Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the Effects of Duration and Size of the Control Zones on the Consequences of a Hypothetical African Swine Fever Epidemic in Denmark

African swine fever (ASF) is a notifiable infectious disease. The disease is endemic in certain regions in Eastern Europe constituting a risk of ASF spread toward Western Europe. Therefore, as part of contingency planning, it is important to continuously explore strategies that can effectively control an epidemic of ASF. A previously published and well documented simulation model for ASF virus spread between herds was used to examine the epidemiologic and economic impacts of the duration and size of the control zones around affected herds. In the current study, scenarios were run, where the duration of the protection and surveillance zones were reduced from 50 and 45 days to 35 and 25 days or to 35 and 25 days, respectively. These scenarios were run with or without enlargement of the surveillance zone around detected herds from 10 to 15 km. The scenarios were also run with only clinical or clinical and serological surveillance of herds within the zones. Sensitivity analysis was conducted on influential input parameters in the model. The model predicts that reducing the duration of the protection and surveillance zones has no impact on the epidemiological consequences of the epidemics, while it may result in a substantial reduction in the total economic losses. In addition, the model predicts that increasing the size of the surveillance zone from 10 to 15 km may reduce both the epidemic duration and the total economic losses, in case of large epidemics. The ranking of the control strategies by the total costs of the epidemics was not influenced by changes of input parameters in the sensitivity analyses.
Psychological variables and Wechsler Adult Intelligence Scale-IV performance

ABSTRACT The MMPI-2 and WAIS-IV are commonly used together in neuropsychological evaluations yet little is known about their interrelationships. This study explored the potential influence of psychological factors on WAIS-IV performance in a sample of 180 predominantly male veteran referrals that underwent a comprehensive neuropsychological examination in a VA Medical Center. Exclusionary criteria included failed performance validity testing and self-report distortion on the MMPI-2. A Principal Components Analysis was performed on the 15 MMPI-2 content scales, yielding three broader higher-order psychological dimensions: Internalized Emotional Dysfunction (IED), Externalized Emotional Dysfunction (EED), and Fear. Level of IED was not related to performance on the WAIS-IV Full Scale IQ or its four indexes: (Verbal Comprehension, Perceptual Reasoning, Working Memory, and Processing Speed). EED was not related to WAIS-IV performance. Level of Fear, which encompasses health preoccupations (HEA) and distorted perceptions (BIZ), was significantly related to WAIS-IV Full Scale IQ and Verbal Comprehension. These results challenge the common use of high scores on the MMPI-2 IED measures (chiefly depression and anxiety) to explain deficient WAIS-IV performance. In addition, they provide impetus for further investigation of the relation between verbal intelligence and Fear.
Expected Time to Extinction of SIS Epidemic Model Using Quasy Stationary Distribution

We study that the breakdown of epidemic depends on some parameters, that is expressed in epidemic reproduction ratio number. It is noted that when $R_0 $ exceeds 1, the stochastic model have two different results. But, eventually the extinction will be reached even though the major epidemic occurs. The question is how long this process will reach extinction. In this paper, we will focus on the Markovian process of SIS model when major epidemic occurs. Using the approximation of quasi--stationary distribution, the expected mean time of extinction only occurs when the process is one step away from being extinct. Combining the theorm from Ethier and Kurtz, we use CLT to find the approximation of this quasi distribution and successfully determine the asymptotic mean time to extinction of SIS model without demography.
Effect of Silkworm Litter - Pupal Waste (SLPW) Compost on Mulberry Leaf Yield

An experiment was conducted to study the influence of composted silkworm litter - pupal waste (SLPW) and other organic manures on growth parameters and leaf yield of mulberry. The compost made of SLPW (Silkworm litter pupal waste) was rich in nutrient content than the farm yard manure and vermicompost used in the experiment. The results clearly indicated that the application of SLPW + Vermicompost recorded significantly higher leaf yield (32,098.5 kg) and NPK content (3.11%, 0.39% and 2.48 %) respectively. Further, there was no significant difference in the quantity of chemical components of the leaves raised completely either on SLPW or other manures. These results are discussed in relation to the suitability of SLPW compost in improving the mulberry leaf quality. Key word: Silkworm litter – pupal waste, FYM, Vermicompost, Mulberry.
Agricultural land application of municipal biosolids : PBDE and metal levels in cow ' s milk

The impact of land application of biosolids (treated municipal sewage sludge) on dairy milk quality was measured in real farm operating conditions where biosolids were applied in accordance with the regulatory framework prescribed in the province of Quebec (Canada). The milk from 14 farms receiving biosolids were sampled in the Saguenay region in December 2009 and compared to the milk from 14 control farms. The tested farms had used biosolids an average of 11 years. Statistical analysis revealed no difference in the content of inorganic contaminants (arsenic, copper, molybdenum, zinc and thallium) in milk. These results suggest absence of induced hypocupriosis for dairy cows from farms using biosolids. However, the content of polybrominated diphenyl ethers (PBDEs) was higher in milk sampled from the farms using biosolids. Differences could be due, in part, by variability of exposition to dust among farm buildings. PBDE levels were however very low (mean value of 7,2 ng/L), and remained 3-7 times lower than the average levels recorded for various dairy products in the United States and
Diversity and Complexity of the Mouse Saa1 and Saa2 genes

Mouse strains show polymorphisms in the amino acid sequences of serum amyloid A 1 (SAA1) and serum amyloid A 2 (SAA2). Major laboratory mouse strains are classified based on the sequence as carrying the A haplotype (e.g., BALB/c) or B haplotype (e.g., SJL/J) of the Saa1 and Saa2 gene unit. We attempted to elucidate the diversity of the mouse Saa1 and Saa2 family genes at the nucleotide sequence level by a systematic survey of 6 inbred mouse strains from 4 Mus subspecies, including Mus musculus domesticus, Mus musculus musculus, Mus musculus castaneus, and Mus spretus. Saa1 and Saa2 genes were obtained from the mouse genome by PCR amplification, and each full-length nucleotide sequence was determined. We found that Mus musculus castaneus mice uniquely possess 2 divergent Saa1 genes linked on chromosome 7. Overall, the mouse strains had distinct composite patterns of amino acid substitutions at 9 positions in SAA1 and SAA2 isoforms. The mouse strains also had distinct composite patterns of 2 polymorphic upstream regulatory elements that influenced gene transcription in in vitro reporter assays. B haplotype mice were revealed to possess an LTR insertion in the downstream region of Saa1. Collectively, these results indicate that the mouse Saa genes hold broader diversity and greater complexity than previously known, and these characteristics were likely attained through gene duplication and repeated gene conversion events in the Mus lineage.
Open and closed loops: A computational approach to attention and consciousness

Within recent years, researchers have proposed the independence of attention and consciousness on both empirical and conceptual grounds. However, the elusive nature of these constructs complicates progress in the investigation of their interaction. We present a framework within which we conceptualize attention and consciousness in computational terms. Here, the concepts are consi-dered as large-scale, functionally and structurally different processes, embedded in a biologically inspired architecture, spanning the full arc from stimulus to response. Our architecture assumes a general independence of attention and consciousness, but supposes strong interactions. Furthermore, it addresses the developmental aspect, stressing that these functions have to gradually develop through learning.
Arachidonic Acid-metabolizing Cytochrome P450 Enzymes Are Targets of ω-3 Fatty Acids*

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) protect against cardiovascular disease by largely unknown mechanisms. We tested the hypothesis that EPA and DHA may compete with arachidonic acid (AA) for the conversion by cytochrome P450 (CYP) enzymes, resulting in the formation of alternative, physiologically active, metabolites. Renal and hepatic microsomes, as well as various CYP isoforms, displayed equal or elevated activities when metabolizing EPA or DHA instead of AA. CYP2C/2J isoforms converting AA to epoxyeicosatrienoic acids (EETs) preferentially epoxidized the ω-3 double bond and thereby produced 17,18-epoxyeicosatetraenoic (17,18-EEQ) and 19,20-epoxydocosapentaenoic acid (19,20-EDP) from EPA and DHA. We found that these ω-3 epoxides are highly active as antiarrhythmic agents, suppressing the Ca2+-induced increased rate of spontaneous beating of neonatal rat cardiomyocytes, at low nanomolar concentrations. CYP4A/4F isoforms ω-hydroxylating AA were less regioselective toward EPA and DHA, catalyzing predominantly ω- and ω minus 1 hydroxylation. Rats given dietary EPA/DHA supplementation exhibited substantial replacement of AA by EPA and DHA in membrane phospholipids in plasma, heart, kidney, liver, lung, and pancreas, with less pronounced changes in the brain. The changes in fatty acids were accompanied by concomitant changes in endogenous CYP metabolite profiles (e.g. altering the EET/EEQ/EDP ratio from 87:0:13 to 27:18:55 in the heart). These results demonstrate that CYP enzymes efficiently convert EPA and DHA to novel epoxy and hydroxy metabolites that could mediate some of the beneficial cardiovascular effects of dietary ω-3 fatty acids.
Diagnostic indicator of acute lung injury for pediatric critically ill patients at a tertiary pediatric hospital

Abstract Early identification of acute lung injury (ALI) in pediatric patients at risk of mortality is important for improving outcome. Assessment of soluble form of receptor for advanced glycation end products (sRAGE) as a valid biomarker for diagnosis of ALI among critically ill, pediatric patients in addition to correlating levels of sRAGE and different outcomes of those patients. A Hospital-based case-control study was conducted in pediatric intensive care units (PICUs) at Cairo University Hospital, along a period of 6 months. Total of 68 pediatric patients following inclusion criteria were classified into: patients with ALI; with both ALI and sepsis; with sepsis and control patients. They were prospectively followed and their laboratory and immunological workup (at days 1 and 9) was done to measure serum sRAGE levels and detect (sRAGE) genotypes. The age of the included children ranged from 8 to 84 months. Plasma level of sRAGE was significantly higher in plasma from patients with ALI regardless of associated sepsis. Plasma sRAGE levels were positively correlated with lung injury score. When assessing sRAGE genotypes, TA and TT genotypes were significant in most of the ALI with and without sepsis patients. Monitoring levels of sRAGE and genotypes can significantly affect the survival of ALI children.
Older adults show a self-reference effect for narrative information

ABSTRACT The self-reference effect (SRE), enhanced memory for information encoded through self-related processing, has been established in younger and older adults using single trait adjective words. We sought to examine the generality of this phenomenon by studying narrative information in these populations. Additionally, we investigated retrieval experience at recognition and whether valence of stimuli influences memory differently in young and older adults. Participants encoded trait adjectives and narratives in self-reference, semantic, or structural processing conditions, followed by tests of recall and recognition. Experiment 1 revealed an SRE for trait adjective recognition and narrative cued recall in both age groups, although the existence of an SRE for narrative recognition was unclear due to ceiling effects. Experiment 2 revealed an SRE on an adapted test of narrative recognition. Self-referential encoding was shown to enhance recollection for both trait adjectives and narrative material in Experiment 1, whereas similar estimates of recollection for self-reference and semantic conditions were found in Experiment 2. Valence effects were inconsistent but generally similar in young and older adults when they were found. Results demonstrate that the self-reference technique extends to narrative information in young and older adults and may provide a valuable intervention tool for those experiencing age-related memory decline.
Integrative and systemic approaches for evaluating PPARβ/δ (PPARD) function

The peroxisome proliferator-activated receptors (PPARs) are a group of nuclear receptors that function as transcription factors regulating the expression of genes involved in cellular differentiation, development, metabolism and also tumorigenesis. Three PPAR isotypes (α, β/δ and γ) have been identified, among which PPARβ/δ (PPARD) is the most difficult to functionally examine due to its tissue-specific diversity in cell fate determination, energy metabolism and housekeeping activities. PPARβ/δ acts both in a ligand-dependent and -independent manner. The specific type of regulation, activation or repression, is determined by many factors, among which the type of ligand, the presence/absence of PPARβ/δ-interacting corepressor or coactivator complexes and PPARβ/δ protein post-translational modifications play major roles. Recently, new global approaches to the study of nuclear receptors have made it possible to evaluate their molecular activity in a more systemic fashion, rather than deeply digging into a single pathway/function. This systemic approach is ideally suited for studying PPARβ/δ, due to its ubiquitous expression in various organs and its overlapping and tissue-specific transcriptomic signatures. The aim of the present review is to present in detail the diversity of PPARβ/δ function, focusing on the different information gained at the systemic level, and describing the global and unbiased approaches that combine a systems view with molecular understanding.
Expression of GFP-Actin Leads to Failure of Nuclear Elongation and Cytokinesis in Tetrahymena thermophila

Abstract Green fluorescent protein (GFP)-tagged actin was used to investigate the distribution and function of actin in Tetrahymena. A strain that expresses both GFP-actin and endogenous actin was developed by transformation of Tetrahymena thermophila with a ribosomal DNA-based replicative vector. Confocal microscopy of living cells and immunogold electron microscopy confirmed localization of GFP-actin to basal bodies and the contractile ring. Incorporation of the fusion protein into these and other actin-related structures correlated with severe impairment of macronuclear elongation and cytokinesis. At 30 °C macronuclear elongation failed to occur in 25% of the transformants despite completion of micronuclear division. At 20 °C macronuclear elongation failed to occur in 2% of the population. Arrest of cytokinesis coincided with failure of macronuclear elongation. Arrested cells developed into homopolar doublets with two sets of oral structures. This study indicates a requirement for actin in nuclear elongation and cytokinesis. Although GFP-actin can interfere with the functioning of actin-containing structures, the GFP-actin transformant strain can be used to monitor actin distribution and dynamics and is therefore an important new tool for further studies of Tetrahymena actin.
A Dataset and Reranking Method for Multimodal MT of User-Generated Image Captions

We present a dataset and method for improving the translation of noisy image captions that were created by users of Wikimedia Commons. The dataset is multilingual but non-parallel, and is several orders of magnitude larger than existing parallel data for multimodal machine translation. Our retrieval-based method pivots on similar images and uses the associated cap-tions in the target language to rerank translation outputs. This method only requires small amounts of parallel captions to ﬁnd the optimal ensemble of retrieval features based on textual and visual similarity. Furthermore, our method is compatible with any machine translation system, and allows to quickly integrate new data without the need of re-training the translation system. Tests on three different datasets showed that size and diversity of the data is crucial for the performance of our method. On the introduced dataset we observe consistent improvements of up to 5 BLEU points and 3 points in Character F-score over strong neural MT baselines for three different language pairs.
Multimodal approaches to functional connectivity in autism spectrum disorders: An integrative perspective

Atypical functional connectivity has been implicated in autism spectrum disorders (ASDs). However, the literature to date has been largely inconsistent, with mixed and conflicting reports of hypo‐ and hyper‐connectivity. These discrepancies are partly due to differences between various neuroimaging modalities. Functional magnetic resonance imaging (fMRI), electroencephalography (EEG), and magnetoencephalography (MEG) measure distinct indices of functional connectivity (e.g., blood‐oxygenation level‐dependent [BOLD] signal vs. electrical activity). Furthermore, each method has unique benefits and disadvantages with respect to spatial and temporal resolution, vulnerability to specific artifacts, and practical implementation. Thus far, functional connectivity research on ASDs has remained almost exclusively unimodal; therefore, interpreting findings across modalities remains a challenge. Multimodal integration of fMRI, EEG, and MEG data is critical in resolving discrepancies in the literature, and working toward a unifying framework for interpreting past and future findings. This review aims to provide a theoretical foundation for future multimodal research on ASDs. First, we will discuss the merits and shortcomings of several popular theories in ASD functional connectivity research, using examples from the literature to date. Next, the neurophysiological relationships between imaging modalities, including their relationship with invasive neural recordings, will be reviewed. Finally, methodological approaches to multimodal data integration will be presented, and their future application to ASDs will be discussed. Analyses relating transient patterns of neural activity (“states”) are particularly promising. This strategy provides a comparable measure across modalities, captures complex spatiotemporal patterns, and is a natural extension of recent dynamic fMRI research in ASDs. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 78: 456–473, 2018
Double Bank Runs and Liquidity Risk Management

By providing liquidity to depositors and credit line borrowers, banks are exposed to double-runs on assets and liabilities. For identification, we exploit the 2007 freeze of the European interbank market and the Italian Credit Register. After the shock, there are sizeable, aggregate double-runs. In the cross-section, pre-shock interbank exposure is (unconditionally) unrelated to post-shock credit line drawdowns. However, conditioning on firm observable and unobservable characteristics, higher pre-shock interbank exposure implies more post-shock drawdowns. We show that is the result of active pre-shock liquidity risk management by more exposed banks granting credit lines to firms that run less in a crisis.
Spin‐lock imaging of early tissue pH changes in ischemic rat brain

We have previously reported that the dispersion of spin‐lattice relaxation rates in the rotating frame (R1ρ) of tissue water protons at high field can be dominated by chemical exchange contributions. Ischemia in brain causes changes in tissue pH, which in turn may affect proton exchange rates. Amide proton transfer (APT, a form of chemical exchange saturation transfer) has been shown to be sensitive to chemical exchange rates and able to detect pH changes non‐invasively following ischemic stroke. However, the specificity of APT to pH changes is decreased because of the influence of several other factors that affect magnetization transfer. R1ρ is less influenced by such confounding factors and thus may be more specific for detecting variations in pH. Here, we applied a spin‐locking sequence to detect ischemic stroke in animal models. Although R1ρ images acquired with a single spin‐locking amplitude (ω1) have previously been used to assess stroke, here we use ΔR1ρ, which is the difference in R1ρ values acquired with two different locking fields to emphasize selectively the contribution of chemical exchange effects. Numerical simulations with different exchange rates and measurements of tissue homogenates with different pH were performed to evaluate the specificity of ΔR1ρ to detect tissue acidosis. Spin‐lock and APT data were acquired on five rat brains after ischemic strokes induced via middle cerebral artery occlusions. Correlations between these data were analyzed at different time points after the onset of stroke. The results show that ΔR1ρ (but not R1ρ acquired with a single ω1) was significantly correlated with APT metrics consistent with ΔR1ρ varying with pH.
Rethinking Antillothrix: The Mandible and Its Implications

A mandible of the Hispaniolan primate Antillothrix bernensis, virtually complete and providing the only definitive evidence of the species' lower dentition, has been discovered in a submerged Dominican Republic cave. The new specimen enables a more certain assessment of the species' phylogenetic position than previously possible. It belongs to the same individual as the nearly complete young adult cranium and postrcranial elements found earlier at the same site. Of the extinct Caribbean platyrrhines, the jaw compares well with partial mandibles representing Xenothrix mcgregori, from Jamaica. Among living platyrrhines, it closely resembles Callicebus and Aotus, as documented in a biometric analysis employing three‐dimensional geometric morphometrics of Callicebus, Aotus, Pithecia, Chiropotes, Cacajao, Cebus, and Saimiri. The jaw falls within the morphological variability of Callicebus and Aotus in this three‐dimensional analysis, is otherwise most similar to Pithecia, and is distinct from cebines. Lower molars resemble the Haitian primate, Insulacebus, a genus known by a full dentition and gnathic fragments with a pattern of derived features also present in Xenothrix. Considering the available craniodental and postcranial evidence, we conclude that Antillothrix is not properly classified as cebid but rather is best grouped with Pitheciidae, an idea long central to discussions of the phylogenetic affinities of the Greater Antillean primates. Since Antillothrix and Insulacebus are more primitive anatomically than the highly modified Xenothrix, it is tempting to surmise that the origins of the latter involved a vicariance or dispersal event via Hispaniola isolating it on Jamaica. Am. J. Primatol. 75:825–836, 2013. © 2013 Wiley Periodicals, Inc.