Miracle-dz/UniFAR-FTUs huggingface dataset:
Predation Risk Perception, Food Density and Conspecific Cues Shape Foraging Decisions in a Tropical Lizard

When foraging, animals can maximize their fitness if they are able to tailor their foraging decisions to current environmental conditions. When making foraging decisions, individuals need to assess the benefits of foraging while accounting for the potential risks of being captured by a predator. However, whether and how different factors interact to shape these decisions is not yet well understood, especially in individual foragers. Here we present a standardized set of manipulative field experiments in the form of foraging assays in the tropical lizard Anolis cristatellus in Puerto Rico. We presented male lizards with foraging opportunities to test how the presence of conspecifics, predation-risk perception, the abundance of food, and interactions among these factors determines the outcome of foraging decisions. In Experiment 1, anoles foraged faster when food was scarce and other conspecifics were present near the feeding tray, while they took longer to feed when food was abundant and when no conspecifics were present. These results suggest that foraging decisions in anoles are the result of a complex process in which individuals assess predation risk by using information from conspecific individuals while taking into account food abundance. In Experiment 2, a simulated increase in predation risk (i.e., distance to the feeding tray) confirmed the relevance of risk perception by showing that the use of available perches is strongly correlated with the latency to feed. We found Puerto Rican crested anoles integrate instantaneous ecological information about food abundance, conspecific activity and predation risk, and adjust their foraging behavior accordingly.
Embryonic expression patterns of the Hox genes of the crayfish Procambarus clarkii (Crustacea, Decapoda)

SUMMARY Higher crustaceans (class Malacostraca) represent the most species‐rich and morphologically diverse group of non‐insect arthropods. The superorders Eucarida and Peracarida, two large groups that separated over 350 million years ago, encompass most malacostracan diversity. Recently, the Hox genes of the peracarid woodlouse Porcellio scaber (Isopoda) were shown to be expressed in domains that coincide with morphological boundaries of body tagmata, which differ from those in insects ( Abzhanov and Kaufman 1999a,b ). Moreover, observed changes in Hox expression domains during ontogeny correlate with morphological remodeling, such as a transformation of the first thoracic leg into mouthpart maxillipeds, which occurs in the trunk of the embryo. Decapods have a different modification of the malacostracan bodyplan, with up to three pairs of maxillipeds and extensive fusion and cephalization of the thorax. Here we describe expression patterns of the trunk Hox genes Scr, Antp, Ubx, abd‐A and cad in the eucarid crayfish Procambarus clarkii (Decapoda). We find that the crayfish expression patterns, for the most part, resemble those of the woodlouse Porcellio scaber (Isopoda), but are more modulated and complex. Nevertheless, as in Porcellio the boundaries of the Hox expression domains do correlate with morphological features and their modulations to transformations in the embryo. Thus we propose that the trunk Hox genes were likely important in the evolution of and currently play an essential role in the development of the complex decapod bodyplan.
Sexual maturity in growing dinosaurs does not fit reptilian growth models

Recent histological studies suggest relatively rapid growth in dinosaurs. However, the timing of reproductive maturity (RM) in dinosaurs is poorly known because unambiguous indicators of RM are rare. One exception is medullary bone (MB), which is an ephemeral bony tissue that forms before ovulation in the marrow cavities of birds as a calcium source for eggshelling. Recently, MB also was described in a single specimen of the saurischian dinosaur Tyrannosaurus rex. Here, we report two other occurrences of MB: in another saurischian dinosaur, Allosaurus, and in the ornithischian dinosaur Tenontosaurus. We show by counting lines of arrested growth and performing growth curve reconstructions that Tenontosaurus, Allosaurus, and Tyrannosaurus were reproductively mature by 8, 10, and 18 years, respectively. RM in these dinosaurs coincided with a transition from growth acceleration to deceleration. It also far precedes predictions based on the growth rates of living reptiles scaled to similar size. Despite relatively rapid growth, dinosaurs were similar to reptiles in that RM developed before reaching asymptotic size. However, this reproductive strategy also occurs in medium- to large-sized mammals and correlates with a strategy of prolonged multiyear growth. RM in actively growing individuals suggests that these dinosaurs were born relatively precocial and experienced high adult mortality. The origin of the modern avian reproductive strategy in ornithuran birds likely coincided with their extreme elevations in growth rate and truncations to growth duration.
Family solidarity in the Netherlands

So far, little is understood about the causes and potential implications of changing family patterns. Insight into these processes is essential in framing policies to safeguard the solidarity thal families help providing.This volume aims to contribute to this insight by offering a first overview of empirical results of the so-called Netherlands Kinship Panel Study (NKPS), a large-scale database on family and kinship in the Netherlands. How much family solidarity is there in the Netherlands and what forms does it take? The popular idea of a middle generation that has to cope with a double caring task has to be qualified: the so-called "sandwich generation" is quite limited in size. The often assumed "lack" of intergenerational solidarity seems to be mainly a problem of those with higher education: the more highly educated have less contact with their parents and children than do those with lower education. Strong family bonds tend to accrue mainly to those who are already in a stronger social position because they are more highly educated, more wealthy and are involved in a partner relationship. Family obligations are much more strongly felt by migrants than by the native Dutch, a finding that is constistent with popular notions of the collectivistic character of family relationships in ethnic communities.
Corynebacterium pseudotuberculosis infection in horses: 538 cases (1982-1993).

OBJECTIVE To describe clinical manifestations of Corynebacterium pseudotuberculosis infection in horses and to evaluate diagnostic methods for identification of this disease. DESIGN Retrospective case series. ANIMALS 538 horses with a diagnosis of C pseudotuberculosis infection. RESULTS Median age of horses with external abscesses was similar to that in horses with internal abscesses. Breed and sex did not appear to be associated with infection. Cases were detected during all 12 months; however, the disease was most common in the fall and early winter, with the highest incidence in September, October, and November in every year. Most horses (492/538, 91.4%) had a single episode of infection, without recurrence in subsequent years. Of 538 horses, 308 had pectoral abscesses, although infection was documented in many other anatomic locations. Forty-two horses had internal abscesses involving the abdomen or thoracic cavity. Corynebacterium pseudotuberculosis infection was readily identified by bacterial culture of aspirate samples from abscesses. The synergistic hemolysis inhibition test was useful for diagnosis of internal abscesses; however, it was unreliable for the diagnosis of external abscesses. Horses with external abscesses responded well to conventional treatment, in contrast to those with internal abscesses. The overall case fatality was low (3.9%), and was considerably lower for horses with external abscesses (0.8%) than for horses with internal abscesses (40.5%). CLINICAL IMPLICATIONS Serology (synergistic hemolysis inhibition titers > or = 512) is useful for diagnosis of internal abscesses, but not reliable for diagnosis in horses with external abscesses. Prognosis for horses with internal abscesses is considerably poorer than for those with external abscesses.
Effect of the 5-HT3 receptor antagonist ondansetron on amphetamine-induced hyperactivity and stereotypy in rats.

The effects of different doses of ondansetron (0.1, 0.5, 1, 2 mg/kg) administered intra-peritoneally were studied on amphetamine-induced hyperactivity and stereotypy in wistar rats. Ondansetron was administered 30 minutes prior to d-amphetamine (3 mg/kg, i.p.). Ondansetron in doses of 0.5 and 1 mg/kg significantly decreased the mean number of head dippings and crossings in the hole board test and in doses of 0.1 and 0.5 mg/kg significantly decreased the average stereotypic score. Since the hyperactivity and stereotypy are dopamine mediated, the effect of ondansetron to reduce these states suggests a potential role for ondansetron in conditions with dopamine excess.
XRCC1 Gene Polymorphism, Clinicopathological Characteristics and Stomach Cancer Survival in Thailand.

BACKGROUND Stomach cancer is one of leading causes of death worldwide. In Thailand, the incidence and mortality of stomach cancer are in the top ten for cancers. Effects of DNA repair gene X-ray repair cross complementary protein 1 (XRCC1) polymorphisms and clinicopathological characteristics on survival of stomach cancer in Thailand have not been previously reported. The aim of this study was to investigate the effects of XRCC1 gene and clinicopathological characteristics on survival of stomach cancer patients in Thailand. MATERIALS AND METHODS Data and blood samples were collected from 101 newly diagnosed stomach cancer cases pathologically confirmed and recruited during 2002 to 2006 and followed-up for vital status until 31 October 2012. Genotype analysis was performed using real-time PCR-HRM. The data were analyzed using the Kaplan-Meier method to yield cumulative survival curve, log-rank test to assess statistical difference of survival and Cox proportional hazard models to estimate adjusted hazard ratio. RESULTS The total followed-up times were 2,070 person-months, and the mortality rate was 4.3 per 100 person-months. The median survival time after diagnosis was 8.07 months. The cumulative 1-, 3-, 5-years survival rates were 40.4%, 15.2 % and 10.1 % respectively. After adjustment, tumour stage were associated with an increased risk of death (p= 0.036). The XRCC1 Gln339Arg, Arg/Arg homozygote was also associated with increased risk but statistically this was non-significant. CONCLUSIONS In addition to tumour stage, which is an important prognostic factor affecting to the survival of stomach cancer patients, the genetic variant Gln339Arg in XRCC1 may non-significantly contribute to risk of stomach cancer death among Thai people. Larger studies with different populations are need to verify ours findings.
Identification of an Intrinsic Determinant Critical for Maspin Subcellular Localization and Function

Maspin, a multifaceted tumor suppressor, belongs to the serine protease inhibitor superfamily, but only inhibits serine protease-like enzymes such as histone deacetylase 1 (HDAC1). Maspin is specifically expressed in epithelial cells and it is differentially regulated during tumor progression. A new emerging consensus suggests that a shift in maspin subcellular localization from the nucleus to the cytoplasm stratifies with poor cancer prognosis. In the current study, we employed a rational mutagenesis approach and showed that maspin reactive center loop (RCL) and its neighboring sequence are critical for maspin stability. Further, when expressed in multiple tumor cell lines, single point mutation of Aspartate346 (D346) to Glutamate (E346), maspinD346E, was predominantly nuclear, whereas wild type maspin (maspinWT) was both cytoplasmic and nuclear. Evidence from cellular fractionation followed by immunological and proteomic protein identification, combined with the evidence from fluorescent imaging of endogenous proteins, fluorescent protein fusion constructs, as well as bimolecular fluorescence complementation (BiFC) showed that the increased nuclear enrichment of maspinD346E was, at least in part, due to its increased affinity to HDAC1. MaspinD346E was also more potent than maspinWT as an HDAC inhibitor. Taken together, our evidence demonstrates that D346 is a critical cis-element in maspin sequence that determines the molecular context and subcellular localization of maspin. A mechanistic model derived from our evidence suggests a new window of opportunity for the development of maspin-based biologically competent HDAC inhibitors for cancer treatment.
Primary and Secondary Reinforcers in Performance of a 1.0-Mile Walk/Jog by Adolescents with Moderate Mental Retardation

Based on visual inspection of data, reinforcement procedures, namely, use of verbal praise and verbal praise plus token exchange, were at least mildly influential in improving performance of 5 youth with moderate mental retardation compared to their initial performance without reinforcers. These findings suggest specific reinforcement may improve the time for aerobic activity by adolescents with moderate mental retardation.
First steps in modelling turbulence and its origins: a commentary on Reynolds (1895) ‘On the dynamical theory of incompressible viscous fluids and the determination of the criterion’

Reynolds' paper sought to explain the change in character of flow through a pipe from laminar to turbulent that his earlier experiments had shown to occur when the dimensionless group that today bears his name exceeded approximately 2000. This he did by decomposing the velocity into mean and fluctuating components and noting how the average kinetic energy generation and dissipation rates changed with Reynolds number. The paper was only grudgingly accepted by two very distinguished referees and initially raised little external interest. As years went by, however, the averaged form of the equations of motion, known as the Reynolds equations (which were an intermediate stage in Reynolds' analysis) became the acknowledged starting point for computing turbulent flows. Moreover, some 50 years after his paper, a refinement of his strategy for predicting transition was also successfully taken up. For some engineering problems, the continual rapid growth of computing resources has meant that more detailed approaches for computing turbulent flow phenomena can nowadays be employed. However, this growth of computing power likewise makes possible a Reynolds-averaging strategy for complex flow systems in industry or the environment which formerly had to adopt less comprehensive analyses. Thus, Reynolds' approach may well remain in use throughout the present century. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
Middle and inner ear modelling: From microCT images to 3D reconstruction and coupling of models

We present finite element (FE) modeling approaches of ear mechanics including 3-dimensional (3D) reconstruction of the human middle and inner ear. Specifically, we demonstrate a semi-automatic methodology for the 3D reconstruction of the inner ear structures, a FE harmonic response model of the middle ear to predict the stapes footplate frequency response, a 2D FE slice model of the cochlea for the coupled response at the micromechanical level for either acoustic or electrical excitation and a coupled FE middle ear model with a simplified cochlea box model to simulate the basilar membrane velocity in response to acoustic excitation. The proposed methodologies are validated against experimental and literature data and the results are in good agreement.
Data-oriented locality sensitive hashing

Locality Sensitive Hashing (LSH) has been proposed as a scalable and high-dimensional index for approximate similarity search. Euclidean LSH is a variation of LSH and has been successfully used in many multimedia applications. However, hash functions of the basic Euclidean LSH project data points over randomly selected directions, which reduces accuracy when data are non-uniformly distributed. So more hash tables are needed to guarantee the accuracy, and thus more memory is consumed. Since heavy memory cost is a significant drawback of Euclidean LSH, we propose Data-Oriented LSH to reduce memory consumption when data are non-uniformly distributed. Most of existing methods are query-directed, such as multi-probe and query expansion methods. We focused on the hash table construction, and thus the query-directed methods can be applied to our index to improve further. The experiment shows that to achieve the same accuracy, our method uses less time and less memory compared with original Euclidean LSH.
The Fallacy of Treating the Ad Baculum as a Fallacy

The ad baculum is not a fallacy in an argument, but is offered instead of an argument to put an end to further argument. This claim is the basis for criticizing Michael Wreen's "neo-traditionalism," which yields misreadings of supposed cases of the ad baculum because of its rejection of any consideration of what the person using the ad baculum, or someone who refers to that use as an "argument," is doing. The paper concludes with reflections on the values that should inform talk of a fallacy in an argument such as the one that Wreen is giving.
Transgenic Rabbits Expressing Ovine PrP Are Susceptible to Scrapie

Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative diseases affecting a wide range of mammalian species. They are caused by prions, a proteinaceous pathogen essentially composed of PrPSc, an abnormal isoform of the host encoded cellular prion protein PrPC. Constrained steric interactions between PrPSc and PrPC are thought to provide prions with species specificity, and to control cross-species transmission into other host populations, including humans. Transgenetic expression of foreign PrP genes has been successfully and widely used to overcome the recognized resistance of mouse to foreign TSE sources. Rabbit is one of the species that exhibit a pronounced resistance to TSEs. Most attempts to infect experimentally rabbit have failed, except after inoculation with cell-free generated rabbit prions. To gain insights on the molecular determinants of the relative resistance of rabbits to prions, we generated transgenic rabbits expressing the susceptible V136R154Q171 allele of the ovine PRNP gene on a rabbit wild type PRNP New Zealand background and assessed their experimental susceptibility to scrapie prions. All transgenic animals developed a typical TSE 6–8 months after intracerebral inoculation, whereas wild type rabbits remained healthy more than 700 days after inoculation. Despite the endogenous presence of rabbit PrPC, only ovine PrPSc was detectable in the brains of diseased animals. Collectively these data indicate that the low susceptibility of rabbits to prion infection is not enciphered within their non-PrP genetic background.
Recognition of Altered Deoxyribonucleic Acid in Recombination

Kinetics of inactivation of transduction by phage P1bt which had been treated with ultraviolet light (UV) or nitrous acid (NA) was examined. With Escherichia coli B/r (radiation-resistant), low doses of UV increased transduction frequency, but the frequency was exponentially inactivated by higher doses. Little initial stimulus was observed in strain Bs−1 (radiation-sensitive). The final rate of decay was the same as in B/r. The initial stimulus of transduction in B/r was probably a consequence of increased recombination resulting from dark repair. It was estimated that another nucleotide within 1000 nucleotide pairs had to be damaged by UV to prevent a given nucleotide from successful transduction. The NA dose response was the same for the two strains. An initial stimulus of transduction was followed by exponential decline. The UV-repair enzymes missing in Bs−1 were not required for repair of NA-induced damage to transducing or lytic phage DNA. Low recovery of new mutations in the transductants showed that mutagen-induced damage to transducing DNA was excluded from recombinant chromosomes. The few recovered mutants may have resulted from “normal” error in recombination.
Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors

Molecular dynamics (MD) simulations of 12 aqueous systems of the NADH-dependent enoyl-ACP reductase from Mycobacterium tuberculosis (InhA) were carried out for up to 20–40 ns using the GROMACS 4.5 package. Simulations of the holoenzyme, holoenzyme-substrate, and 10 holoenzyme-inhibitor complexes were conducted in order to gain more insight about the secondary structure motifs of the InhA substrate-binding pocket. We monitored the lifetime of the main intermolecular interactions: hydrogen bonds and hydrophobic contacts. Our MD simulations demonstrate the importance of evaluating the conformational changes that occur close to the active site of the enzyme-cofactor complex before and after binding of the ligand and the influence of the water molecules. Moreover, the protein-inhibitor total steric (ELJ) and electrostatic (EC) interaction energies, related to Gly96 and Tyr158, are able to explain 80% of the biological response variance according to the best linear equation, pKi = 7.772 − 0.1885 × Gly96 + 0.0517 × Tyr158 (R2 = 0.80; n = 10), where interactions with Gly96, mainly electrostatic, increase the biological response, while those with Tyr158 decrease. These results will help to understand the structure-activity relationships and to design new and more potent anti-TB drugs.
Apnoea–Hypopnoea Index during Rapid Eye Movement and Non-Rapid Eye Movement Sleep in Obstructive Sleep Apnoea

This study investigated the differences in apnoea-hypopnoea index (AHI) during rapid eye movement (REM) sleep (AHI-REM) and AHI during non-REM (NREM) sleep (AHI-NREM) in patients with obstructive sleep apnoea (OSA). Nocturnal polysomnography was performed in 102 Japanese OSA patients and their AHI along with a variety of other factors were retrospectively evaluated. Regardless of the severity of AHI, mean apnoea duration was longer and patients' lowest recorded oxygen saturation measured by pulse oximetry was lower during REM sleep than during NREM sleep. Approximately half of the patients (n = 50) had a higher AHI-NREM than AHI-REM. In subjects with AHI ≤ 60 events/h, AHI-NREM was significantly higher than AHI-REM. On multivariate logistic regression, severe AHI ≤ 30 events/h was the only predictor of a higher AHI-NREM than AHI-REM. This may indicate that important, but unknown, factors related to the mechanism responsible for the severity of OSA are operative during NREM sleep.
Reverse Anthropology

@fmct:Contents @toc4:A note to the reader iii List of illustrations iii Acknowledgements iii A note on language iii @toc2:Introduction 000 1 Historical encounters 000 2 The enchantment of place 000 3 Unrequited reciprocity 000 4 Sorcery and the mine 000 5 Mythical encounters 000 6 Divining violence 000 7 Loss and the future imagined 000 Conclusions 000 @toc4:Notes 000 References 000 Index 000