Miracle-dz/UniFAR-FTUs huggingface dataset:
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation.
Regional groundwater flow dynamics and residence times in Chaudière-Appalaches, Québec, Canada: Insights from numerical simulations

As part of the Quebec PACES III provincial groundwater resources assessment programme (Programme d’acquisition des connaissances en eaux souterraines), a regional-scale two-dimensional numerical groundwater model was developed in the Chaudière-Appalaches region, Québec, Canada. The model considers groundwater flow, transport of groundwater age and the influence of a fault on the flow system and its implications for groundwater quality. By including deep and shallow flow systems, the study helps fill a knowledge gap with respect to intermediate flow systems and the role they would play during potential energy resource development including shale gas exploitation from the Utica Shale. Physical and chemical hydrogeological data, including an analysis of 14C in dissolved inorganic carbon in sampled groundwater, supported a regional conceptual flow model forming the basis for numerical simulations. The numerical model is first calibrated to regional piezometry through a semi-automated workflow using the inverse model PEST. Although some evidence for deeper regional flow exists, the area appears to be dominated by local flow systems on maximum length scales of about 5 km, with significant flow through the top 40 to 60 m of the fractured sedimentary rock aquifer. This regional-scale flow model is also supported by the local hydrogeochemical signatures. Simulated mean groundwater ages show young shallow water of < 100 years with rapid increases in age with depth suggesting diffusion-controlled age evolution. Groundwater age is likely being perturbed in the vicinity of the Jacques Cartier River fault, which can act as both a barrier and a preferential pathway, provided permeability contrasts with the surrounding rock are at least two orders of magnitude.
Toric Calabi-Yau Fourfolds Duality Between N=1 Theories and Divisors that Contribute to the Superpotential *

We study issues related to F-theory on Calabi-Yau fourfolds and its duality to heterotic theory for Calabi–Yau threefolds. We discuss principally fourfolds that are described by reflexive polyhedra and show how to read off some of the data for the heterotic theory from the polyhedron. We give a procedure for constructing examples with given gauge groups and describe some of these examples in detail. Interesting features arise when the local pieces are fitted into a global manifold. An important issue is how to compute the superpotential explicitly. Witten has shown that the condition for a divisor to contribute to the superpotential is that it have arithmetic genus 1. Divisors associated with the short roots of non-simply laced gauge groups do not always satisfy this condition while the divisors associated to all other roots do. For such a ‘dissident’ divisor we distinguish cases for which χ(OD) > 1 corresponding to an X that is not general in moduli (in the toric case this corresponds to the existence of non-toric parameters). In these cases the ‘dissident’ divisor D does not remain an effective divisor for general complex structure. If however χ(OD) ≤ 0, then the divisor is general in moduli and there is a genuine instability.
Association of duration and severity of diabetes mellitus with mild cognitive impairment.

BACKGROUND It remains unknown whether diabetes mellitus (DM) is a risk factor for mild cognitive impairment (MCI). OBJECTIVE To investigate the association of DM with MCI using a population-based case-control design. DESIGN Population-based case-control study. SETTING Academic research. PARTICIPANTS Our study was conducted, among subjects aged 70 to 89 years on October 1, 2004, who were randomly selected from the Olmsted County (Minnesota) population. Main Outcome Measure We administered to all participants a neurologic examination, the Clinical Dementia Rating Scale, and a neuropsychological evaluation (including 9 tests in 4 cognitive domains) to diagnose normal cognition, MCI, or dementia. We assessed history of DM, DM treatment, and DM complications by interview, and we measured fasting blood glucose levels. History of DM was also confirmed using a medical records linkage system. RESULTS We compared 329 subjects having MCI with 1640 subjects free of MCI and dementia. The frequency of DM was similar in subjects with MCI (20.1%) and in subjects without MCI (17.7%) (odds ratio [OR], 1.16; 95% confidence interval [CI], 0.85-1.57). However, MCI was associated with onset of DM before age 65 years (OR, 2.20; 95% CI, 1.29-3.73), DM duration of 10 years or longer (OR, 1.76; 95% CI, 1.16-2.68), treatment with insulin (OR, 2.01; 95% CI, 1.22-3.31), and the presence of DM complications (OR, 1.80; 95% CI, 1.13-2.89) after adjustment for age, sex, and education. Analyses using alternative definitions of DM yielded consistent findings. CONCLUSION These findings suggest an association of MCI with earlier onset, longer duration, and greater severity of DM.
Misdiagnosis of High Function Autism Spectrum Disorders in Adults: An

High Function (HF) Autism Spectrum Disorders (ASD) in adulthood is highly prevalent but insufficiently recognized. In Italy, in particular, awareness of this condition is still insufficient and many psychiatrists have no cases of HF ASD to mention. Adult patients with HF ASD come to the attention of Mental Health Services complaining of difficulties within their social context and interpersonal relationships. Objectives: Describe emblematic clinical examples of misdiagnosed HF ASD to understand reasons that conducted to misdiagnosis. Procedure: We contact five specialized Italian Center in diagnosis of ASD. Each center have to describe two or three emblematic cases of adult patient with diagnosis of ASD validated by ADOS-4 but referred to clinicians with another diagnosis, discussing about possible reasons of misdiagnosis. Sample and Results: We have collected 12 case reports (2 from Bologna center, 3 from Torino center, 3 from Pavia center, 2 from Verona center and 2 from Catania center) of adult HF ASD previously misdiagnosed. These cases shows important similarity across centers and highlight that if are taken into account only problems or symptoms that conduct patients to ask help, cases can easily suggest other psychiatric or personality disorders. Diagnosis becomes clear only after considering all the clinical features and a detailed developmental history. Conclusion: Psychiatrists who have insufficient experience of ASD may overlook some symptoms of the overall clinical picture and misdiagnose ASD as personality disorders, schizophrenia, phobia or even as a non-psychiatric condition, so is hopeful for future increased knowledge about HF ASD in adulthood.
Kinesin-dependent mechanism for controlling triglyceride secretion from the liver

Significance The liver secretes lipids in a controlled manner despite vast changes in its internal lipid content. This buffering function of the liver is essential for lipid/energy homeostasis, but its molecular and cellular mechanism is unknown. We show that motor protein kinesin transports lipid droplets (LDs) to the endoplasmic reticulum (ER) in liver cells, engineering ER−droplet contacts and supplying lipids to the ER for secretion as lipoprotein. However, when fasting induces massive lipid accumulation in liver, kinesin is removed from LDs, inhibiting lipid supply to the ER and homeostatically tempering lipid secretion from liver in a fasted state. Interestingly, reducing kinesin also blocks propagation of hepatitis-C virus inside liver cells, possibly because viral proteins cannot transfer from the ER to LDs. Despite massive fluctuations in its internal triglyceride content, the liver secretes triglyceride under tight homeostatic control. This buffering function is most visible after fasting, when liver triglyceride increases manyfold but circulating serum triglyceride barely fluctuates. How the liver controls triglyceride secretion is unknown, but is fundamentally important for lipid and energy homeostasis in animals. Here we find an unexpected cellular and molecular mechanism behind such control. We show that kinesin motors are recruited to triglyceride-rich lipid droplets (LDs) in the liver by the GTPase ARF1, which is a key activator of lipolysis. This recruitment is activated by an insulin-dependent pathway and therefore responds to fed/fasted states of the animal. In fed state, ARF1 and kinesin appear on LDs, consequently transporting LDs to the periphery of hepatocytes where the smooth endoplasmic reticulum (sER) is present. Because the lipases that catabolize LDs in hepatocytes reside on the sER, LDs can now be catabolized efficiently to provide triglyceride for lipoprotein assembly and secretion from the sER. Upon fasting, insulin is lowered to remove ARF1 and kinesin from LDs, thus down-regulating LD transport and sER–LD contacts. This tempers triglyceride availabiity for very low density lipoprotein assembly and allows homeostatic control of serum triglyceride in a fasted state. We further show that kinesin knockdown inhibits hepatitis-C virus replication in hepatocytes, likely because translated viral proteins are unable to transfer from the ER to LDs.
Insect oral secretions suppress wound-induced responses in Arabidopsis

The induction of plant defences and their subsequent suppression by insects is thought to be an important factor in the evolutionary arms race between plants and herbivores. Although insect oral secretions (OS) contain elicitors that trigger plant immunity, little is known about the suppressors of plant defences. The Arabidopsis thaliana transcriptome was analysed in response to wounding and OS treatment. The expression of several wound-inducible genes was suppressed after the application of OS from two lepidopteran herbivores, Pieris brassicae and Spodoptera littoralis. This inhibition was correlated with enhanced S. littoralis larval growth, pointing to an effective role of insect OS in suppressing plant defences. Two genes, an ERF/AP2 transcription factor and a proteinase inhibitor, were then studied in more detail. OS-induced suppression lasted for at least 48 h, was independent of the jasmonate or salicylate pathways, and was not due to known elicitors. Interestingly, insect OS attenuated leaf water loss, suggesting that insects have evolved mechanisms to interfere with the induction of water-stress-related defences.
Drosophila germ-line modulation of insulin signaling and lifespan

Ablation of germ-line precursor cells in Caenorhabditis elegans extends lifespan by activating DAF-16, a forkhead transcription factor (FOXO) repressed by insulin/insulin-like growth factor (IGF) signaling (IIS). Signals from the gonad might thus regulate whole-organism aging by modulating IIS. To date, the details of this systemic regulation of aging by the reproductive system are not understood, and it is unknown whether such effects are evolutionarily conserved. Here we report that eliminating germ cells (GCs) in Drosophila melanogaster increases lifespan and modulates insulin signaling. Long-lived germ-line-less flies show increased production of Drosophila insulin-like peptides (dilps) and hypoglycemia but simultaneously exhibit several characteristics of IIS impedance, as indicated by up-regulation of the Drosophila FOXO (dFOXO) target genes 4E-BP and l (2)efl and the insulin/IGF-binding protein IMP-L2. These results suggest that signals from the gonad regulate lifespan and modulate insulin sensitivity in the fly and that the gonadal regulation of aging is evolutionarily conserved.
Cosparse analysis modeling - uniqueness and algorithms

In the past decade there has been a great interest in a synthesis-based model for signals, based on sparse and redundant representations. Such a model assumes that the signal of interest can be composed as a linear combination of few columns from a given matrix (the dictionary). An alternative analysis-based model can be envisioned, where an analysis operator multiplies the signal, leading to a cosparse outcome. In this paper, we consider this analysis model, in the context of a generic missing data problem (e.g., compressed sensing, inpainting, source separation, etc.). Our work proposes a uniqueness result for the solution of this problem, based on properties of the analysis operator and the measurement matrix. This paper also considers two pursuit algorithms for solving the missing data problem, an L1-based and a new greedy method. Our simulations demonstrate the appeal of the analysis model, and the success of the pursuit techniques presented.
Opus: University of Bath Online Publication Store Divorce and Infidelity Are Associated with Skewed Adult Sex Ratios in Birds 2 3

(2014) Divorce and infidelity are associated with skewed adult sex ratios in birds. This version is made available in accordance with publisher policies. Please cite only the published version using the reference above. 20 Running head: Divorce and infidelity are related to sex ratio 21 22 Word count (without title page, references and figure legends): 2663 23 2 Summary 24 Adult sex ratio (ASR) is a fundamental concept in population demography, and 25 recent theory suggests that ASR plays a central role in social behaviour, mating 26 systems and parental care [1-6]. Unbalanced ASRs are predicted to influence 27 pair-bond and mating behaviour since the rarer sex in the population has more 28 potential partners to mate with than the more common sex [1, 4]. Here we use 29 phylogenetic comparative analyses to test whether ASR is related to three major 30 aspects of mating behaviour: divorce, social polygamy and pair-bond infidelity. 31 ASR is strongly correlated with long-term pair-bonds since divorce rate is higher 32 in species with female-biased sex ratio, indicating that mate change by pair 33 members and/or breaking of pair-bonds by unmated individuals is more 34 frequent when females outnumber males. Short-term pair-bonds are also 35 associated with unbalanced ASRs: males are more commonly polygamous when 36 females outnumber males, and conversely, females are more polygamous when 37 males outnumber females. Furthermore, infidelity increases with male-biased 38 ASR in socially monogamous birds, suggesting that male coercion and/or female 39 willingness to cheat the partner are facilitated by male-biased ASR. Our results 40 provide the first comprehensive support for the proposition that ASR influences 41 multiple aspects of pair-bonds and mating behaviour in wild populations. 42 43 44 3 Results and Discussion 45 The significance of adult sex ratios 46 Adult sex ratio (ASR, defined here as the proportion of adult males in the adult 47 population) is one of the fundamental demographic characteristics that impacts on 48 population growth, demography and extinctions [3, 5, 6]. Recent theoretical models 49 predict that ASR also influences social behaviour including pair-bonds, mating 50 behaviour and parental care [1, 2, 4]. Relationships between ASR and mating 51 behaviour are expected since the members of the rarer sex have more potential 52 partners to mate with, so they may obtain (or change) mate more easily than members 53 of the common sex [1, 2, 4, 7]. For example, in a population …
Specific airway resistance, interrupter resistance, and respiratory impedance in healthy children aged 2–7 years

We report data on respiratory function in healthy children aged 2–7 years in whom we measured respiratory resistance by the interrupter technique (Rint); total respiratory impedance (Zrs), respiratory resistance (Rrs), and reactance (Xrs) by the impulse oscillation technique; and specific airway resistance (sRaw) by a modified procedure method in the whole body plethysmograph. Measurements were attempted in 151 children and were successfully obtained in 121 children with a mean (SD) age of 5.3 (1.5) years; no measurements were possible in 30 children (mean age 3 (0.9) years).
Balloon Catheter Injury to Rabbit Carotid Artery: II. Selective Increase in Reactivity to Some Vasoconstrictor Drugs

The present study examined the changes in reactivity to a variety of vasoconstrictor drugs of the rabbit carotid artery during development of an Intlmal thickening induced by Injury with an Inflated balloon catheter. The Injured and the unoperated contralateral carotid arteries were studied at 2 and 6 weeks after the operation. To differentiate areas of the Injured artery lined by modified smooth muscle cells from areas lined by regenerated endothellal cells, each rabbit was Injected with Evans blue dye before sacrifice. Ring segments (3 mm length) from the control and injured arteries were mounted In organ baths to record the circumferential Isometric force with a technique that ensured that all rings were set to equivalent Initial resting conditions of passive transmural stretch. Compared with the controls, the experimental arteries had a significantly decreased maximum contraction (E) In response to KCI at both 2 and 6 weeks. The experimental arteries were also significantly less sensitive to the a1-adrenoceptor agonist, methoxamlne, at both 2 weeks (approximately sevenfold) and 6 weeks (fourfold), with a marked decrease in Emax at 2 weeks, which returned to control values at 6 weeks. There was no change In Emax, to either serotonin or the thromboxane Aj-mlmetic, U46619, In the experimental arteries at either time. There was, however, a small but significant Increase In the sensitivity to both drugs. There was no difference In response to any of the constrictor agents between the white and blue regions of the experimental vessels. We propose that the selective increase in responsiveness to certain platelet-derived autocotds In the Injured artery may be related to the changes In smooth muscle cell phenotype observed throughout the media and neolntima and reported In our companion article. These modifications In arterial reactivity may contribute to the development of spasm In arteries with atherosclerotic lesions.
Effects of different ratios and storage periods of liquid brewer’s yeast mixed with cassava pulp on chemical composition, fermentation quality and in vitro ruminal fermentation

Objective This study aims to evaluate the chemical composition, fermentation quality and in vitro ruminal fermentation of various ratios and storage periods of liquid brewer’s yeast (LBY) mixed with cassava pulp (CVP). Methods Four mixtures of fresh LBY and CVP were made (LBY0, LBY10, LBY20, and LBY30 for LBY:CVP at 0:100, 10:90, 20:80, and 30:70, respectively) on a fresh matter basis, in 500 g in plastic bags and stored at 30 to 32°C. After storage, the bags were opened weekly from weeks 0 to 4. Fermentation quality and in vitro gas production (IVGP) were determined, as well as the dry matter (DM), organic matter (OM), crude protein (CP), ether extract (EE), neutral detergent fiber, acid detergent fiber and acid detergent lignin contents. Results The contents of CP and EE increased, whereas all other components decreased, in proportion to LBY inclusion (p<0.01). The DM and OM contents gradually decreased in weeks 3 and 4 (p<0.05), while EE contents were lowest in week 0. The pH, ammonia nitrogen per total nitrogen (NH3-N/TN) and V-score in each mixture and storage period demonstrated superior fermentation quality (pH≤4.2, NH3-N/TN≤12.5%, and V-score>90%). The pH increased and NH3-N/TN decreased, with proportionate increases of LBY, whereas the pH decreased and NH3-N/TN increased, as the storage periods were extended (p<0.01). Although IVGP decreased in proportion to the amount of LBY inclusion (p<0.01), in vitro organic matter digestibility (IVOMD) was unaffected by the mixture ratios. The highest IVGP and IVOMD were observed in week 0 (p<0.01). Conclusion The inclusion of LBY (as high as 30%) into CVP improves the chemical composition of the mixture, thereby increasing the CP content, while decreasing IVGP, without decreasing fermentation quality and IVOMD. In addition, a preservation period of up to four weeks can guarantee superior fermentation quality in all types of mixtures. Therefore, we recommend limiting the use of CVP as a feed ingredient, given its low nutritional value and improving feed quality with the inclusion of LBY.
Three counting methods agree on cell and neuron number in chimpanzee primary visual cortex

Determining the cellular composition of specific brain regions is crucial to our understanding of the function of neurobiological systems. It is therefore useful to identify the extent to which different methods agree when estimating the same properties of brain circuitry. In this study, we estimated the number of neuronal and non-neuronal cells in the primary visual cortex (area 17 or V1) of both hemispheres from a single chimpanzee. Specifically, we processed samples distributed across V1 of the right hemisphere after cortex was flattened into a sheet using two variations of the isotropic fractionator cell and neuron counting method. We processed the left hemisphere as serial brain slices for stereological investigation. The goal of this study was to evaluate the agreement between these methods in the most direct manner possible by comparing estimates of cell density across one brain region of interest in a single individual. In our hands, these methods produced similar estimates of the total cellular population (approximately 1 billion) as well as the number of neurons (approximately 675 million) in chimpanzee V1, providing evidence that both techniques estimate the same parameters of interest. In addition, our results indicate the strengths of each distinct tissue preparation procedure, highlighting the importance of attention to anatomical detail. In summary, we found that the isotropic fractionator and the stereological optical fractionator produced concordant estimates of the cellular composition of V1, and that this result supports the conclusion that chimpanzees conform to the primate pattern of exceptionally high packing density in V1. Ultimately, our data suggest that investigators can optimize their experimental approach by using any of these counting methods to obtain reliable cell and neuron counts.