Miracle-dz/UniFAR-FTUs huggingface dataset:
Dental ontogeny in the most primitive bony fish Lophosteus reveals the developmental relationship between teeth and dermal odontodes

Ontogenetic data obtained by synchrotron microtomography of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically basalmost stem osteichthyan, reveal developmental relationships between teeth and ornament that are not obvious from the adult morphology. The earliest odontodes are two longitudinal founder ridges formed at the ossification center. Subsequent odontodes that are added lingually to the ridges turn into conical teeth and undergo cyclic replacement, while those added labially achieve a stellate appearance. The stellate odontodes deposited directly on the bony plate are aligned with the alternate files of the teeth. Successive odontodes overgrowing the labial tooth rows become tooth-like and the replacement teeth near to them are ornament-like. We propose that teeth and ornament are modifications of a single odontode system regulated and differentiated by the oral and dermal signals; signal cross-communication between the two domains can occur around the oral-dermal boundary.
Prognostic factors for local recurrence and survival and impact of local treatments on survival in lacrimal gland carcinoma

Background/aims To identify prognostic factors for local recurrence, distant metastasis and disease-specific survival (DSS) for lacrimal gland carcinoma. Methods All consecutive patients with lacrimal gland carcinoma treated from January 1998 through December 2018 were included. Log-rank tests and univariate Cox proportional hazards regression models were used to study risk factors and survival. Results Overall, 55 patients were included in this study, and 5 patients were excluded from the survival analysis. Median age was 46 years (range: 10–76). 43 patients (78%) had adenoid cystic carcinoma (ACC). 31 patients (56%) had T2 disease at presentation. 28 patients (51%) underwent orbital exenteration with or without adjuvant radiotherapy or chemoradiation, 26 (47%) underwent eye-sparing surgery with or without adjuvant radiotherapy or chemoradiation, and 1 received palliative chemoradiation. 11 patients (22%) experienced local recurrence; 14 (29%) experienced distant metastasis. Five- and 10-year local-recurrence-free survival rates were 0.71 (95% CI 0.58 to 0.88), and 5- and 10-year distant-metastasis-free survival rates were 0.67 (95% CI 0.53 to 0.85) and 0.49 (95% CI 0.30 to 0.81), respectively. There was no significant difference in risks of local recurrence, distant metastasis or DSS between ACC patients who had orbital exenteration and those who had eye-sparing surgery. Perineural invasion was negatively associated with local-recurrence-free survival (p=0.02). Among patients with ACC, basaloid/solid histologic type was associated with significantly worse DSS than non-basaloid/solid histologic type (p<0.01). Conclusions For lacrimal gland carcinoma, orbital exenteration with adjuvant therapy and eye-sparing surgery with adjuvant therapy are associated with similar recurrence outcomes. Eye-sparing surgery is associated with better DSS. Perineural invasion is a risk factor for local recurrence. ACC with basaloid/solid subtype correlates with worse DSS.
Identification of annually produced opaque bands in the shell of the freshwater mussel Elliptio complanata using the seasonal cycle of δ18 Ο

On a compare trois methodes de determination de l'âge de Elliptio complanata, soit (i) le compte des bandes opaques a l'exterieur de la coquille observees en lumiere transmise, (ii) le compte des bandes opaques observees dans des sections longitudinales polies de la coquille et (iii) le compte des bandes opaques identifiees comme etant annuelles d'apres leur concentration de δ 18 O. En moyenne, le nombre de bandes opaques comptees a l'interieur de la coquille etait superieur a celui obtenu pour l'exterieur de la coquille. Le nombre de bandes opaques annuelles, qu'on distingue des bandes parasites par leur position dans le cycle saisonnier de δ 18 O dans la coquille, concordait avec le nombre de bandes comptees dans les sections interieures polies. Les bandes opaques causees par des evenements annuels etaient soit non continues de l'extremite en croissance a l'umbo, soit non continues jusqu'a leur fusion avec d'autres bandes pres de la ligne palleale. C'est le compte des bandes opaques internes, a l'aide des methodes decrites dans cette etude, qui a permis d'obtenir la meilleure estimation de l'âge reel d'Elliptio complanata.
TROPICAL MARSH AND SAVANNA OF THE LATE PLEISTOCENE IN NORTHEASTERN SONORA, MEXICO

Abstract We recovered Pleistocene fossils from a lava-dammed river deposit along the Río de Moctezuma in northeastern Sonora, at 29°41′N, 109°39′W, and 605 m elevation. Today the region is semiarid, with a foothills thornscrub community. The impoundment that resulted from the lava dam produced a short-lived marsh with an adjacent savanna. The extraordinary fauna is both diverse and rich, and includes ostracods, mollusks, fish, amphibians, turtles, a crocodilian, snakes, lizards, birds, and mammals, many with tropical affinities today. Most of the animals are either extralimital to the setting today or extinct. The recovery of Bison dictates a Rancholabrean Land Mammal Age for the fauna; a preliminary 40Ar/39Ar age suggests that the deposit is between 570,000 and 310,000 years old. The occurrence of cf. Crocodylus acutus (a crocodilian; generic assignment uncertain) and Pampatherium, the giant armadillo, is unique in the northern interior Sonora setting. We speculate that a well-developed riparian corridor along the Río Yaqui, from the Gulf of California to the mountain-valley setting at Térapa, permitted the animals with tropical affinities to extend 350 km inland.
Altered Cortical Functional Networks in Patients With Schizophrenia and Bipolar Disorder: A Resting-State Electroencephalographic Study

Background Pathologies of schizophrenia and bipolar disorder have been poorly understood. Brain network analysis could help understand brain mechanisms of schizophrenia and bipolar disorder. This study investigates the source-level brain cortical networks using resting-state electroencephalography (EEG) in patients with schizophrenia and bipolar disorder. Methods Resting-state EEG was measured in 38 patients with schizophrenia, 34 patients with bipolar disorder type I, and 30 healthy controls. Graph theory based source-level weighted functional networks were evaluated: strength, clustering coefficient (CC), path length (PL), and efficiency in six frequency bands. Results At the global level, patients with schizophrenia or bipolar disorder showed higher strength, CC, and efficiency, and lower PL in the theta band, compared to healthy controls. At the nodal level, patients with schizophrenia or bipolar disorder showed higher CCs, mostly in the frontal lobe for the theta band. Particularly, patients with schizophrenia showed higher nodal CCs in the left inferior frontal cortex and the left ascending ramus of the lateral sulcus compared to patients with bipolar disorder. In addition, the nodal-level theta band CC of the superior frontal gyrus and sulcus (cognition-related region) correlated with positive symptoms and social and occupational functioning scale (SOFAS) scores in the schizophrenia group, while that of the middle frontal gyrus (emotion-related region) correlated with SOFAS scores in the bipolar disorder group. Conclusions Altered cortical networks were revealed and these alterations were significantly correlated with core pathological symptoms of schizophrenia and bipolar disorder. These source-level cortical network indices could be promising biomarkers to evaluate patients with schizophrenia and bipolar disorder.
Control of Heterofermentative Bacteria During Cheddar Cheese Maturation by Homofermentative Lactobacillus Starters

Abstract Aged Cheddar cheese was manufactured by a two-phase starter addition. Initially, a commercial mixed Streptococcus starter was used according to conventional practice. Just before rennet addition selected mixtures of homofermentative and heterofermentative lactobacilli or heterofermentauves alone were added to yield a final cell concentration of 10 5 /mL. Use of the homofermentative Lactobacillus strains Lactobacillus casei ssp. casei, Lactobacillus casei ssp. pseudoplantarum , and Lactobacillus plantarum each with the heterofermentative strains Lactobacillus brevis and Lactobacillus fermentum in cheese production resulted in an inhibitory effect of the former upon development of the latter in aging cheeses. Addition of heterofermentative lactobacilli cultures did not contribute significantly to proteolysis, as measured by soluble N extracted by 5% TCA (150 to 225 mg/100g), whereas mixtures of homofermentative and heterofermentative strains produced soluble N in the range of 175 to 250 mg/100g in cheeses aged 4 mo.
A 2.4 GHz SiGe Envelope Tracking Power Amplifier for LTE Applications

This paper presents a 2.4 GHz SiGe Power Amplifier based on envelope tracking (ET) technology for long term evolution (LTE) application, aiming to improve efficiency. The ET consists of envelope detector and envelope modulator. Using linear amplifier assisted switching amplifier to improve the system bandwidth, the proposed technique enhances the PA’s back-off efficiency. The power amplifier is designed in 0.18um SiGe process and simulated with LTE16QAM signal. The simulated peak output power is 30.1 dBm at 2.4 GHz with 42% peak power added efficiency (PAE) and average output power is 24.6 dBm with 24% average PAE.
Plant diversity and community age shape soil microbial communities

Plants influence belowground microbial communities, which in turn drive nutrient cycling, plant productivity, and the maintenance of plant diversity. Over time, associations between plant communities and their belowground microbiota may strengthen and become more specific. However, we do not know whether plant diversity affects bulk soil microbial community composition and diversity, and whether this association strengthens as micro-evolutionary processes modify plant communities through time. To address this, we used plant communities and soil from an eight-year-old biodiversity experiment (the Jena Experiment; “old” plant communities and “old” soil), plant communities without such history (“new” plants), and soil from which any soil legacy was removed by sterilization (“new” soil) to set up a field biodiversity experiment in which we factorially crossed plant community age with soil legacy for 52 different plant species compositions. We grew these plant-soil communities for four years in experimental plots with plant species richness ranging from 1, 2, 4, 8 to 60 species. At the end of the experiment, we sequenced bacterial 16S rRNA and fungal ITS fragments to compare soil microbial communities under new vs. old plant communities in new vs. old soils. Soil microbial diversity was positively but weakly associated with plant diversity, with the strongest difference in microbial diversity between plant monocultures and any community of more than one plant species. Particular plant community compositions were associated with particular microbial community compositions. Soil legacy (old soil) increased soil bacterial richness and evenness more strongly than did plant community age. Plant community age (old plant communities) significantly affected the abundance of 10% of fungal OTUs. Some of the effects of soil legacy on bacterial and fungal diversity were indirect via changes in soil abiotic and biotic properties. Our findings suggest that as experimental ecosystems develop over time, plant communities associate with specific microbiomes and plant species associate with specific soil microbial species. With increasing knowledge about the taxonomic identities of the microbial OTUs, our dataset in the future may be used for function-based analyses of the detected associations. This may eventually help to identify microbiomes that improve plant health and consequently plant community productivity.
Bone Marrow Stromal Cells With Exercise and Thyroid Hormone Effect on Post-Stroke Injuries in Middle-aged Mice

Introduction: Based on our previous findings, the treatment of stem cells alone or in combination with thyroid hormone (T3) and mild exercise could effectively reduce the risk of stroke damage in young mice. However, it is unclear whether this treatment is effective in aged or middle-aged mice. Therefore, this study designed to assess whether combination of Bone Marrow Stromal Cells (BMSCs) with T3 and mild treadmill exercise can decrease stroke complications in middle-aged mice. Methods: Under laser Doppler flowmetry monitoring, transient focal cerebral ischemia was produced by right Middle Cerebral Artery Occlusion (MCAO) for 45 min followed by 7 days of reperfusion in middle-aged mice. BMSCs (1×105) were injected into the right cerebral ventricle 24 h after MCAO, followed by daily injection of triiodothyronine (T3) (20 μg/100 g/d SC) and 6 days of running on a treadmill. Infarct size, neurological function, apoptotic cells and expression levels of Glial Fibrillary Acidic Protein (GFAP) were evaluated 1 week after stroke. Results: Post-ischemic treatment with BMSCs or with T3 and or mild treadmill exercise alone or in combination did not significantly change neurological function, infarct size, and apoptotic cells 7 days after ischemia in middle-aged mice (P>0.05). However, the expression of GFAP significantly reduced after treatment with BMSCs and or T3 (P<0.01). Conclusion: Our findings indicate that post-stroke treatment BMSCs with exercise and thyroid hormone cannot reverse neuronal damage 7 days after ischemia in middle-aged mice. These findings further support that age is an important variable in stroke treatment
Enrofloxacin Shifts Intestinal Microbiota and Metabolic Profiling and Hinders Recovery from Salmonella enterica subsp. enterica Serovar Typhimurium Infection in Neonatal Chickens

In this study, we examined the effects of S. Typhimurium infection and enrofloxacin treatment on the microbiota and metabolite synthesis in chicken cecum, in order to identify target metabolites that may promote S. Typhimurium colonization and aggravate inflammation and to evaluate the important microbiota that may be associated with these metabolites. Our findings may facilitate the use of antibiotics to prevent S. Typhimurium infection. ABSTRACT Enrofloxacin is an important antibiotic used for prevention and treatment of Salmonella infection in poultry in many countries. However, oral administration of enrofloxacin may lead to the alterations in the microbiota and metabolome in the chicken intestine, thereby reducing colonization resistance to the Salmonella infection. To study the effect of enrofloxacin on Salmonella in the chicken cecum, we used different concentrations of enrofloxacin to feed 1-day-old chickens, followed by oral challenge with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). We then explored the distribution pattern of S. Typhimurium in cecum contents in vivo and analyzed the microbial community structure of cecum contents using microbial 16S amplicon sequencing. Untargeted metabolomics was used to explore the gut metabolome on day 14. Faecalibacterium and Anaerostipes, which are closely related to the chicken intestinal metabolome, were screened using a multi-omics technique. The abundance of S. Typhimurium was significantly higher in the enrofloxacin-treated group than in the untreated group, and S. Typhimurium persisted longer. Moreover, the cecal colony structures of the three groups exhibited different characteristics, with Lactobacillus reaching its highest abundance on day 21. Notably, S. Typhimurium infection is known to affect the fecal metabolome of chickens differently. Thus, our results suggested that enrofloxacin and Salmonella infections completely altered the intestinal microbiota and metabolism of chickens. IMPORTANCE In this study, we examined the effects of S. Typhimurium infection and enrofloxacin treatment on the microbiota and metabolite synthesis in chicken cecum, in order to identify target metabolites that may promote S. Typhimurium colonization and aggravate inflammation and to evaluate the important microbiota that may be associated with these metabolites. Our findings may facilitate the use of antibiotics to prevent S. Typhimurium infection.
Forest Rotation and Streamflow Benefits

Summary This paper analyses the optimal rotation of a forest when the forest provides streamflow benefits. While timber values are typically assumed concave in stand age, streamflow benefits may be quasiconvex, with maximum current benefit flows being realised when the forest is either very young or very old. These features can explain the divergent views held by forestry and water management specialists concerned with managing the Thomson River Catchment area in Gippsland, Victoria. Optimal management may call for extremes of either short or very long forest rotations. It is in the mid-range of forest ages that streamflow benefits are mainly lost. Using realistic data a case is made for never harvesting the Thomson Catchment forest.
Efficient and Meaningful Multi-secret Image Sharing Based on Block Imitation

Chen et al. proposed a deterministic algorithm to create a new secret sharing scheme for multiple secret images ( n +1, n +1), by Boolean-based visual secret sharing. This algorithm achieves no pixel expansion, reversibility, and no codebook required. However, this scheme has the disadvantage that the shared images are all meaningless shares, becoming very suspicious in the attackers’ eyes. To solve the above problem, this paper proposes a new multi-secret image sharing algorithm to share n secret images into n meaningful shared images using halftone images. The proposed scheme can encode multiple secrets in fewer shares than Chen et al.’s scheme, and also achieves a reversible secret construction. Most important this technique can avoid attracting the attention of attackers by using meaningful shared images rather than showing meaningless shares to attackers.
Putative linear motifs mediate the trafficking to apical and basolateral membranes

Cell polarity refers to the asymmetric organisation of cellular components in various cells. Epithelial cells are the best known examples of polarized cells, featuring apical and basolateral membrane domains. Despite huge efforts, the exact rules governing the protein distribution in such domains are still elusive. In this study we examined linear motifs accumulating in these parts and based on the results we prepared ‘Classical’ and Convolutional Neural Networks to classify human transmembrane proteins localizing into apical/basolateral membranes. Asymmetric expression of drug transporters results in vectorial drug transport, governing the pharmacokinetics of numerous substances, yet the data on how proteins are sorted in epithelial cells is very scattered. The provided dataset may offer help to experimentalists to characterize novel molecular targets to regulate transport processes more precisely.
Would East African savanna rodents inhibit woody encroachment? Evidence from stable isotopes and microhistological analysis of feces

Abstract It is well established that massive consumption of plants by the abundant and diverse assemblage of savanna ungulates in East Africa competitively suppresses the native guild of herbivorous to omnivorous small mammals. An important role of woody plant suppression in the Acacia-dominated savannas for this guild of rodents, when released from ungulate competition, has been demonstrated only recently, but without direct evidence of which species are involved. In an effort to establish which of the common species in this guild are most likely to impact growth of trees and forbs, as opposed to grasses or insects, or both, I present data on atomic and isotopic ratios of fecal carbon and nitrogen from 8 commonly occurring muroid rodents from savanna and bush habitats on the Laikipia Plateau of central Kenya: Acomys percivali, Acomys wilsoni, Aethomys hindei, Arvicanthis niloticus, Mastomys natalensis, Mus spp. (thought to be mostly M. minutoides), Saccostomus mearnsi, and Gerbilliscus robustus. In this region where all grasses are C4 and all trees and other nongrasses are C3, different ratios of 13C:12C (δ13C) in plant tissues give pure grazers, pure browsers, and mixed-feeding herbivores distinctive carbon isotope signatures. Degree of omnivory is revealed by C:N and, arguably, by δ15N, but the latter is influenced by dietary protein quality and varies widely by plant species and soil type. Joint consideration of stable-isotope data, total C:N, and microhistological analysis of feces allowed better resolution of dietary niche of each species than any of these data sets could, alone. Grass was either coequal to browse (dicots) or dominated the plant portion of each species' diet, which was somewhat unexpected given rodents' hypothesized role in limiting Acacia recruitment. All species consumed some arthropods. A. niloticus, the only diurnal species, was the most herbivorous, being largely a grazer. S. mearnsi, A. hindei, and M. natalensis were mixed-feeding (grass–browse) herbivores. Mus spp. and Acomys spp. were omnivores whose plant components were largely grass. G. robustus was primarily an insectivore–omnivore whose smaller plant component was grass. Both S. mearnsi and A. niloticus displayed a significant increase in proportion of C4 grasses in the diet in periods following significant rains, a pattern previously documented from δ13C diet studies in large mammalian herbivores. Fecal δ15N was significantly higher for rodents that consumed more grass and for rodents released from competition with ungulates, suggesting a partial mechanism for that competitive release. S. mearnsi, followed by A. hindei and M. natalensis, were most likely to feed on woody dicots including Acacia.
Glutathione S-transferase: A Candidate Gene for Berry Color in Muscadine Grapes (Vitis rotundifolia)

Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n=40) belong to the Muscadinia subgenus of Vitis, while all other cultivated grape species belong to the subgenus Euvitis (2n=38). The berry color locus in muscadines has been mapped to a 0.8 Mbp region syntenic with chromosome 4 of V. vinifera. In this study, we identified glutathione S-transferase4 (GST4) as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and KASP genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadine GST4 (VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 65 breeding selections, 14 cultivars, and 320 progeny from two mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominant VrGST4 action, with no allele dosage effect on total anthocyanin content or composition of individual anthocyanins. Proanthocyanidin content was similar in the seeds of both black and bronze genotypes, and seeds had much higher VrGST3 expression and lower VrGST4 expression than skins. VrGST4 expression was higher in post-veraison berries of black muscadines compared to pre-veraison berries, but no changes in gene expression in pre- and post-veraison berries were observed in the bronze muscadine cultivar. VrMybA1 expression was higher in post-veraison berries of both black and bronze muscadines. These results suggest that berry pigmentation in muscadines is regulated by a mechanism distinct from the MybA gene cluster that is responsible for berry color variation in V. vinifera.