Miracle-dz/UniFAR-FTUs huggingface dataset:
EFFECT PROPAGATION IN A TOXICOKINETIC/TOXICODYNAMIC MODEL EXPLAINS DELAYED EFFECTS ON THE GROWTH OF UNICELLULAR GREEN ALGAE SCENEDESMUS VACUOLATUS

Ecotoxicological standard tests assess toxic effects by exposing an organism to high concentrations over defined periods of time. To evaluate toxicity under field conditions such as fluctuating and pulsed exposures, process‐based toxicokinetic/toxicodynamic (TK/TD) models may be used for extrapolation from the existing evidence. A TK/TD model was developed that simulates the effect on growth of the green algae Scenedesmus vacuolatus continuously exposed to the model chemicals norflurazon, triclosan, and N‐phenyl‐2‐naphthylamine. A pharmacological time–response model describing the effects of anticancer treatments on cancer cell growth was adapted and modified to model the affected growth of synchronized algae cells. The TK/TD model simulates the temporal effect course by linking the ambient concentration of a chemical to the observable adverse effect via an internal concentration and a sequence of biological events in the organism. The parameters of the toxicodynamic model are related to the growth characteristics of algae cells, a no effect concentration, the chemical efficacy as well as the ability of recovery and repair, and the delay during damage propagation. The TK/TD model fits well to the observed algae growth. The effect propagation through cumulative cell damage explained the observed delayed responses better than just the toxicokinetics. The TK/TD model could facilitate the link between several effect levels within damage propagation, which prospectively may be helpful to model adverse outcome pathways and time‐dependent mixture effects. Environ. Toxicol. Chem. 2013;32:1161–1172. © 2013 SETAC
Satisfaction of Patients After Treatment With Botulinum Toxin for Dynamic Facial Lines

OBJECTIVE To gain first evidence on the patient satisfaction after treatment with botulinum toxin type A (BTX-A) and to check for differences in satisfaction with respect to clinical, psychologic, and sociodemographic parameters. METHODS In this pilot study, 30 patients who had been treated with BTX-A within the last 3 months answered a standardized questionnaire (the Freiburg questionnaire on aesthetic dermatology and cosmetic surgery). The items assessed were attitudes on beauty and body, satisfaction with treatment outcome, and general quality of life. A prospective study consisting of the same items runs parallel and will be published later. RESULTS More than 80% of the patients answered that the treatment had been beneficial to them. All patients would recommend treatment completely or mostly. Only a very small part of the patients was moderately stressed by the treatment. CONCLUSION Injections with BTX-A is a satisfying and well-tolerated treatment of dynamic facial lines for all patients in this pilot study.
Select and Sample - A Model of Efficient Neural Inference and Learning

An increasing number of experimental studies indicate that perception encodes a posterior probability distribution over possible causes of sensory stimuli, which is used to act close to optimally in the environment. One outstanding difficulty with this hypothesis is that the exact posterior will in general be too complex to be represented directly, and thus neurons will have to represent an approximation of this distribution. Two influential proposals of efficient posterior representation by neural populations are: 1) neural activity represents samples of the underlying distribution, or 2) they represent a parametric representation of a variational approximation of the posterior. We show that these approaches can be combined for an inference scheme that retains the advantages of both: it is able to represent multiple modes and arbitrary correlations, a feature of sampling methods, and it reduces the represented space to regions of high probability mass, a strength of variational approximations. Neurally, the combined method can be interpreted as a feed-forward preselection of the relevant state space, followed by a neural dynamics implementation of Markov Chain Monte Carlo (MCMC) to approximate the posterior over the relevant states. We demonstrate the effectiveness and efficiency of this approach on a sparse coding model. In numerical experiments on artificial data and image patches, we compare the performance of the algorithms to that of exact EM, variational state space selection alone, MCMC alone, and the combined select and sample approach. The select and sample approach integrates the advantages of the sampling and variational approximations, and forms a robust, neurally plausible, and very efficient model of processing and learning in cortical networks. For sparse coding we show applications easily exceeding a thousand observed and a thousand hidden dimensions.
Nursing a Patient during and after 90Y-Ibritumomab Tiuxetan (Zevalin™) Therapy

Radioimmunotherapy (RIT) is a new cancer therapy that uses monoclonal antibodies to deliver targeted radiation to cancer cells, allowing multiple sites of disseminated disease to be treated simultaneously, while limiting toxicity to normal healthy tissue. 90Y-ibritumomab tiuxetan was the first RIT to be approved for the treatment of relapsed and refractory B-cell non-Hodgkin's lymphoma (NHL), and consists of the anti-CD20 murine monoclonal antibody, ibritumomab, covalently bound to the linker tiuxetan, which securely chelates the radioactive isotope 90Y. Effective RIT demands a multidisciplinary approach to patient care, which places considerable emphasis on the role of the nurse. This review explores the role of the nurse in 90Y-ibritumomab tiuxetan therapy.
CD8+ T Cells and Macrophages Regulate Pathogenesis in a Mouse Model of Middle East Respiratory Syndrome

ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) is an important emerging pathogen that was first described in 2012. While the cell surface receptor for MERS-CoV has been identified as dipeptidyl peptidase 4 (DPP4), the mouse DPP4 homologue does not allow virus entry into cells. Therefore, development of mouse models of MERS-CoV has been hampered by the fact that MERS-CoV does not replicate in commonly available mouse strains. We have previously described a mouse model in which mDPP4 was replaced with hDPP4 such that hDPP4 is expressed under the endogenous mDPP4 promoter. In this study, we used this mouse model to analyze the host response to MERS-CoV infection using immunological assays and transcriptome analysis. Depletion of CD4+ T cells, CD8+ T cells, or macrophages has no effect on MERS-CoV replication in the lungs of infected mice. However, we found that depletion of CD8+ T cells protects and depletion of macrophages exacerbates MERS-CoV-induced pathology and clinical symptoms of disease. Overall, we demonstrate an important role for the inflammatory response in regulating MERS-CoV pathogenesis in vivo. IMPORTANCE The Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly pathogenic respiratory virus that emerged from zoonotic sources in 2012. Human infections are still occurring throughout Saudi Arabia at a 38% case fatality rate, with the potential for worldwide spread via air travel. In this work, we identify the host response to the virus and identify inflammatory pathways and cell populations that are critical for protection from severe lung disease. By understanding the immune response to MERS-CoV we can develop targeted therapies to inhibit pathogenesis in the future.
German children's productivity with tense morphology: the Perfekt (present perfect)

Two nonce-word studies examined German-speaking children's productivity with the Perfekt (present perfect) from 2;6 to 3;6. The German Perfekt consists of the past participle of the main verb and an inflected form of an auxiliary (either haben ‘have’ or sein ‘be’). In Study 1, nonce verbs were either introduced in the infinitival form, and children (seventy-two children, aged 2;6 to 3;6) were tested on their ability to produce the Perfekt, or introduced in the Perfekt, and children were tested on their ability to produce the infinitive. In Study 2 twenty-four children aged 3;6 were given the past participle form of nonce verbs to see if they could supply the appropriate auxiliary (based mainly on verb semantics). The results were that many children as young as 2;6 used past participles productively (more than used infinitival forms productively), but all children had much difficulty in supplying both auxiliaries appropriately. The current findings suggest that mastery of the Perfekt construction as a whole does not take place before the age of four and that frequency of exposure is an important factor in determining the age at which children acquire grammatical constructions.
A Spatial Statistical Model for Landscape Genetics

Landscape genetics is a new discipline that aims to provide information on how landscape and environmental features influence population genetic structure. The first key step of landscape genetics is the spatial detection and location of genetic discontinuities between populations. However, efficient methods for achieving this task are lacking. In this article, we first clarify what is conceptually involved in the spatial modeling of genetic data. Then we describe a Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits. In this method, the global set of sampled individuals is modeled as a spatial mixture of panmictic populations, and the spatial organization of populations is modeled through the colored Voronoi tessellation. In addition to spatially locating genetic discontinuities, the method quantifies the amount of spatial dependence in the data set, estimates the number of populations in the studied area, assigns individuals to their population of origin, and detects individual migrants between populations, while taking into account uncertainty on the location of sampled individuals. The performance of the method is evaluated through the analysis of simulated data sets. Results show good performances for standard data sets (e.g., 100 individuals genotyped at 10 loci with 10 alleles per locus), with high but also low levels of population differentiation (e.g., FST < 0.05). The method is then applied to a set of 88 individuals of wolverines (Gulo gulo) sampled in the northwestern United States and genotyped at 10 microsatellites.
The Malignant Brain Tumor (MBT) Domain Protein SFMBT1 Is an Integral Histone Reader Subunit of the LSD1 Demethylase Complex for Chromatin Association and Epithelial-to-mesenchymal Transition*

Background: The LSD1 histone demethylase regulates gene expression by demethylating chromatin. Results: SFMBT1 associates with the LSD1 complex and is essential for its chromatin association, histone demethylation, and induction of EMT. Conclusion: SFMBT1 is a novel, integral component of the LSD1 complex. Significance: Understanding how the LSD1 complex is recruited to chromatin may offer new opportunities for therapeutic intervention. Chromatin readers decipher the functional readouts of histone modifications by recruiting specific effector complexes for subsequent epigenetic reprogramming. The LSD1 (also known as KDM1A) histone demethylase complex modifies chromatin and represses transcription in part by catalyzing demethylation of dimethylated histone H3 lysine 4 (H3K4me2), a mark for active transcription. However, none of its currently known subunits recognizes methylated histones. The Snai1 family transcription factors are central drivers of epithelial-to-mesenchymal transition (EMT) by which epithelial cells acquire enhanced invasiveness. Snai1-mediated transcriptional repression of epithelial genes depends on its recruitment of the LSD1 complex and ensuing demethylation of H3K4me2 at its target genes. Through biochemical purification, we identified the MBT domain-containing protein SFMBT1 as a novel component of the LSD1 complex associated with Snai1. Unlike other mammalian MBT domain proteins characterized to date that selectively recognize mono- and dimethylated lysines, SFMBT1 binds di- and trimethyl H3K4, both of which are enriched at active promoters. We show that SFMBT1 is essential for Snai1-dependent recruitment of LSD1 to chromatin, demethylation of H3K4me2, transcriptional repression of epithelial markers, and induction of EMT by TGFβ. Carcinogenic metal nickel is a widespread environmental and occupational pollutant. Nickel alters gene expression and induces EMT. We demonstrate the nickel-initiated effects are dependent on LSD1-SFMBT1-mediated chromatin modification. Furthermore, in human cancer, expression of SFMBT1 is associated with mesenchymal markers and unfavorable prognosis. These results highlight a critical role of SFMBT1 in epigenetic regulation, EMT, and cancer.
Detection of Viable Cryptosporidium parvum in Soil by Reverse Transcription–Real-Time PCR Targeting hsp70 mRNA

ABSTRACT Extraction of high-quality mRNA from Cryptosporidium parvum is a key step in PCR detection of viable oocysts in environmental samples. Current methods for monitoring oocysts are limited to water samples; therefore, the goal of this study was to develop a rapid and sensitive procedure for Cryptosporidium detection in soil samples. The efficiencies of five RNA extraction methods were compared (mRNA extraction with the Dynabeads mRNA Direct kit after chemical and physical sample treatments, and total RNA extraction methods using the FastRNA Pro Soil-Direct, PowerSoil Total RNA, E.Z.N.A. soil RNA, and Norgen soil RNA purification kits) for the direct detection of Cryptosporidium with oocyst-spiked sandy, loamy, and clay soils by using TaqMan reverse transcription-PCR. The study also evaluated the presence of inhibitors by synthesis and incorporation of an internal positive control (IPC) RNA into reverse transcription amplifications, used different facilitators (bovine serum albumin, yeast RNA, salmon DNA, skim milk powder, casein, polyvinylpyrrolidone, sodium hexametaphosphate, and Salmonella enterica serovar Typhi) to mitigate RNA binding on soil components, and applied various treatments (β-mercaptoethanol and bead beating) to inactivate RNase and ensure the complete lysis of oocysts. The results of spiking studies showed that Salmonella cells most efficiently relieved binding of RNA. With the inclusion of Salmonella during extraction, the most efficient mRNA method was Dynabeads, with a detection limit of 6 × 102 oocysts g−1 of sandy soil. The most efficient total RNA method was PowerSoil, with detection limits of 1.5 × 102, 1.5 × 103, and 1.5 × 104 C. parvum oocysts g−1 soil for sandy, loamy, and clay samples, respectively.
HEMOPROTOZOA OF FRESHWATER TURTLES IN QUEENSLAND

Blood smears from 27 turtles (15 Emydura signata, nine Elseya latisternum, and three Chelodina longicollis) from southeastern Queensland (Australia) were examined for infections by hemoprotozoan parasites between January and June 1999. Infections were found in 26 (96%) of the turtles. Twenty five (93%) were infected with the adeleorin coccidian Haemogregarina clelandi, eight (30%) with the hemosporidian Haemoproteus chelodinae, 11 (41%) with the kinetoplastid flagellate Trypanosoma chelodinae, and eight (30%) with a novel Trypanosoma sp. Despite the high prevalence and intensity of infections, there was no evidence of clinical disease in any of the turtles.
Loss of Heterozygosity on Chromosomes 1, 2, 8, 9 and 17 in Cerebral Atherosclerotic plaques

Objective Atherosclerosis is a fibroproliferative disease which has been attributed to several factors including genetic and molecular alterations. Initial studies have shown genetic alterations at the microsatellite level in the DNA of atherosclerotic plaques. Extending our initial findings, we performed a microsatellite analysis on cerebral atherosclerotic plaques. Methods Twenty-seven cerebral atherosclerotic plaques were assessed for loss of heterozygosity (LOH) and microsatellite instability (MI) using 25 microsatellite markers located on chromosomes 2, 8, 9 and 17. DNA was extracted from the vessels as well as the respective blood from each patient and subjected to polymerase chain reaction. Results Our analyses revealed that specific loci on chromosomes 2, 8, 9 and 17 exhibited a significant incidence of LOH. Forty-six percent of the specimens showed loss of heterozygosity at 2p13–p21, 48% exhibited LOH at 8p12–q11.2, while allelic imbalance was detected in 47% of the cases. The LOH incidence was 39%, 31% and 27% at 17q21, 9q31–34 and 17p13, respectively. Genetic alterations were detected at a higher rate as compared to the corresponding alterations observed in plaques from other vessels. Discussion This is the first microsatellite analysis using atherosclerotic plaques obtained from cerebral vessels. Our results indicate an elevated mutational rate on specific chromosomal loci, suggesting a potential implication of these regions in atherogenesis.
The Evolution of the Dark Halo Spin Parameters lambda and lambda' in a LCDM Universe: The Role of Minor and Major Mergers

The evolution of the spin parameter of dark halos and the dependence on the halo merging history in a set of dissipationless cosmological LCDM simulations is investigated. Special focus is placed on the differences of the two commonly used versions of the spin parameter, namely lambda=J*E^1/2/(G*M^5/2) (Peebles 80) and lambda'=J/(sqrt(2)*M_vir*R_vir*V_vir) (Bullock et al. 01). Though the distribution of the spin transfer rate defined as the ratio of the spin parameters after and prior to a merger is similar to a high degree for both, lambda and lambda', we find considerable differences in the time evolution: while lambda' is roughly independent of redshift, lambda turns out to increase significantly with decreasing redshift. This distinct behaviour arises from small differences in the spin transfer during accretion events. The evolution of the spin parameter is strongly coupled with the virial ratio eta:=2*E_kin/|E_pot| of dark halos. Major mergers disturb halos and increase both their virial ratio and spin parameter for 1-2 Gyrs. At high redshifts (z=2-3) many halos are disturbed with an average virial ratio of eta = 1.3 which approaches unity until z=0. We find that the redshift evolution of the spin parameters is dominated by the huge number of minor mergers rather than the rare major merger events.
Mobile Robot Localization and Mapping by Scan Matching using Laser Reflection Intensity of the SOKUIKI Sensor

This paper describes a new scan matching method for mobile robot localization and mapping. The proposed method "intensity-ICP" uses laser reflection intensity obtained by a laser range scanner named "SOKUIKI sensor". Compared with conventional scan matching methods which are effective just in geometric featured environments, intensity-ICP is effective in both geometric featured and featureless environments if there are some features like colors or materials. This method can build a map with laser reflection intensity data. The map will be effective to robust localization because it has abundant information; not only geometric data but also laser reflection intensity
Learning Optimal Parameters For Multi-target Tracking

We describe an end-to-end framework for learning parameters of min-cost flow multitarget tracking problem with quadratic trajectory interactions including suppression of overlapping tracks and contextual cues about co-occurrence of different objects. Our approach utilizes structured prediction with a tracking-specific loss function to learn the complete set of model parameters. Under our learning framework, we evaluate two different approaches to finding an optimal set of tracks under quadratic model objective based on an LP relaxation and a novel greedy extension to dynamic programming that handles pairwise interactions. We find the greedy algorithm achieves almost equivalent accuracy to the LP relaxation while being 2-7x faster than a commercial solver. We evaluate trained models on the challenging MOT and KITTI benchmarks. Surprisingly, we find that with proper parameter learning, our simple data-association model without explicit appearance/motion reasoning is able to outperform many state-of-the-art methods that use far more complex motion features and affinity metric learning.
Stimulus Parameters for Multifocal Pupillographic Objective Perimetry

PurposeWe compared the diagnostic power of 10 stimulus variants that assessed the visual fields of both eyes by recording pupillary responses to multifocal stimuli. The 10 variants comprised 6 initial tests, and 4 subsequent variants whose design was informed by the initial results. MethodsTwo study groups containing 16 normal and 22 primary open angle glaucoma subjects, and 15 normal and 20 primary open angle glaucoma subjects had their diagnostic status verified by a slit-lamp investigation, applanation tonometry, 3 forms of perimetry, and Stratus OCT. Stereoscopically arranged displays presented multifocal stimulus arrays having 24 stimulus regions/eye within the central 60 degrees. Pupil responses were recorded by video cameras under infrared illumination. The 10 stimulus conditions varied in presentation rate, duration, stimulus luminance, and flicker rate. Stimuli were 4 minutes in duration, presented in 8 segments of 30 seconds. Up to 15% of the data of a segment could be lost owing to blinks and fixation losses without repeating the segment. ResultsEach recording gave 96 direct and consensual responses/subject. The best performing stimulus method gave a sensitivity of 1.0±0.0 (mean±SE) for moderate and severe glaucomatous fields combined at a false positive rate of 0.05. Median signal to noise ratios for peak response amplitude expressed as t-statistics exceeded 4 for several variants. ConclusionsStimulus delivery rates of about 1 presentation/region/s and test luminance around 150 cd/m2 performed best diagnostically. Unlike automated perimetry, the mfPOP method provides information on response delays and afferent and efferent defects at each region of the visual field.
Digital Piracy, Teens, and the Source of Advice: An Experimental Study

The objective of our paper is to determine the effect of piracy advice from various sources on the behavior of the music consumer. Specifically, does it matter if the source of advice has a stake in the outcome of the piracy decision? Does it matter if the source of advice has a social tie with the advisee? Accordingly, we conduct a laboratory experiment using teenagers and their parents as subjects, increasing the realism of the context by sampling potential pirates and their parents. Treatments represent various sources of piracy advice (e.g., the teen's parent, a record label, or an external regulator). Subjects make decisions playing our new experimental game—The Piracy Game—extended from the volunteer's dilemma literature. Interestingly, subjects respond negatively to advice from record labels over time, purchasing fewer songs as compared to other sources such as the subject's parent. The existence of a social tie between the adviser and the subject assists in mitigating piracy, especially when a parent is facing potential penalties due to his or her child's behavior. An external regulator, having no social tie or stake in the decision, provides the least credible source of advice, leading to the greatest amount of piracy. Our analyses not only provide managerial insights but also develop theoretical understanding of the role of social ties in the context of advice.