Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach

Abstract The branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth–death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation]
Pheromonally mediated mate attraction by males of the burying beetle Nicrophorus orbicollis: alternative calling tactics conditional on both intrinsic and extrinsic factors

Male burying beetles attract females using a pheromonal signal and can provide parental care and a food resource, vertebrate carrion, for their developing offspring. But males attempt to attract females even when they have no carrion. We examined the factors that influence male behavior directed toward finding or attracting mates in both field-caught and laboratory-reared Nicrophorus orbicollis, a North American burying beetle. We investigated whether male behavior differed based on both intrinsic (size) and extrinsic (resources held) differences among males. Further, we examined repeatability of individual behaviors and the effect of holding or lacking resources on these repeatabilities. Field-caught and laboratory-reared individuals differed in overall activity but not in their behavioral repertoire, making studies of laboratory-reared males relevant. The behavior of individual males was very consistent within a condition, but plastic between resource conditions. The frequency of calling (adopting a posture that indicates pheromone release to attract females) depended on male size when males did not hold resources, but this relationship disappeared when males held resources. Without carrion, smaller males called more frequently than did larger males. When holding carrion, smaller males reduced their calling, whereas larger males significantly increased the frequency with which they attempted to attract females and reduced the amount of time they spent searching. Thus, calling behavior of males was conditional on not only intrinsic and extrinsic factors, but also an interaction between them. We suggest that the changes in calling represent alternative tactics based on the costs and benefits of attracting both potential mates and competitors, which differ for males of different sizes.
Influence of stream size on ammonium and suspended particulate nitrogen processing

We used 15NH4 tracer additions to determine travel distances of ammonium (NH4 ) and suspended particulate organic nitrogen (SPON) in six streams ranging from second to fifth order located within a single watershed on the North Slope of Alaska. Based on the distribution of 15N stored in stream bottom compartments (primary producers or grazers), we estimated NH4 travel lengths. We used a two‐compartment model to estimate the travel length of SPON based on the distribution of source 15N on the stream bottom and SPO 15N in the water column. Both NH4 and SPON travel lengths (Sw and Sp, respectively) increased with discharge primarily due to changes in depth and velocity. Variation in the vertical mass transfer coefficient (vf) of both NH4 and SPON did occur among the streams but was not related to stream size and was relatively small compared to the change in physical characteristics. Thus, in the Kuparuk watershed, physical gradients outweighed biological or chemical changes as controls on NH4 and SPON travel length. The one exception was the Kuparuk fertilized reach, where phosphorus fertilization greatly increased biological activity and NH4 processing compared to unaltered streams. Longitudinal gradients in major biological driving variables such as litter inputs, debris dams, and shading are absent in the Arctic, perhaps explaining the relatively uniform NH4 ‐ vf. Watersheds in other biomes may show differing degrees of physical versus biological/chemical controls. A conceptual model is presented for comparing the relative strength of these controls among different watersheds. Strong relationships between discharge and travel length should greatly aid development of watershed models of nutrient dynamics.
Histopathologic Assessment of Suspected Idiopathic Pulmonary Fibrosis: Where We Are and Where We Need to Go.

CONTEXT. — Accurate diagnosis of idiopathic pulmonary fibrosis (IPF) requires multidisciplinary diagnosis that includes clinical, radiologic, and often pathologic assessment. In 2018, the American Thoracic Society, European Respiratory Society, Japanese Respiratory Society, and the Latin American Thoracic Society (ATS/ERS/JRS/ALAT) and the Fleischner Society each published guidelines for the diagnosis of IPF, which include criteria for 4 categories of confidence of a histologic usual interstitial pneumonia (UIP) pattern. OBJECTIVE. — To (1) identify the role of the guidelines in pathologic assessment of UIP; (2) analyze the 4 guideline categories, including potential areas of difficulty; and (3) determine steps the Pulmonary Pathology Society and the greater pulmonary pathology community can take to improve current guideline criteria and histopathologic diagnosis of interstitial lung disease. DATA SOURCES. — Data were derived from the guidelines, published literature, and clinical experience. CONCLUSIONS. — Both guidelines provide pathologists with a tool to relay to the clinician the likelihood that a biopsy represents UIP, and serve as an adjunct, not a replacement, for traditional histologic diagnosis. There are multiple challenges with implementing the guidelines, including (1) lack of clarity on the quantity and quality of histologic findings required, (2) lack of recognition that histologic features cannot be assessed independently, and (3) lack of guidance on how pathologists should incorporate clinical and radiographic information. Current criteria for "probable UIP" and "indeterminate for UIP" hinder accurate reflection of the likelihood of IPF. These challenges highlight the need for further morphologic-based investigations in the field of pulmonary pathology.
Genetic suppression of defective profilin by attenuated Myosin II reveals a potential role for Myosin II in actin dynamics in vivo in fission yeast

The actin cytoskeleton plays a variety of roles in eukaryotic cell physiology, ranging from cell polarity and migration to cytokinesis. Key to the function of the actin cytoskeleton is the mechanisms that control its assembly, stability, and turnover. Through genetic analyses in Schizosaccharomyces pombe, we found that myo2-S1 (myo2-G515D), a Myosin II mutant allele, was capable of rescuing lethality caused by partial defects in actin nucleation/stability caused, for example, through compromised function of the actin-binding protein Cdc3-profilin. The mutation in myo2-S1 affects the activation loop of Myosin II, which is involved in physical interaction with subdomain 1 of actin and in stimulating the ATPase activity of Myosin. Consistently, actomyosin rings in myo2-S1 cell ghosts were unstable and severely compromised in contraction on ATP addition. These studies strongly suggest a role for Myo2 in actin cytoskeletal disassembly and turnover in vivo, and that compromise of this activity leads to genetic suppression of mutants defective in actin filament assembly/stability at the division site.
Dual versus single vessel normothermic ex vivo perfusion of rat liver grafts using metamizole for vasodilatation

Background Normothermic ex vivo liver perfusion (NEVLP) is a promising strategy to increase the donor pool in liver transplantation. Small animal models are essential to further investigate questions regarding organ preservation and reconditioning by NEVLP. A dual vessel small animal NEVLP (dNEVLP) model was developed using metamizole as a vasodilator and compared to conventional portovenous single vessel NEVLP (sNEVLP). Methods Livers of male Wistar rats were perfused with erythrocyte-supplemented culture medium for six hours by either dNEVLP via hepatic artery and portal vein or portovenous sNEVLP. dNEVLP was performed either with or without metamizole treatment. Perfusion pressure and flow rates were constantly monitored. Transaminase levels were determined in the perfusate at the start and after three and six hours of perfusion. Bile secretion was monitored and bile LDH and GGT levels were measured hourly. Histopathological analysis was performed using liver and bile duct tissue samples after perfusion. Results Hepatic artery pressure was significantly lower in dNEVLP with metamizole administration. Compared to sNEVLP, dNEVLP with metamizole treatment showed higher bile production, lower levels of transaminases during and after perfusion as well as significantly lower necrosis in liver and bile duct tissue. Biochemical markers of bile duct injury showed the same trend. Conclusion Our miniaturized dNEVLP system enables normothermic dual vessel rat liver perfusion. The administration of metamizole effectively ameliorates arterial vasospasm allowing for six hours of dNEVLP, with superior outcome compared to sNEVLP.
Managing Evolving Fish Stocks

Darwinian evolution is the driving process of innovation and adaptation across the world’s biota. Acting on top of natural selection, human-induced selection pressures can also cause rapid evolution. Sometimes such evolution has undesirable consequences, one example being the spreading resistance to antibiotics and pesticides, which causes suffering and billion-dollar losses annually (1). A comparable anthropogenic selection pressure originates from fishing, which has become the main source of mortality in many fish stocks, and may exceed natural mortality by more than 400% (2). This has, however, been largely ignored, even though studies based on fisheries data and controlled experiments have provided strong empirical evidence for fisheries-induced evolution over a range of species and regions (see table, page 1248). These evolutionary changes are unfolding on decadal time scales—much faster than previously thought. Life-history theory predicts that increased mortality generally favors evolution toward earlier sexual maturation at smaller size and elevated reproductive effort. Fishing that is selective with respect to size, maturity status, behavior, or morphology causes further evolutionary pressures (3). Evidence that harvesting can bring about genetic changes comes from breeding programs in aquaculture, which have shown heritable genetic variation in numerous traits (4), and from experiments
Draft Genome Sequence of Putative 2-Methylisoborneol-Producing Pseudanabaena yagii Strain GIHE-NHR1, Isolated from the North Han River in South Korea

The draft genome sequence of Pseudanabaena yagii GIHE-NHR1, a filamentous cyanobacterium, is reported here. Comparative genome analysis suggests that this strain can produce an odor-causing compound (2-methylisoborneol) in water. The genome information is expected to improve the understanding of the putative 2-methylisoborneol production by the bacterium. ABSTRACT The draft genome sequence of Pseudanabaena yagii GIHE-NHR1, a filamentous cyanobacterium, is reported here. Comparative genome analysis suggests that this strain can produce an odor-causing compound (2-methylisoborneol) in water. The genome information is expected to improve the understanding of the putative 2-methylisoborneol production by the bacterium.
Pediatric Distraction on Induction of Anesthesia With Virtual Reality and Perioperative Anxiolysis: A Randomized Controlled Trial.

BACKGROUND Perioperative pediatric anxiety is common and can have a negative psychological impact on children undergoing surgery and anesthesia. Studies have shown an incidence of anxiety at induction of up to 50%. Audiovisual distraction, including virtual reality (VR), is a noninvasive, nonpharmacological modality that may reduce perioperative anxiety. The goal of this study was to determine whether immersive audiovisual distraction with a VR headset during induction of general anesthesia (GA) in pediatric patients reduced preoperative anxiety. METHODS In this randomized-controlled, parallel-group study, 71 children 5-12 years of age scheduled for elective surgery with GA were randomly allocated to a VR group or a non-VR (No VR) control group. VR group patients underwent audiovisual distraction with a VR headset during induction in the operating room, whereas the control group received no audiovisual distraction. The primary outcome was the Modified Yale Preoperative Anxiety Scale (mYPAS), which was measured at 3 time points to assess patient anxiety: in the preoperative holding area before randomization, on entering the operating room, and during induction of GA. The primary outcome was analyzed using univariate analysis and a linear mixed-effects model. Secondary outcomes included postinduction parental anxiety measured by the State-Trait Anxiety Inventory, pediatric induction compliance, and parental satisfaction. RESULTS Average patient age was 8.0 ± 2.3 years (mean ± standard deviation [SD]), and 51.4% of patients were female. Baseline variables were not substantially different between the VR group (33 patients) and the No VR group (37 patients). No patients received preoperative anxiolytic medication. Baseline mYPAS scores were not different between the groups, with scores of 28.3 (23.3-28.3) (median [interquartile range {IQR}]) in both. The change in mYPAS scores from baseline to time of induction was significantly lower in the VR group versus control group (0.0 [0.0-5.0] vs 13.3 [5.0-26.7]; P< .0001). In the mixed-effects model, the VR group had an estimated 6.0-point lower mYPAS score (95% confidence interval [CI], 0.7-11.3; P= .03) at room entry than the No VR group, and 14.5-point lower score (95% CI, 9.3-19.8; P< .0001) at induction versus control. Randomization to VR did not alter parental anxiety (0 [-2 to 2]), pediatric induction compliance (0 [0-0]), or parental satisfaction (-3 [-8 to 2]) (difference in medians [95% CI]). CONCLUSIONS This study demonstrates a reduction in pediatric preoperative anxiety with the use of VR. Preoperative VR may be an effective noninvasive modality for anxiolysis during induction of anesthesia in children.
Self-awareness for financial decision-making abilities in healthy adults

Objective Decades of research have established how to measure metacognition (i.e., awareness of one’s cognitive abilities), whereas relatively little is known about how to assess the integrity of financial awareness (FA; awareness of one’s financial abilities), a related construct with practical implications for vulnerable older adults. The current study’s goal was to apply established metacognitive frameworks to identify an objective measure of FA. Methods Metacognitive ratings were integrated into two financial decision making (FDM) assessments in order to derive two types of FA metrics: absolute accuracy (calibration) and relative accuracy (resolution) in each FDM task. Associations between each FA metric, demographic variables, FDM performances, and metamemory were examined. Design & setting Cross-sectional, community-based, prospective study. Participants 93 individuals with mean age = 59 years (SD = 15.12); mean education = 15.70 (SD = 2.39); 60% females. Measures FA was calculated using the Financial Competency Assessment Inventory (FCAI) and Decision Making Competence Assessment Tool, Finance Module (DMC-F), and memory awareness was calculated using an objective metamemory test. Results None of the FA metrics was associated with age, education or gender. FCAI calibration was inversely associated with FDM, and positively correlated with DMC-F calibration and metamemory calibration. None of the FA metrics for DMC-F was associated with metamemory. Conclusions Mirroring findings from metamemory studies, overconfidence in FDM was associated with lower FDM accuracy in healthy adults. Moreover, calibration scores on the FCAI and metamemory were related, suggesting that FA taps into metacognitive abilities. Our findings provide preliminary evidence for how to measure FA in both clinical and research contexts.
Convergent evolution of the cavefish Astyanax (Characidae, Teleostei): genetic evidence from reduced eye‐size and pigmentation

More than 20 populations of the cave-dwelling characid Astyanax occur within a restricted karst area in Mexico. The fish possess reduced eyes without lenses and visual cells. It is still an open question as to whether this condition evolved convergently after multiple entries of the surface ancestor into the different caves or whether a single cave ancestor, already characterized by reduced eyes, spread secondarily within them. In the crosses between specific populations, specimens appear that deviate considerably from those of the parents. They possess larger and better-developed eyes with histologically intact lenses and visual cells; they thus have the structural potential for vision. This indicates that in different cave populations, different mutations in the eye gene system have occurred. In cases where these non-functional rudimentary genes are recombined in hybrid specimens, gene expression may be restored. This is the result of separate evolution of several Astyanax cave populations. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 545−554.
Serotonin 5‐HT3 receptors in rat CA1 hippocampal interneurons: functional and molecular characterization

The molecular makeup of the serotonin 5‐HT3 receptor (5‐HT3R) channel was investigated in rat hippocampal CA1 interneurons in slices using single‐cell RT‐PCR and patch‐clamp recording techniques. We tested for the expression of the 5‐HT3A (both short and long splice variants) and 5‐HT3B subunits, as well as the expression of the α4 subunit of the neuronal nicotinic ACh receptors (nAChRs), the latter of which has been shown to co‐assemble with the 5‐HT3A subunit in heterologous expression systems. Both the 5‐HT3A‐short and α4‐nAChR subunits were expressed in these interneurons, but we could not detect any expression of either the 5‐HT3B or the 5‐HT3A‐long subunits. Furthermore, there was a strong tendency for the 5‐HT3A‐short and α4‐nAChR subunits to be co‐expressed in individual interneurons. To assess whether there was any functional evidence for co‐assembly between the 5‐HT3A‐short and α4‐nAChR subunits, we used the sulphydryl agent 2‐aminoethyl methanethiosulphonate (MTSEA), which has previously been shown to modulate expressed 5‐HT3Rs that contain the α4‐nAChR subunit. In half of the interneurons examined, MTSEA significantly enhanced the amplitude of the 5‐HT3R‐mediated responses, which is consistent with the notion that the α4‐nAChR subunit co‐assembles with the 5‐HT3A subunit to form a native heteromeric 5‐HT3R channel in rat CA1 hippocampal interneurons in vivo. In addition, the single‐channel properties of the 5‐HT3R were investigated in outside‐out patches. No resolvable single‐channel currents were observed. Using non‐stationary fluctuation analysis, we obtained an estimate of the single‐channel conductance of 4 pS, which is well below that expected for channels containing both the 5‐HT3A and 5‐HT3B subunits.
Teriparatide for the Treatment of Medication-Related Osteonecrosis of the Jaw

Medication-related osteonecrosis of the jaw (MRONJ) is a painful and intractable disease of the jaw that clinically presents as an area of ulceration with exposed necrotic bone. In severe cases, it can predispose to jaw fracture, skin fistula, or osteolysis extending beyond the region of the alveolar bone. No effective treatment has been established for this condition. Recently, teriparatide, a recombinant parathyroid hormone, and the only FDA-approved osteoanabolic drug for the treatment of glucocorticoid-induced osteoporosis, has been used for the treatment of MRONJ. We review the literature highlighting the effectiveness of teriparatide alone or as an adjunct in the treatment of MRONJ. Twenty publications met our selection criteria, comprising 54 patients with stage 2 or 3 MRONJ secondary to antiresorptive/antiangiogenic drugs. Trauma due to implant placement was the most common triggering factor for the development of MRONJ. Patients were treated with subcutaneous injections of 20-μg teriparatide for 3–12 months (5 1/2 months average). Symptomatic relief was achieved in almost all cases, with lesions healing completely in 49 of 54 patients. Based on our findings, teriparatide can play an important role in the treatment of MRONJ.
Using Conceptual Norms for Metaphor Detection

This paper reports a linguistically-enriched method of detecting token-level metaphors for the second shared task on Metaphor Detection. We participate in all four phases of competition with both datasets, i.e. Verbs and AllPOS on the VUA and the TOFEL datasets. We use the modality exclusivity and embodiment norms for constructing a conceptual representation of the nodes and the context. Our system obtains an F-score of 0.652 for the VUA Verbs track, which is 5% higher than the strong baselines. The experimental results across models and datasets indicate the salient contribution of using modality exclusivity and modality shift information for predicting metaphoricity.
Distinct neural correlates of social and object reward seeking motivation

The “Choose‐a‐Movie‐CAM” is an established task to quantify the motivation for seeking social rewards. It allows participants to directly assess both the stimulus value and the effort required to obtain it. In the present study, we aimed to identify the neural mechanisms of such cost‐benefit decision‐making. To this end, functional Magnetic Resonance Imaging data were collected from 24 typical adults while they completed the CAM task. We partly replicated the results from our previous behavioural studies showing that typical adults prefer social over object stimuli and low effort over higher effort stimuli but found no interaction between the two. Results from neuroimaging data suggest that there are distinct neural correlates for social and object preferences. The precuneus and medial orbitofrontal cortex, two key areas involved in social processing are engaged when participants make a social choice. Areas of the ventral and dorsal stream pathways associated with object recognition are engaged when making an object choice. These activations can be seen during the decision phase even before the rewards have been consumed, indicating a transfer the hedonic properties of social stimuli to its cues. We also found that the left insula and bilateral clusters in the inferior occipital gyrus and the inferior parietal lobule were recruited for increasing effort investment. We discuss limitations and implications of this study which reveals the distinct neural correlates for social and object rewards, using a robust behavioural measure of social motivation.