Miracle-dz/UniFAR-FTUs huggingface dataset:
String gas cosmology and structure formation

It has recently been shown that a Hagedorn phase of string gas cosmology may provide a causal mechanism for generating a nearly scale-invariant spectrum of scalar metric fluctuations, without the need for an intervening period of de Sitter expansion. A distinctive signature of this structure formation scenario would be a slight blue tilt of the spectrum of gravitational waves. In this paper we give more details of the computations leading to these results, and the assumptions underlying them.
Learning Semantic Grammars with Constructive Inductive Logic Programming

Automating the construction of semantic grammars is a difficult and interesting problem for machine learning. This paper shows how the semantic-grammar acquisition problem can be viewed as the learning of search-control heuristics in a logic program. Appropriate control rules are learned using a new first-order induction algorithm that automatically invents useful syntactic and semantic categories. Empirical results show that the learned parsers generalize well to novel sentences and out-perform previous approaches based on connectionist techniques.
Ozone exposure affects feeding and locomotor behavior of adult Bufo marinus

Ozone (O3), a reactive component of air pollution, depresses feeding and voluntary locomotor behavior in laboratory rodents, but the effects of O3 on amphibian behavior are not known. We evaluated the effects of 4 h of exposure to air or ozone (0.6 μl/L), on two ecologically relevant behaviors of the toad Bufo marinus. Toads were offered five mealworms at 1, 24, and 48 h after exposure. One hour after exposure, O3‐exposed toads ate fewer mealworms than did air‐exposed toads (Fisher exact test, p = 0.005). Within 24 h after exposure, all toads ate four or five mealworms. Because movement is a key component of toad feeding behavior, we tested additional toads (n = 25) for voluntary locomotor behavior during three 1‐h trials in a 2.9‐m2 open‐field arena. Mean (± standard deviation) total distance moved was: pre‐exposure, 29 ± 19.5 m; 1‐h postexposure, 13 ± 15.6 m; and 24‐h postexposure, 17 ± 17.4 m. The means were not statistically different by repeated measures analysis of covariance. Therefore, our results suggest that a single 4‐h exposure to O3 depresses toad feeding behavior after exposure but had little effect on voluntary locomotor behavior.
APOE ε4 allele predicts faster cognitive decline in mild Alzheimer disease

Objective: To determine whether APOE ε4 predicts rate of cognitive change in incident and prevalent Alzheimer disease (AD). Methods: Individuals were recruited from two longitudinal cohort studies—the Washington Heights and Inwood Columbia Aging Project (WHICAP; population-based) and the Predictors Study (clinic-based)—and were followed for an average of 4 years. Three samples of participants diagnosed with AD, with diverse demographic characteristics and baseline cognitive functioning, were studied: 1) 199 (48%) of the incident WHICAP cases; 2) 215 (54%) of the prevalent WHICAP cases; and 3) 156 (71%) of the individuals diagnosed with AD in the Predictors Study. Generalized estimating equations were used to test whether rate of cognitive change, measured using a composite cognitive score in WHICAP and the Mini-Mental State Examination in Predictors, varied as a function of ε4 status in each sample. Results: The presence of at least one ε4 allele was associated with faster cognitive decline in the incident population-based AD group (p = 0.01). Parallel results were produced for the two prevalent dementia samples only when adjusting for disease severity or excluding the most impaired participants from the analyses. Conclusion: APOE ε4 may influence rate of cognitive decline most significantly in the earliest stages of Alzheimer disease.
Brain mechanisms subserving self-generated imagery: electrophysiological specificity and patterning.

The present study was designed to assess the patterning of occipital and sensorimotor EEG activation during self-generated visual and kinesthetic imagery. Twenty subjects were requested to imagine, in separate trials, a flashing light, a tapping sensation on the right forearm, and both the light and the tapping together. Prior to the imagery trials, subjects were exposed to the stimuli which they were asked to subsequently imagine. EEG was recorded from the left occipital and left sensorimotor regions, filtered for alpha and quantified on-line. The results indicated that self-generated visual imagery elicited greater relative occipital activation than comparable kinesthetic imagery. The imagine-both condition fell predictably in between the two unimodal imagery conditions. The difference between visual and kinesthetic imagery was primarily a function of greater occipital activation during the former versus the latter task. No difference in overall alpha abundance among the three imagery tasks was found. These findings suggest that the self-generation of imagery in different modalities elicits specific changes in the sensory regions of the brain responsible for processing information in the relevant modalities.
Assessing Protein Kinase Selectivity with Molecular Dynamics and MM‐PBSA Binding Free Energy Calculations

An application of molecular dynamics and molecular mechanics Poisson–Boltzmann surface area techniques to the prediction of protein kinase inhibitor selectivity is presented. A highly active and selective ERK2 inhibitor was placed in equivalent orientations in five different protein kinases (SRC, LCK, GSK3, JNK3 and Aurora‐A). Binding free energies were then computed with the molecular mechanics Poisson–Boltzmann surface area approach using 15 nanosecond fully solvated molecular dynamics trajectories of the corresponding protein‐ligand complexes. The results show correlation with experimentally determined selectivities and provide useful insights into the underlying structural determinants for selectivity.
Are Consumers Myopic? Evidence from New and Used Car Purchases

We investigate whether car buyers are myopic about future fuel costs. We estimate the effect of gasoline prices on short-run equilibrium prices of cars of different fuel economies. We then compare the implied changes in willingness-to-pay to the associated changes in expected future gasoline costs for cars of different fuel economies in order to calculate implicit discount rates. Using different assumptions about annual mileage, survival rates, and demand elasticities, we calculate a range of implicit discount rates similar to the range of interest rates paid by car buyers who borrow. We interpret this as showing little evidence of consumer myopia. (JEL D12, H25, L11, L62, L71, L81)
Effect of esterified 4-desmethylsterols and -stanols or 4,4′-dimethylsterols on cholesterol and bile acid metabolism in hamsters

4-Desmethylsterols and -stanols reduce plasma total cholesterol (TC) and LDL cholesterol by inhibition of intestinal cholesterol absorption, while the cholesterol-lowering potential of 4,4′-dimethylsterols is less well defined. The present study aimed to compare the effects of 4-desmethylsterols, -stanols, and 4,4′-dimethylsterols on plasma and hepatic cholesterol, sterol excretion and bile acid metabolism. Male golden Syrian hamsters were fed diets containing 13 g/100 g fat, 0·08 g/100 g cholesterol and 0 (control), 0·24 or 0·48 % (w/w) esterified 4-desmethylsterols (sterols) and esterified hydrogenated 4-desmethylsterols (stanols) from common vegetable oils or esterified 4,4′-dimethylsterols from rice bran oil for 5 weeks. Sterol and stanol esters at the dose of 0·24 % were equally effective and significantly (P<0·05) lowered TC by 15 %, while 0·24 % 4,4-dimethylsterols reduced TC by 10 %. Liver total and esterified cholesterol concentrations were significantly (P<0·05) lowered by 40, 22, 43 and 31 % in hamsters fed 0·48 % sterols, 0·24 % stanols, 0·48 % stanols or 0·48 % dimethylsterols, respectively. Daily faecal bile acid excretion and hepatic cholesterol 7α-hydroxylase activity were not altered, indicating that sterols, stanols and dimethylsterols had no effect on the intestinal re-absorption of bile acids or on hepatic bile acid synthesis. Daily excretion of cholesterol was significantly higher in hamsters fed esterified sterols and stanols, but was only slightly increased in those fed dimethylsterols. The results indicate that esterified sterols and stanols were equally effective in lowering plasma TC and LDL cholesterol, while dimethylsterol esters caused a weaker cholesterol-lowering effect. Sterols and stanols achieve their cholesterol-lowering effect by stimulating faecal cholesterol excretion through inhibiting intestinal cholesterol absorption, but do not affect bile acid excretion. Other mechanisms need to be considered to explain the effect on plasma and hepatic cholesterol of dimethylsterols.
An Evaluation of the Pea Pod System for Assessing Body Composition of Moderately Premature Infants

(1) Background: Assessing the quality of growth in premature infants is important in order to be able to provide them with optimal nutrition. The Pea Pod device, based on air displacement plethysmography, is able to assess body composition of infants. However, this method has not been sufficiently evaluated in premature infants; (2) Methods: In 14 infants in an age range of 3–7 days, born after 32–35 completed weeks of gestation, body weight, body volume, fat-free mass density (predicted by the Pea Pod software), and total body water (isotope dilution) were assessed. Reference estimates of fat-free mass density and body composition were obtained using a three-component model; (3) Results: Fat-free mass density values, predicted using Pea Pod, were biased but not significantly (p > 0.05) different from reference estimates. Body fat (%), assessed using Pea Pod, was not significantly different from reference estimates. The biological variability of fat-free mass density was 0.55% of the average value (1.0627 g/mL); (4) Conclusion: The results indicate that the Pea Pod system is accurate for groups of newborn, moderately premature infants. However, more studies where this system is used for premature infants are needed, and we provide suggestions regarding how to develop this area.
The Importance of Being Variable

New work suggests that blood oxygen level-dependent (BOLD) signal variability can be a much more powerful index of human age than mean activation, and that older brains are actually less variable than younger brains. However, little is known of how BOLD variability and task performance may relate. In the current study, we examined BOLD variability in relation to age, and reaction time speed and consistency in healthy younger (20–30 years) and older (56–85 years) adults on three cognitive tasks (perceptual matching, attentional cueing, and delayed match-to-sample). Results indicated that younger, faster, and more consistent performers exhibited significantly higher brain variability across tasks, and showed greater variability-based regional differentiation compared with older, poorer-performing adults. Also, when we compared brain variability- and typical mean-based effects, the respective spatial patterns were essentially orthogonal across brain measures, and any regions that did overlap were largely opposite in directionality of effect. These findings help establish the functional basis of BOLD variability, and further support the statistical and spatial differentiation between BOLD variability and BOLD mean. We thus argue that the precise nature of relations between aging, cognition, and brain function is underappreciated by using mean-based brain measures exclusively.
The roles of stereotypes, phonetic knowledge, and phonological knowledge in the evaluation of dialect

The Viennese dialect belongs to the East Middle-Bavarian dialect group and, consequently, shares the specific dialect features of this group. However, the Viennese dialect also shows some specific characteristics which are, at least historically, restricted to the area of Vienna. When asked for typical characteristics of the Viennese dialect, people spontaneously mention the mono-lateral articulation of the lateral, the monophthongization of the diphthongs, and a drawn-out (=long duration of segments) articulation, referring to specific timing relations. In addition, of all the dialects spoken in Austria, the Viennese dialect is the most negatively evaluated one, connected with unfriendliness and even aggressiveness.
Thyroid Hormone-Regulated Wnt5a/Ror2 Signaling Is Essential for Dedifferentiation of Larval Epithelial Cells into Adult Stem Cells in the Xenopus laevis Intestine

Background and Aims Amphibian intestinal remodeling, where thyroid hormone (T3) induces some larval epithelial cells to become adult stem cells analogous to the mammalian intestinal ones, serves as a unique model for studying how the adult stem cells are formed. To clarify its molecular mechanisms, we here investigated roles of non-canonical Wnt signaling in the larval-to-adult intestinal remodeling during Xenopus laevis metamorphosis. Methods/Findings Our quantitative RT-PCR (qRT-PCR) and immunohistochemical analyses indicated that the expressions of Wnt5a and its receptors, frizzled 2 (Fzd2) and receptor tyrosine kinase-like orphan receptor 2 (Ror2) are up-regulated by T3 and are spatiotemporally correlated with adult epithelial development in the X. laevis intestine. Notably, changes in morphology of larval absorptive epithelial cells expressing Ror2 coincide well with formation of the adult stem cells during metamorphosis. In addition, by using organ cultures of the tadpole intestine, we have experimentally shown that addition of exogenous Wnt5a protein to the culture medium causes morphological changes in the larval epithelium expressing Ror2 even in the absence of T3. In contrast, in the presence of T3 where the adult stem cells are formed in vitro, inhibition of endogenous Wnt5a by an anti-Wnt5a antibody suppressed the epithelial morphological changes, leading to the failure of stem cell formation. Significance Our findings strongly suggest that the adult stem cells originate from the larval absorptive cells expressing Ror2, which require Wnt5a/Ror2 signaling for their dedifferentiation accompanied by changes in cell morphology.
Efficient Distributed Online Prediction and Stochastic Optimization With Approximate Distributed Averaging

We study distributed methods for online prediction and stochastic optimization. Our approach is iterative: In each round, nodes first perform local computations and then communicate in order to aggregate information and synchronize their decision variables. Synchronization is accomplished through the use of a distributed averaging protocol. When an exact distributed averaging protocol is used, it is known that the optimal regret bound of O(√(m)) can be achieved using the distributed minibatch algorithm in [“Optimal distributed online prediction using minibatches,” J. Mach. Learn. Res., vol. 13, pp. 165-202, 2012], where m is the total number of samples processed across the network. We focus on methods using approximate distributed averaging protocols and show that the optimal regret bound can also be achieved in this setting. In particular, we propose a gossip-based optimization method that achieves the optimal regret bound. The amount of communication required depends on the network topology through the second largest eigenvalue of the transition matrix of a random walk on the network. In the setting of stochastic optimization, the proposed gossip-based approach achieves nearly linear scaling: The optimization error is guaranteed to be no more than ∈ after O(1/nϵ2) rounds, each of which involves O(log n) gossip iterations, when n nodes communicate over a well-connected graph.
Improving Public Sector Management at Scale? Experimental Evidence on School Governance in India

We present results from a large-scale experimental evaluation of an ambitious attempt to improve management quality in Indian schools (implemented in 1,774 randomly-selected schools). The intervention featured several global “best practices” including comprehensive assessments, detailed school ratings, and customized school improvement plans. It did not, however, change accountability or incentives. We find that the assessments were near-universally completed, and that the ratings were informative, but the intervention had no impact on either school functioning or student outcomes. Yet, the program was perceived to be successful and scaled up to cover over 600,000 schools nationally. We find using a matched-pair design that the scaled-up program continued to be ineffective at improving student learning in the state we study. We also conduct detailed qualitative interviews with frontline officials and find that the main impact of the program on the ground was to increase required reporting and paperwork. Our results illustrate how ostensibly well-designed programs, that appear effective based on administrative measures of compliance, may be ineffective in practice.
Malignant mesothelioma: a comparison of biopsy and postmortem material by light microscopy and immunohistochemistry.

AIMS The diagnosis of malignant mesothelioma in pleural biopsies can be difficult. Survival is short and consequently many of these cases are submitted to necropsy to assist with medicolegal claims. This study compares the histological appearances and immunohistochemical profile of nine biopsy specimens with corresponding postmortem specimens. METHODS Archival, formalin fixed, paraffin wax embedded material was obtained from nine biopsy and corresponding postmortem cases of malignant mesothelioma. The specimens were examined by light microscopy and stained with an immunohistochemical panel of 12 commercially available antibodies including CAM5.2, HBME-1, and Ber-EP4, and antibodies to thrombomodulin, calretinin, CD44H, WT-1, carcinoembryonic antigen, Leu-M1, epithelial membrane antigen and p53. RESULTS There was greater variation in the range of histological appearances of mesotheliomas in postmortem specimens compared with biopsy specimens. There was also variability in the immunohistochemical staining pattern for certain antibodies including HBME-1, and Ber-EP4 and antibodies to calretinin, CD44H, WT-1, and p53. CONCLUSIONS All available information should be taken into account in the histological diagnosis of malignant mesothelioma. Interpretation of the immunohistochemical profile should be regarded with some caution when only postmortem material is available. When reporting a postmortem case of suspected mesothelioma, the pathologist should seek to review all available biopsy material in conjunction with the necropsy.
Expression Analysis of Flower MADS-box Genes in Saffron Crocus (Crocus sativus L.) Supports a Modified ABCDE Model

Crocus sativus L. is a monocot triploid species, member of the family Iridaceae, and is considered to be the highest priced spice in the world. It is cultivated for its flowers and more specifically for its red stigmas. The flower of Crocus is bisexual and it is sterile. The dry form of stigmas constitutes saffron. In order to uncover and understand the molecular mechanisms controlling flower development in cultivated Crocus and its relative wild progenitor species, and characterize a number of Crocus flower mutants we have cloned and characterized different full length cDNA sequences encoding MADS-box transcription factors belonging to the different ABC and E-class MADS box proteins. Herein, we review the isolation of Crocus MADS box genes and primarily discuss their expression patterns in leaves and the four flower organs: outer tepals, inner tepals, stamens and carpels. Expression analysis of the isolated MADS box genes support the hypothesis that a modified ABCDE model in the flower of Crocus is responsible for the development of the different Crocus flower organs and the transformation of the sepals and petals into tepaloid organs, designated outer tepals and inner tepals, respectively. _____________________________________________________________________________________________________________
Capacity of Byzantine Agreement ( Preliminary Draft – Work in Progress )

Caveat: This report represents work-in-progress, and provides some of our early results on the topic. A more complete version of this report, with additional results not presented in this draft, and improved description of the algorithms and analysis, will be released later this year. This draft version contains known problems with clarity/readability and the descriptions are incomplete/imprecise in some places. The draft is being released nevertheless to seek early feedback from other researchers.
p53 Regulates Oxidative Stress-Mediated Retrograde Signaling: A Novel Mechanism for Chemotherapy-Induced Cardiac Injury

The side effects of cancer therapy on normal tissues limit the success of therapy. Generation of reactive oxygen species (ROS) has been implicated for numerous chemotherapeutic agents including doxorubicin (DOX), a potent cancer chemotherapeutic drug. The production of ROS by DOX has been linked to DNA damage, nuclear translocation of p53, and mitochondrial injury; however, the causal relationship and molecular mechanisms underlying these events are unknown. The present study used wild-type (WT) and p53 homozygous knock-out (p53−/−) mice to investigate the role of p53 in the crosstalk between mitochondria and nucleus. Injecting mice with DOX (20 mg/kg) causes oxidative stress in cardiac tissue as demonstrated by immunogold analysis of the levels of 4-hydroxy-2′-nonenal (4HNE)-adducted protein, a lipid peroxidation product bound to proteins. 4HNE levels increased in both nuclei and mitochondria of WT DOX-treated mice but only in nuclei of DOX-treated p53(−/−) mice, implicating a critical role for p53 in causing DOX-induced oxidative stress in mitochondria. The stress-activated protein c-Jun amino-terminal kinase (JNKs) was activated in response to increased 4HNE in WT mice but not p53(−/−) mice receiving DOX treatment, as determined by co-immunoprecipitation of HNE and pJNK. The activation of JNK in DOX treated WT mice was accompanied by Bcl-2 dissociation from Beclin in mitochondria and induction of type II cell death (autophagic cell death), as evidenced by an increase in LC3-I/LC-3-II ratio and γ-H2AX, a biomarker for DNA damage. The absence of p53 significantly reduces mitochondrial injury, assessed by quantitative morphology, and decline in cardiac function, assessed by left ventricular ejection fraction and fraction shortening. These results demonstrate that p53 plays a critical role in DOX-induced cardiac toxicity, in part, by the induction of oxidative stress mediated retrograde signaling.