal programs, and restored multi-lineage differentiation by scRNA-seq. Expanded chromatin accessibility at regeneration and fetal genes upon Apc inactivation was reduced by concomitant Sox9 suppression. These studies indicate that aberrant cell state plasticity mediated by unabated regenerative activity and developmental reprogramming precedes cancer development.
Decoding Proteoforms with Single Acid Resolution Using a Sub-nanometer Diameter Pore

When a denatured protein isoform (i.e., a proteoform) immersed in electrolyte is impelled by an electric field through a sub-nanometer-diameter pore (i.e., a sub-nanopore) spanning a thin membrane, the sequence of amino acid (AA) residues constituting the proteoform can be directly “read” one at a time by measuring fluctuations in the electrolytic current. Corroborating this assertion, an analysis of the pore current with molecular dynamic (MD) simulations reveals that the fluctuations are correlated to the sequence of AA volumes, the water in the pore and acid mobility. After alignment to account for variations in the acid mobility, the simulated pore current is nearly perfectly correlated to the pattern of empirical fluctuations. To prove out the prospects for decoding proteoforms this way, site-specific post-translational modifications (PTMs) and point mutations in amyloid-beta (Aβ1-42) were analyzed with a sub-nanopore. The results show that single acids can be resolved in proteoforms with a dynamic range limited by the size of phenylalanine and glycine. With this sensitivity and single acid resolution, the sequence of a scrambled variant of Aβ1-42 was discriminated with a p-value < 10-5.
Children Develop Adult-Like Visual Sensitivity to Image Memorability by the Age of Four

Adults have been shown to consistently remember and forget certain images despite large individual differences, suggesting a population-wide sensitivity to an image’s intrinsic memorability—a measure of how successfully an image is remembered. While a decade of research has focused on image memorability among adults, the developmental trajectory of these consistencies in memory is understudied. Here, we investigate by what age children gain adultlike sensitivity to the image memorability effect. We utilized data from Saragosa-Harris et al. (2021), where 137 children aged between 3 and 5 years old encoded animal-scene image pairs and then after a 5-minute, 24-hour, or 1-week delay performed a cued recognition task for each scene target given its animal cue. We tested adults’ memory of the same scene images using ResMem (Needell & Bainbridge, 2022), a pre-trained deep neural network that predicts adult image memorability scores, and using an online behavioral continuous recognition task (N = 116). Results showed that ResMem predictions, as a proxy of adults’ memory, predicted scene memory of children by the age of 4 and were the most predictive of children’s memory across ages after a long, 1-week delay. Children at age 3 show non-adult-like consistent memory patterns, implying that the non-adult-like memory patterns were not due to poor memory performance. Instead, 3-year-olds may have consistently used certain visual memory strategies that become less optimal as they age. Our results suggest that adult-like sensitivity to image memorability emerges by the age of 4 through experience. Public Significance Statement This study strongly suggests that children older than 4 years old tend to remember and forget the same images as adults. We recommend teachers and caregivers to utilize the ResMem DNN to select memorable images to be used in educational settings.
Brassicaceae display diverse photorespiratory carbon recapturing mechanisms

Carbon concentrating mechanisms enhance the carboxylase efficiency of the central photosynthetic enzyme rubisco by providing supra-atmospheric concentrations of CO2 in its surrounding. In the C4 photosynthesis pathway, this is achieved by combinatory changes to leaf biochemistry and anatomy. Carbon concentration by the photorespiratory glycine shuttle requires fewer and less complex modifications. It could represent an early step during evolution from C3 to C4 photosynthesis and an inspiration for engineering approaches. Plants displaying CO2 compensation points between 10 to 40 ppm are therefore often termed ‘C3–C4 intermediates’. In the present study, we perform a physiological, biochemical and anatomical survey of a large number of Brassicaceae species to better understand the C3-C4 intermediate phenotype. Our phylogenetic analysis suggested that C3-C4 metabolism evolved up to five times independently in the Brassicaceae. The efficiency of the pathways showed considerable variation between the species but also within species. Centripetal accumulation of organelles in the bundle sheath was consistently observed in all C3-C4 classified accessions indicating a crucial role of anatomical features for CO2 concentrating pathways. Leaf metabolite patterns were strongly influenced by the individual plant accessions, but accumulation of photorespiratory shuttle metabolites glycine and serine was generally observed. Analysis of PEPC activities suggests that C4-like shuttles have not evolve in the investigated Brassicaceae. Highlight Our physiological, biochemical and anatomical survey of Brassicaceae revels multiple evolution of C3-C4 intermediacy connected to variation in photorespiratory carbon recapturing efficiency and a distinct C3-C4 bundle sheath anatomy.