Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyst-theca relationships of Spiniferites bentorii, S. hyperacanthus, S. ramosus, S. scabratus and molecular phylogenetics of Spiniferites and Tectatodinium (Gonyaulacales, Dinophyceae)

ABSTRACT It is well known that modern resting cysts with morphologies matching those of species of the fossil genus Spiniferites germinate into motile cells of the genus Gonyaulax. Different Spiniferites species have been connected to a single Gonyaulax species, raising the question of whether they are over-classified. Through germination experiments of cysts with the morphological features of four species of Spiniferites, viz. S. bentorii, S. hyperacanthus, S. ramosus and S. scabratus, we established cyst-theca relationships. Cysts with the morphology of S. bentorii gave rise to vegetative, motile cells of Gonyaulax nezaniae sp. nov., which is characterized by two stout antapical spines. Cysts with S. hyperacanthus and S. ramosus morphologies germinated into Gonyaulax whaseongensis and G. spinifera, respectively. Cysts with S. scabratus morphology lacked a ventral pore and were attributed to Gonyaulax cf. spinifera. Gene sequences for SSU, LSU and/or ITS-5.8S rRNA were obtained from these four species, and from cysts with the morphology of Spiniferites belerius, S. mirabilis, S. lazus, Spiniferites cf. bentorii and Tectatodinium pellitum. The maximum likelihood and Bayesian inference analyses based on LSU and SSU rRNA gene sequences revealed that cysts assignable to Spiniferites formed a polyphyletic group, intermingled with Tectatodinium, Bitectatodinium, Ataxiodinium and Impagidinium, whereas Gonyaulax species appeared as monophyletic. From our results we inferred the phylogenetic positions of S. bentorii, S. mirabilis, S. lazus, S. scabratus, Tectatodinium pellitum and Gonyaulax digitale for the first time, supporting the idea that Spiniferites species are not over-classified and each of them may correspond to different Gonyaulax species.
Plicidentine and the repeated origins of snake venom fangs

Snake fangs are an iconic exemplar of a complex adaptation, but despite striking developmental and morphological similarities, they probably evolved independently in several lineages of venomous snakes. How snakes could, uniquely among vertebrates, repeatedly evolve their complex venom delivery apparatus is an intriguing question. Here we shed light on the repeated evolution of snake venom fangs using histology, high-resolution computed tomography (microCT) and biomechanical modelling. Our examination of venomous and non-venomous species reveals that most snakes have dentine infoldings at the bases of their teeth, known as plicidentine, and that in venomous species, one of these infoldings was repurposed to form a longitudinal groove for venom delivery. Like plicidentine, venom grooves originate from infoldings of the developing dental epithelium prior to the formation of the tooth hard tissues. Derivation of the venom groove from a large plicidentine fold that develops early in tooth ontogeny reveals how snake venom fangs could originate repeatedly through the co-option of a pre-existing dental feature even without close association to a venom duct. We also show that, contrary to previous assumptions, dentine infoldings do not improve compression or bending resistance of snake teeth during biting; plicidentine may instead have a role in tooth attachment.
The intrinsically disorderly story of Ki-67

Ki-67 is one of the most famous marker proteins used by histologists to identify proliferating cells. Indeed, over 30 000 articles referring to Ki-67 are listed on PubMed. Here, we review some of the current literature regarding the protein. Despite its clinical importance, our knowledge of the molecular biology and biochemistry of Ki-67 is far from complete, and its exact molecular function(s) remain enigmatic. Furthermore, reports describing Ki-67 function are often contradictory, and it has only recently become clear that this proliferation marker is itself dispensable for cell proliferation. We discuss the unusual organization of the protein and its mRNA and how they relate to various models for its function. In particular, we focus on ways in which the intrinsically disordered structure of Ki-67 might aid in the assembly of the still-mysterious mitotic chromosome periphery compartment by controlling liquid–liquid phase separation of nucleolar proteins and RNAs.
Spatial activation of ezrin by epidermal growth factor receptor and focal adhesion kinase co-ordinates epithelial cell migration

Epidermal growth factor receptor (EGFR) plays a critical role in the promotion of epithelial cell proliferation and migration. Previous studies have suggested a cooperative role between EGFR and integrin signalling pathways that enable efficient adhesion and migration but the mechanisms controlling this remain poorly defined. Here, we show that EGFR forms a complex with focal adhesion kinase in epithelial cells. Surprisingly, this complex enhances local Src activity at focal adhesions to promote phosphorylation of the cytoskeletal adaptor protein ezrin at Y478, leading to actomyosin contractility, suppression of focal adhesion dynamics and slower migration. We further demonstrate this regulation of Src is due to the suppression of PTP1B activity. Our data provide new insight into EGF-independent cooperation between EGFR and integrins and suggest transient interactions between these kinases at the leading edge of cells act to spatially control signalling to permit efficient motility.
Many ways to land upright: novel righting strategies allow spotted lanternfly nymphs to land on diverse substrates

Unlike large animals, insects and other very small animals are so unsusceptible to impact-related injuries that they can use falling for dispersal and predator evasion. Reorienting to land upright can mitigate lost access to resources and predation risk. Such behaviours are critical for the spotted lanternfly (SLF) (Lycorma delicatula), an invasive, destructive insect pest spreading rapidly in the USA. High-speed video of SLF nymphs released under different conditions showed that these insects self-right using both active midair righting motions previously reported for other insects and novel post-impact mechanisms that take advantage of their ability to experience near-total energy loss on impact. Unlike during terrestrial self-righting, in which an animal initially at rest on its back uses appendage motions to flip over, SLF nymphs impacted the surface at varying angles and then self-righted during the rebound using coordinated body rotations, foot–substrate adhesion and active leg motions. These previously unreported strategies were found to promote disproportionately upright, secure landings on both hard, flat surfaces and tilted, compliant host plant leaves. Our results highlight the importance of examining biomechanical phenomena in ecologically relevant contexts, and show that, for small animals, the post-impact bounce period can be critical for achieving an upright landing.
Urban rat exposure to anticoagulant rodenticides and zoonotic infection risk

Anticoagulant rodenticides (ARs) deployed to control rodent pest populations can increase the risk of pathogen infection for some wildlife. However, it is unknown whether ARs also increase infection risk for target rodents, which are common hosts for zoonotic (animal-to-human transmitted) pathogens. In this study, we tested whether rats exposed to ARs were more likely to be infected with zoonotic pathogens, specifically Leptospira spp. or Escherichia coli, after controlling for known predictors of infection (i.e. sex, age, body condition). We collected biological samples from 99 rats trapped in Chicago alleys and tested these for Leptospira infection, E. coli shedding and AR exposure. We found that rats that had been exposed to ARs and survived until the time of trapping, as well as older rats, were significantly more likely to be infected with Leptospira spp. than other rats. We found no significant association between E. coli shedding and any predictors. Our results show that human actions to manage rats can affect rat disease ecology and public health risks in unintended ways, and more broadly, contribute to a growing awareness of bidirectional relationships between humans and natural systems in cities.
AIC Algorithm for the Behavioral Intention by R Soft-Ware

The pursuit of a sustainable environment has a significant connection to the knowledge level of society. In today's world, the primary means of acquiring knowledge is through educational institutions. Besides, even if inclusive and equal quality education and lifelong training chances for all are ensured and promoted, there is a need to apply the recognizing beneficial information obtained from the educational institutions. This study set out to investigate and explain the factors of student trust (ST), student identity (SI) and student commitment (SC), and university reputation (UR) affecting behavioral intention (BI). This paper presents an empirically chosen model from a sample size of 1538 Vietnamese graduates. The result of the AIC algorithm pointed out that the factors impacting on the behavioral intention for a continuous sustainable future are positive. The results suggest that some factors can be a driving force toward students having the behavioral intention to achieve positive goals.
Impact of vitamin D serum levels on clinicopathological features and outcome in advanced pancreatic carcinoma

Abstract Background Growing evidence encourages the preventive role of vitamin D in pancreatic carcinoma (PC). Meanwhile, the prognostic or predictive role needs more investigations. This study aimed to evaluate the correlation between serum vitamin D levels and the clinicopathological features with the outcome in advanced pancreatic carcinoma (APC). Materials and methods The current prospective study included 176 patients with APC. Assessing 25-hydroxy vitamin D is the most accurate method to measure the serum vitamin D levels. Serum vitamin D levels <20 ng/ml are defined as vitamin D deficiency, while levels ranging from 20 to 29 ng/ml are defined as vitamin D insufficiency. Before any treatment modalities were administered, the serum vitamin D levels were measured by enzyme-linked immunosorbent assay (ELISA). Results Serum vitamin D insufficiency and deficiency were detected in 28.4% and 31.8%, respectively. A large tumor size, higher grade, liver metastasis, higher serum level of CA 19-9, poor ECOG PS, and low overall response rate (ORR) were associated with lower serum vitamin D levels (p = 0.000). The median follow-up period was 7.6 months (range 0.6–18.6). The ORR was 23.2%, 54%, and 82.9% of vitamin D deficiency, insufficiency, and normal levels of vitamin D, respectively. The median OS was 11.4 months for patients with normal serum vitamin D levels, compared with 2.7 and 7.03 months for serum vitamin D deficiency and insufficiency, respectively. Conclusions Among patients with APC, serum vitamin D levels are considered a promising prognostic factor. It is associated with various poor prognostic features and worse survival outcome.
Reliability of DNMSQuest as a Screening Tool for Mood Disorders in Cervical Dystonia

The high prevalence of mood disorders in cervical dystonia, often unaddressed in botulinum toxin clinics, is a major factor in impaired quality of life. There is a clear need for a brief screening method for identifying these disorders; the Dystonia non‐motor symptoms questionnaire (DNMSQuest) has been proposed as such.
Model‐based evaluation for online shopping platform with probabilistic double hierarchy linguistic CODAS method

With the rapid advancement of Internet technology, the number of online shopping platforms has been increasing. Poor online shopping platform causes all sorts of trouble among the people despite convenience. A comprehensive and reasonable evaluation of online shopping platforms is of great significance. Therefore, this study establishes an online shopping platform evaluation model based on probability double linguistic‐combinative distance‐based assessment (PDHL‐CODAS). First, the notion of probabilistic double hierarchy linguistic term sets (PDHLTSs) is reviewed. Then the distance formulas of PDHLTS are defined. Thereafter, cumulative prospect theory is used to generate the cumulative weight of probabilistic double hierarchy linguistic information. Additionally, the integrated determination of objective criteria weights method is introduced to calculate the objective weight. PDHL‐CODAS method is established and applied to the evaluation of online shopping platforms. Finally, unlike the available probabilistic double hierarchy linguistic multiple attribute decision making methods, the defined method is scientifically effective.
Emigration Effects on Estimates of Age- and Sex-specific Survival of Small Mammals

Age- and sex-specific survival estimates are crucial to understanding important life-history characteristics and variation in these estimates can be a key driver of population dynamics. When estimating survival using Cormack–Jolly–Seber (CJS) models and capture–recapture data, emigration is typically assumed to have a negligible effect on estimates such that apparent survival is indistinguishable from true survival. Consequently, especially for populations or age classes with high dispersal rates, apparent survival estimates are often biased low and temporal patterns in survival might be masked when site fidelity varies temporally. We used 9 years of annual mark-recapture data to estimate age-, sex-, and time-specific apparent survival of Humboldt’s flying squirrels (Glaucomys oregonensis) and Townsend’s chipmunks (Neotamias townsendii). For Humboldt’s flying squirrels, these estimates support a small body of research investigating potential variation of survival among age and sex classes, but age- and sex-specific survival has not been evaluated for Townsend’s chipmunks. We also quantified the effects of age- and sex-specific emigration on confounded estimates of apparent survival. Our estimates of juvenile flying squirrel survival were high relative to other small mammal species and estimates for both species were variable among years. We found survival differed moderately among age and sex classes for Humboldt’s flying squirrels, but little among age and sex classes for Townsend’s chipmunks, and that the degree to which emigration confounded apparent survival estimates varied substantially among years. Without correcting for emigration, apparent survival estimates were lower and temporal variation was obscured, particularly for male Humboldt’s flying squirrels and female Townsend’s chipmunks. Our results demonstrate that emigration can influence commonly used estimates of apparent survival. Unadjusted estimates confounded the interpretation of differences in survival between age and sex classes and masked potential temporal patterns in survival because the magnitude of adjustment varied among years. We conclude that apparent survival estimators are robust during some time periods; however, when emigration rates vary in time the effects of emigration should be carefully considered and accounted for, especially in comparative studies and those with policy and conservation implications.
Mitonuclear co-introgression opposes genetic differentiation between phenotypically divergent songbirds

Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the relative effective population sizes of these genomic components. Differential introgression can cause some species pairs to deviate dramatically from this pattern. The yellowhammer (Emberiza citrinella) and the pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance but show no mtDNA differentiation. This discordance might be explained by mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). We investigated genome-wide nuclear differentiation between yellowhammers and pine buntings and compared it to what was seen previously in the mitochondrial genome. We found clear nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further tested for preferential introgression of mitonuclear genes and detected evidence for such biased introgression in yellowhammers. Mitonuclear co-introgression can remove post-zygotic incompatibilities between species and may contribute to the continued hybridization between yellowhammers and pine buntings despite their clear morphological and genetic differences. As such, our results highlight the potential ramifications of co-introgression in species evolution.
Phyllotaxis Models: from the Inhibition Potential to the Real Plant

Previous phyllotaxis models allowed the initiation of new primordia when a threshold of inhibition potential is reached on the meristem front: their adequacy to botanical reality is only qualitative. We formulated the hypothesis that it is not the value of the inhibition threshold that remains constant as the meristem develops, but the difference of the inhibition thresholds during the initiation of two successive primordia. We were thus able to model with accuracy the sequence of plastochron ratios observed by Williams (1975) on the leaf meristem of flax: an outstanding result. More generally, we have shown that the evolution trajectories of the phyllotaxis modes as a function of the plastochron ratios follow the minima of the potential under decreasing plastochron ratios constraint and bifurcate when the number of these minima increases, thus giving physicochemical foundations to the famous van Iterson diagram. This historical representation of rising phyllotaxis shows the trajectories, but doesn’t give the velocity of the movement: our plastochron ratio sequence adds this major dynamical information.
Thalamocortical and intracortical contributions to stimulus-evoked and oscillatory activity in rodent primary auditory cortex

Intracortical, horizontal connections seem ideally suited to contribute to cortical processing by spreading information across cortical space and coordinating activity between distant cortical sites. In sensory systems experiments have implicated horizontal connections in the generation of receptive fields and have in turn led to computational models of receptive field generation that rely on the contribution of horizontal connections. Testing the contribution of horizontal connections at the mesoscopic level has been difficult due to the lack of a suitable method to observe the activity of intracortical horizontal connections. Here, we develop such a method based on the analysis of the relative residues of the cortical laminar current source density reconstructions. In the auditory cortex of Mongolian gerbils, the method is then tested by manipulating the contribution of horizontal connections by surgical dissection. Our results indicate that intracortical horizontal connections contribute to the frequency-tuning of mesoscopic cortical patches. Futhermore, we dissociated a type of cortical gamma oscillation based on horizontal connections between mesoscopic patches from gamma oscillations locally generated within mesoscopic patches. The data further imply that global and local coordination of activity during sensory stimulation occur in a low and high gamma frequency band, respectively. Taken together the present data demonstrate that intracortical horizontal connections play an important role in generating cortical feature tuning and coordinate neuronal oscillations across cortex.
In Vitro Activity of Bedaquiline and Imipenem against Actively Growing, Nutrient-Starved, and Intracellular Mycobacterium abscessus

Mycobacterium abscessus lung disease is difficult to treat due to intrinsic drug resistance and the persistence of drug-tolerant bacteria. Currently, the standard of care is a multi-drug regimen with at least 3 active drugs, preferably including a β-lactam (imipenem or cefoxitin). ABSTRACT Mycobacterium abscessus lung disease is difficult to treat due to intrinsic drug resistance and the persistence of drug-tolerant bacteria. Currently, the standard of care is a multidrug regimen with at least 3 active drugs, preferably including a β-lactam (imipenem or cefoxitin). These regimens are lengthy and toxic and have limited efficacy. The search for more efficacious regimens led us to evaluate bedaquiline, a diarylquinoline licensed for treatment of multidrug-resistant tuberculosis. We performed in vitro time-kill experiments to evaluate the activity of bedaquiline alone and in combination with the first-line drug imipenem against M. abscessus under various conditions. Against actively growing bacteria, bedaquiline was largely bacteriostatic and antagonized the bactericidal activity of imipenem. Contrarily, against nutrient-starved persisters, bedaquiline was bactericidal, while imipenem was not, and bedaquiline drove the activity of the combination. In an intracellular infection model, bedaquiline and imipenem had additive bactericidal effects. Correlations between ATP levels and the bactericidal activity of imipenem and its antagonism by bedaquiline were observed. Interestingly, the presence of Tween 80 in the media affected the activity of both drugs, enhancing the activity of imipenem and reducing that of bedaquiline. Overall, these results show that bedaquiline and imipenem interact differently depending on culture conditions. Previously reported antagonistic effects of bedaquiline on imipenem were limited to conditions with actively multiplying bacteria and/or the presence of Tween 80, whereas the combination was additive or indifferent against nutrient-starved and intracellular M. abscessus, where promising bactericidal activity of the combination suggests it may have a role in future treatment regimens.
A Multisubcellular Compartment Model of AMPA Receptor Trafficking for Neuromodulation of Hebbian Synaptic Plasticity

Neuromodulation can profoundly impact the gain and polarity of postsynaptic changes in Hebbian synaptic plasticity. An emerging pattern observed in multiple central synapses is a pull–push type of control in which activation of receptors coupled to the G-protein Gs promote long-term potentiation (LTP) at the expense of long-term depression (LTD), whereas receptors coupled to Gq promote LTD at the expense of LTP. Notably, coactivation of both Gs- and Gq-coupled receptors enhances the gain of both LTP and LTD. To account for these observations, we propose a simple kinetic model in which AMPA receptors (AMPARs) are trafficked between multiple subcompartments in and around the postsynaptic spine. In the model AMPARs in the postsynaptic density compartment (PSD) are the primary contributors to synaptic conductance. During LTP induction, AMPARs are trafficked to the PSD primarily from a relatively small perisynaptic (peri-PSD) compartment. Gs-coupled receptors promote LTP by replenishing peri-PSD through increased AMPAR exocytosis from a pool of endocytic AMPAR. During LTD induction AMPARs are trafficked in the reverse direction, from the PSD to the peri-PSD compartment, and Gq-coupled receptors promote LTD by clearing the peri-PSD compartment through increased AMPAR endocytosis. We claim that the model not only captures essential features of the pull–push neuromodulation of synaptic plasticity, but it is also consistent with other actions of neuromodulators observed in slice experiments and is compatible with the current understanding of AMPAR trafficking.