Miracle-dz/UniFAR-FTUs huggingface dataset:
Policing of reproduction by hidden threats in a cooperative mammal

Significance In social insects, selfish reproduction by workers is suppressed by “policing” behavior, whereby queens and workers identify and destroy worker-laid eggs. An alternative method of policing is to use deterrent threats to prevent offspring production in the first place. Our 7-y field experiment on wild banded mongooses, Mungos mungo, shows that selection to evade the threat of infanticide by older, socially dominant females can explain the evolution of remarkable birth synchrony in this species. The results suggest that reproduction in animal societies can be shaped by threats of punishment that remain hidden until they are triggered experimentally. It follows that coercion may be more widespread than we currently realize. The evolution of cooperation in animal and human societies is associated with mechanisms to suppress individual selfishness. In insect societies, queens and workers enforce cooperation by “policing” selfish reproduction by workers. Insect policing typically takes the form of damage limitation after individuals have carried out selfish acts (such as laying eggs). In contrast, human policing is based on the use of threats that deter individuals from acting selfishly in the first place, minimizing the need for damage limitation. Policing by threat could in principle be used to enforce reproductive suppression in animal societies, but testing this idea requires an experimental approach to simulate reproductive transgression and provoke out-of-equilibrium behavior. We carried out an experiment of this kind on a wild population of cooperatively breeding banded mongooses (Mungos mungo) in Uganda. In this species, each group contains multiple female breeders that give birth to a communal litter, usually on the same day. In a 7-y experiment we used contraceptive injections to manipulate the distribution of maternity within groups, triggering hidden threats of infanticide. Our data suggest that older, socially dominant females use the threat of infanticide to deter selfish reproduction by younger females, but that females can escape the threat of infanticide by synchronizing birth to the same day as older females. Our study shows that reproduction in animal societies can be profoundly influenced by threats that remain hidden until they are triggered experimentally. Coercion may thus extend well beyond the systems in which acts of infanticide are common.
Approximating the set of separable states using the positive partial transpose test

The positive partial transpose test is one of the main criteria for detecting entanglement, and the set of states with positive partial transpose is considered as an approximation of the set of separable states. However, we do not know to what extent this criterion, as well as the approximation, is efficient. In this paper, we show that the positive partial transpose test gives no bound on the distance of a density matrix from separable states. More precisely, we prove that, as the dimension of the space tends to infinity, the maximum trace distance of a positive partial transpose state from separable states tends to 1. Using similar techniques, we show that the same result holds for other well-known separability criteria such as reduction criterion, majorization criterion, and symmetric extension criterion. We also bring in evidence that the sets of positive partial transpose states and separable states have totally different shapes.
Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations

Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low‐resolution experimental data by transforming a known structure. A common application is against data from cryo‐electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants. Application to simulated maps of Ca2+ ATPase and diphtheria toxin as well as experimental data of release factor 2 revealed that for these systems, multiple conformations with similar agreement with the density map exist and a large number of fitting trials are necessary to generate good models. Clustering analysis can be an effective approach to avoid over‐fitting models. In addition, we show that an automatic adjustment of the biasing force constants during the fitting process, implemented as replica‐exchange scheme, can improve the success rate. © 2017 Wiley Periodicals, Inc.
Fine‐scale distribution of moisture in the surface of a degraded blanket bog and its effects on the potential spread of smouldering fire

During rain‐free periods, the water table in peatlands falls and the moisture content (MC) of top 10 cm, including the moss layer, depends upon the hydrophysical properties and the responses of the local composition of species to water deficit. Thus, the ecosystem becomes vulnerable to surface peat fires. The spread of such fires is often irregular; however, there is little understanding of how the fine‐scale variation of peat MC can affect the spread of smouldering fire.
Practical Application of Methanol-Mediated Mutualistic Symbiosis between Methylobacterium Species and a Roof Greening Moss, Racomitrium japonicum

Bryophytes, or mosses, are considered the most maintenance-free materials for roof greening. Racomitrium species are most often used due to their high tolerance to desiccation. Because they grow slowly, a technology for forcing their growth is desired. We succeeded in the efficient production of R. japonicum in liquid culture. The structure of the microbial community is crucial to stabilize the culture. A culture-independent technique revealed that the cultures contain methylotrophic bacteria. Using yeast cells that fluoresce in the presence of methanol, methanol emission from the moss was confirmed, suggesting that it is an important carbon and energy source for the bacteria. We isolated Methylobacterium species from the liquid culture and studied their characteristics. The isolates were able to strongly promote the growth of some mosses including R. japonicum and seed plants, but the plant-microbe combination was important, since growth promotion was not uniform across species. One of the isolates, strain 22A, was cultivated with R. japonicum in liquid culture and in a field experiment, resulting in strong growth promotion. Mutualistic symbiosis can thus be utilized for industrial moss production.
Speech recognition error analysis on the English MALACH corpus

This paper presents an analysis of the word recognition error rate on an English subset of the MALACH corpus. The MALACH project is an NSF-funded research program related to the development of multilingual access to large audio archives. The archive of interest is a large collection of testimonies from 52,000 survivors, liberators, rescuers and witnesses of the Nazi Holocaust, assembled by the Shoah Visual History Foundation. This data has some unique characteristics that make it quite unusual in the speech recognition community such as elderly speech, noisy conditions, heavily accented speech. Hence, it is a challenging task for automatic speech recognition (ASR). This paper attempts to identify the factors affecting the ASR performance on that task. It was found that the signal-to-noise ratio and syllable rate were two dominant factors in explaining the overall word error rate, while we observed no evidence of the impact of accent and speaker’s age on the recognition performance. Based on this evidence, noise compensation experiments were carried out and led to a 1.1% absolute reduction of the word error rate.
Functional Analysis of Neutralizing Antibodies against Clostridium perfringens Epsilon-Toxin

ABSTRACT The Clostridium perfringens epsilon-toxin causes a severe, often fatal illness (enterotoxemia) characterized by cardiac, pulmonary, kidney, and brain edema. In this study, we examined the activities of two neutralizing monoclonal antibodies against the C. perfringens epsilon-toxin. Both antibodies inhibited epsilon-toxin cytotoxicity towards cultured MDCK cells and inhibited the ability of the toxin to form pores in the plasma membranes of cells, as shown by staining cells with the membrane-impermeant dye 7-aminoactinomycin D. Using an antibody competition enzyme-linked immunosorbent assay (ELISA), a peptide array, and analysis of mutant toxins, we mapped the epitope recognized by one of the neutralizing monoclonal antibodies to amino acids 134 to 145. The antibody competition ELISA and analysis of mutant toxins suggest that the second neutralizing monoclonal antibody also recognizes an epitope in close proximity to this region. The region comprised of amino acids 134 to 145 overlaps an amphipathic loop corresponding to the putative membrane insertion domain of the toxin. Identifying the epitopes recognized by these neutralizing antibodies constitutes an important first step in the development of therapeutic agents that could be used to counter the effects of the epsilon-toxin.
Prostate Segmentation: An Efficient Convex Optimization Approach With Axial Symmetry Using 3-D TRUS and MR Images

We propose a novel global optimization-based approach to segmentation of 3-D prostate transrectal ultrasound (TRUS) and T2 weighted magnetic resonance (MR) images, enforcing inherent axial symmetry of prostate shapes to simultaneously adjust a series of 2-D slice-wise segmentations in a “global” 3-D sense. We show that the introduced challenging combinatorial optimization problem can be solved globally and exactly by means of convex relaxation. In this regard, we propose a novel coherent continuous max-flow model (CCMFM), which derives a new and efficient duality-based algorithm, leading to a GPU-based implementation to achieve high computational speeds. Experiments with 25 3-D TRUS images and 30 3-D T2w MR images from our dataset, and 50 3-D T2w MR images from a public dataset, demonstrate that the proposed approach can segment a 3-D prostate TRUS/MR image within 5-6 s including 4-5 s for initialization, yielding a mean Dice similarity coefficient of 93.2% ± 2.0% for 3-D TRUS images and 88.5% ± 3.5% for 3-D MR images. The proposed method also yields relatively low intra- and inter-observer variability introduced by user manual initialization, suggesting a high reproducibility, independent of observers.
THE PHYLOGENETIC PATTERN OF SPECIATION AND WING PATTERN CHANGE IN NEOTROPICAL ITHOMIA BUTTERFLIES (LEPIDOPTERA: NYMPHALIDAE)

Abstract Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification.
Ly6c+ “inflammatory monocytes” are microglial precursors recruited in a pathogenic manner in West Nile virus encephalitis

In a lethal West Nile virus (WNV) model, central nervous system infection triggered a threefold increase in CD45int/CD11b+/CD11c− microglia at days 6–7 postinfection (p.i.). Few microglia were proliferating, suggesting that the increased numbers were derived from a migratory precursor cell. Depletion of “circulating” (Gr1−(Ly6Clo)CX3CR1+) and “inflammatory” (Gr1hi/Ly6Chi/CCR2+) classical monocytes during infection abrogated the increase in microglia. C57BL/6 chimeras reconstituted with cFMS–enhanced green fluorescent protein (EGFP) bone marrow (BM) showed large numbers of peripherally derived (GFP+) microglia expressing GR1+(Ly6C+) at day 7 p.i. , suggesting that the inflammatory monocyte is a microglial precursor. This was confirmed by adoptive transfer of labeled BM (Ly6Chi/CD115+) or circulating inflammatory monocytes that trafficked to the WNV-infected brain and expressed a microglial phenotype. CCL2 is a chemokine that is highly expressed during WNV infection and important in inflammatory monocyte trafficking. Neutralization of CCL2 not only reduced the number of GFP+ microglia in the brain during WNV infection but prolonged the life of infected animals. Therefore, CCL2-dependent inflammatory monocyte migration is critical for increases in microglia during WNV infection and may also play a pathogenic role during WNV encephalitis.
ALMA SURVEY OF LUPUS PROTOPLANETARY DISKS. I. DUST AND GAS MASSES

We present the first high-resolution sub-millimeter survey of both dust and gas for a large population of protoplanetary disks. Characterizing fundamental properties of protoplanetary disks on a statistical level is critical to understanding how disks evolve into the diverse exoplanet population. We use the Atacama Large Millimeter/Submillimeter Array (ALMA) to survey 89 protoplanetary disks around stars with in the young (1–3 Myr), nearby (150–200 pc) Lupus complex. Our observations cover the 890 μm continuum and the 13CO and C18O 3–2 lines. We use the sub-millimeter continuum to constrain to a few Martian masses (0.2–0.4 M⊕) and the CO isotopologue lines to constrain to roughly a Jupiter mass (assuming an interstellar medium (ISM)-like abundance). Of 89 sources, we detect 62 in continuum, 36 in 13CO, and 11 in C18O at significance. Stacking individually undetected sources limits their average dust mass to Lunar masses (0.03 M⊕), indicating rapid evolution once disk clearing begins. We find a positive correlation between and M*, and present the first evidence for a positive correlation between and M*, which may explain the dependence of giant planet frequency on host star mass. The mean dust mass in Lupus is 3× higher than in Upper Sco, while the dust mass distributions in Lupus and Taurus are statistically indistinguishable. Most detected disks have and gas-to-dust ratios , assuming an ISM-like abundance; unless CO is very depleted, the inferred gas depletion indicates that planet formation is well underway by a few Myr and may explain the unexpected prevalence of super-Earths in the exoplanet population.
Alaskan Polar Bear Denning

: Information on 35 overwinter maternity dens of Alaskan polar bears (Ursus maritimnus Phipps) and on 101 female polar bears with cubs, recently emerged from dens, was obtained by aerial and ground surveys, interviews with Arctic coast residents, and literature review. Pregnant females form snow dens in October and November and give birth in December and January. Females and cubs emerge from dens in late March and April. Factors necessary for continued successful denning in an area include ice movements that enable bears to reach the area in the fall; the availability of seals as a food source and ice conditions facilitating their capture during the predenning and postdenning periods; and suitable weather conditions (snowfall, wind, and ambient temperatures) and topography that combine to produce snowdrifts that do not thaw during the denning period. Dens consist of 1 or more chambers, connecting tunnels, and entrance-exit tunnels. Alaskan dens were found as far inland as 48 km from the coast, along the coast, on offshore islands, on shorefast ice, and on drifting sea ice. Bears denning in the coastal zone are subject to human disturbance and should receive protection.
Comparison the effects of paracetamol with sufentanil infusion on postoperative pain control after craniotomy in patients with brain tumor

Background: Patients experience severe pain after craniotomy surgery that leads to discomfort. Our target in this study that performed in interventional method is an evaluation of sufentanil and paracetamol effect on postoperative pain control in patients undergone craniotomy surgery at Urmia Imam Khomeini Hospital. Materials and Methods: Totally, 45 patients between the ages 18 and 65 were studied. The effect of sufentanil and paracetamol medicines in pain management, hemodynamic stability, and side effects compared with control group that were receiving morphine (subcutaneous [SC]) in 3 groups of 15 people at time 0, 2, 4, 12 and 24-h were evaluated. Collected data were included and monitoring blood pressure, O 2 Sat, heart rate (HR) and pain, nausea, vomiting and use of morphine. Results: According to the analysis of results, there was a significant difference between 3 groups on postoperative pain (P < 0.05). In patients that used sufentanil, pain score of visual analog scale (VAS) is lowest and in the paracetamol group the highest VAS score was seen. There was a significant difference in HR between 3 groups (P < 0.05). Maximum average of HR was observed in the paracetamol group. There was a significant difference in mean arterial pressure between 3 groups (P < 0.05). In paracetamol group, there was the highest value (99.3). There was no significant difference in Glasgow Coma scale and SPO 2 between 3 groups (P > 0.05). Conclusion: Sufentanil compared to morphine (which is routinely used for patients pain control after craniotomy surgery) has better pain control, less nausea and vomiting, and better hemodynamic stability. Although paracetamol has the least nausea and vomiting, it has the lowest quality of pain relief.
A polytope calculus for semisimple groups

We define a collection of polytopes associated to a semisimple group G. Weight multiplicities and tensor product multiplicities may be computed as the number of such polytopes fitting in a certain region. The polytopes are defined as moment map images of algebraic cycles discovered by I. Mirkovi ć and K. Vilonen. These cycles are a canonical basis for the intersection homology of (the closures of the strata of) the loop Grassmannian.
Adaptation of Ritchie's Method for Parasites Diagnosing with Minimization of Chemical Products

Latin America, Africa, and Asia present wide dissemination and high prevalence rates of waterborne parasitic diseases, which is a strong indicative of the fragility of public sanitation systems. In this context, parasitological analyses represent extremely relevant instruments. Several parasite diagnosis methods exist, among which Ritchie's method (1948) stands out. This method uses formaldehyde and ether, two reagents of toxicological importance that can cause damages to environmental and occupational health. The present study aimed to compare Ritchie's method modified by Régis Anécimo, without use of solvents, with the traditional Ritchie's method, routinely used for helminth and protozoa diagnosing in Brazil. Some changes were introduced in the modified method, such as controlled increase of water temperature used after stool dilution and substitution of formaldehyde and ether by a neutral detergent before material centrifugation for observation of parasites. In examined samples by both methods, multiple infections were commonly observed; the modified method presented a similar sensitivity to identify the parasites. The development of analytic diagnosis methods that minimize the use of chemical products like ether and formaldehyde represents an important tool to prevent occupational diseases among exposed professionals, as well as to preserve environmental quality through the use of clean techniques.
Neuroendocrine Regulation of GnRH Release in Induced Ovulators

GnRH is the key neuropeptide controlling reproductive function in all vertebrate species. Two different neuroendocrine mechanisms have evolved among female mammals to regulate the mediobasal hypothalamic (MBH) release of GnRH leading to the preovulatory secretion of LH by the anterior pituitary gland. In females of spontaneously ovulating species, including rats, mice, guinea pigs, sheep, monkeys, and women, ovarian steroids secreted by maturing ovarian follicles induce a pulsatile pattern of GnRH release in the median eminence that, in turn, stimulates a preovulatory LH surge. In females of induced ovulating species, including rabbits, ferrets, cats, and camels, the preovulatory release of GnRH, and the resultant preovulatory LH surge, is induced by the receipt of genital somatosensory stimuli during mating. Induced ovulators generally do not show "spontaneous" steroid-induced LH surges during their reproductive cycles, suggesting that the positive feedback actions of steroid hormones on GnRH release are reduced or absent in these species. By contrast, mating-induced preovulatory surges occasionally occur in some spontaneously ovulating species. Most research in the field of GnRH neurobiology has been performed using spontaneous ovulators including rat, guinea pig, sheep, and rhesus monkey. This review summarizes the literature concerning the neuroendocrine mechanisms controlling GnRH biosynthesis and release in females of several induced ovulating species, and whenever possible it contrasts the results with those obtained for spontaneously ovulating species. It also considers the adaptive, evolutionary benefits and disadvantages of each type of ovulatory control mechanism. In females of induced ovulating species estradiol acts in the brain to induce aspects of proceptive and receptive sexual behavior. The primary mechanism involved in the preovulatory release of GnRH among induced ovulators involves the activation of midbrain and brainstem noradrenergic neurons in response to genital-somatosensory signals generated by receipt of an intromission from a male during mating. These noradrenergic neurons project to the MBH and, when activated, promote the release of GnRH from nerve terminals in the median eminence. In contrast to spontaneous ovulators, there is little evidence that endogenous opioid peptides normally inhibit MBH GnRH release among induced ovulators. Instead, the neural signals that induce a preovulatory LH surge in these species seem to be primarily excitatory. A complete understanding of the neuroendocrine control of ovulation will only be achieved in the future by comparative studies of several animal model systems in which mating-induced as well as spontaneous, hormonally stimulated activation of GnRH neurons drives the preovulatory LH surge.