Miracle-dz/UniFAR-FTUs huggingface dataset:
Proof of classical versions of the Bousso entropy bound and of the generalized second law

Bousso has conjectured that in any spacetime satisfying Einstein's equation and satisfying the dominant energy condition, the "entropy flux" S through any null hypersurface L generated by geodesics with non-positive expansion starting from some spacelike 2 surface of area A must satisfy S<=A/4. This conjecture reformulates earlier conjectured entropy bounds of Bekenstein and also of Fischler and Susskind, and can be interpreted as a statement of the so-called holographic principle. We show that Bousso's entropy bound can be derived from either of two sets of hypotheses. The first set of hypotheses is (i) associated with each null surface L in spacetime there is an entropy flux 4-vector s^a_L whose integral over L is the entropy flux through L, and (ii) along each null geodesic generator of L, we have $|s^a_L k_a| \le \pi (\lambda_\infty - \lambda) T_{ab} k^a k^b$, where $T_{ab}$ is the stress-energy tensor, $\lambda$ is an affine parameter, $k^a = (d / d\lambda)^a$, and $\lambda_\infty$ is the value of affine parameter at the endpoint of the geodesic. The second (purely local) set of hypotheses is (i) there exists an absolute entropy flux 4-vector s^a such that the entropy flux through any null surface L is the integral of s^a over L, and (ii) this entropy flux 4-vector obeys the pointwise inequalities $(s_a k^a)^2 \le T_{ab} k^a k^b / (16 \pi)$ and $|k^a k^b \nabla_a s_b| \le \pi T_{ab} k^a k^b /4$ for any null vector k^a. Under the first set of hypotheses, we also show that a stronger entropy bound can be derived, which directly implies the generalized second law of thermodynamics.
Extracellular vaccinia virus formation and cell-to-cell virus transmission are prevented by deletion of the gene encoding the 37,000-Dalton outer envelope protein

There are two types of infectious vaccinia virus particles: intracellular naked virions and extracellular enveloped virions (EEV). To determine the biological role of the enveloped form of vaccinia virus, we produced and characterized a mutant that is defective in EEV formation. The strategy involved replacement by homologous recombination of the gene F13L, encoding a 37,000-Da protein (VP37) that is specific for the outer envelope of EEV, with a selectable antibiotic resistance marker, the Escherichia coli gpt gene. Initial experiments, however, suggested that such a mutation was lethal or prevented plaque formation. By employing a protocol consisting of high-multiplicity passages of intracellular virus from the transfected cells and then limiting dilution cloning, we succeeded in isolating the desired mutant, which was defective in production of plaques and extracellular virus but made normal amounts of intracellular naked virions. Electron microscopic examination indicated that the mutant virus particles, unlike wild type, were neither wrapped with Golgi-derived membranes nor associated with the cell surface. The absence of VP37 did not prevent the transport of the viral hemagglutinin to the plasma membrane but nevertheless abrogated both low-pH- and antibody-mediated cell fusion. These results indicate that VP37 is required for EEV formation and also plays a critical role in the local cell-to-cell transmission of vaccinia virus, perhaps via enveloped virions attached to or released from the cell membrane. By contrast, a mutated virus with a deletion of the K4L open reading frame, which is a homolog of the VP37 gene, was not defective in formation of plaques or EEV.
Genetic effects on children's conversational language use.

PURPOSE The present study examined the extent of genetic and environmental influences on individual differences in children's conversational language use. METHOD Behavioral genetic analyses focused on conversational measures and 2 standardized tests from 380 twins (M = 7.13 years) during the 2nd year of the Western Reserve Reading Project (S. A. Petrill, K. Deater-Deckard, L. A. Thompson, L. S. DeThorne, & C. Schatschneider, 2006) Multivariate analyses using latent factors were conducted to examine the extent of genetic overlap and specificity between conversational and formalized language. RESULTS Multivariate analyses revealed a heritability of . 70 for the conversational language factor and . 45 for the formal language factor, with a significant genetic correlation of . 37 between the two factors. Specific genetic effects were also significant for the conversational factor. CONCLUSIONS The current study indicated that over half of the variance in children's conversational language skills can be accounted for by genetic effects with no evidence of significant shared environmental influence. This finding casts an alternative lens on past studies that have attributed differences in children's spontaneous language use to differences in environmental language exposure. In addition, multivariate results generally support the context-dependent construction of language knowledge, as suggested by the theory of activity and situated cognition (J. S. Brown, A. Collins, & P. Duguid, 1989; T. A. Ukrainetz, 1998), but also indicate some degree of overlap between language use in conversational and formalized assessment contexts.
Corticocortical feedback increases the spatial extent of normalization

Normalization has been proposed as a canonical computation operating across different brain regions, sensory modalities, and species. It provides a good phenomenological description of non-linear response properties in primary visual cortex (V1), including the contrast response function and surround suppression. Despite its widespread application throughout the visual system, the underlying neural mechanisms remain largely unknown. We recently observed that corticocortical feedback contributes to surround suppression in V1, raising the possibility that feedback acts through normalization. To test this idea, we characterized area summation and contrast response properties in V1 with and without feedback from V2 and V3 in alert macaques and applied a standard normalization model to the data. Area summation properties were well explained by a form of divisive normalization, which computes the ratio between a neuron's driving input and the spatially integrated activity of a "normalization pool. " Feedback inactivation reduced surround suppression by shrinking the spatial extent of the normalization pool. This effect was independent of the gain modulation thought to mediate the influence of contrast on area summation, which remained intact during feedback inactivation. Contrast sensitivity within the receptive field center was also unaffected by feedback inactivation, providing further evidence that feedback participates in normalization independent of the circuit mechanisms involved in modulating contrast gain and saturation. These results suggest that corticocortical feedback contributes to surround suppression by increasing the visuotopic extent of normalization and, via this mechanism, feedback can play a critical role in contextual information processing.
The roles of FGF and MAP kinase signaling in the segregation of the epiblast and hypoblast cell lineages in bovine and human embryos

INTRODUCTION Mammalian pre-implantation development is characterized by the development of the trophectoderm (TE), the hypoblast (primitive endoderm) and the epiblast cell lineages. The three different cell types in peri-implantation embryos are the result of two consecutive lineage segregation events. The first lineage specification occurs at the morula stage, when outer cells segregate from the inner cells and differentiate into the TE. The second lineage specification takes place in the inner cell mass (ICM) of blastocyst stage embryos, where the precursors of the hypoblast segregate from precursors of the epiblast. In the mouse (Mus musculus), the TE gives rise to parts of the trophoblast/placenta and the chorion, whereas the primitive endoderm (PE) develops primarily to parietal endoderm and visceral endoderm, and the epiblast gives rise to the embryo proper, the umbilical cord, the amnion and part of the chorion (Ralston and Rossant, 2005). In bovine (Bos taurus) and human (Homo sapiens) embryos, the hypoblast gives rise to the primitive yolk sac and the secondary yolk sac (Docherty et al., 1996; Maddox-Hyttel et al., 2003). In the ICM of embryonic day (E) 3.5 mouse blastocysts, the epiblast and PE progenitors can be recognized by the mosaic expression of the transcription factors NANOG and GATA6, respectively (Chazaud et al., 2006). Mouse embryos that lack Nanog do not develop epiblast cells (Mitsui et al., 2003; Silva et al., 2009), whereas embryos mutant for Gata6 initiate the formation of the PE but fail to develop functional visceral endoderm (Morrisey et al., 1998; Koutsourakis et al., 1999). Various lines of evidence indicate that the formation of the murine PE is initiated upon FGF-mediated activation of GRB2 and subsequent activation of the mitogen-activated protein kinase (MAP kinase) signal transduction pathway. Indeed, mouse embryos that lack Fgf4, Fgfr2 or Grb2 fail to develop PE cells and all ICM cells of E3.5 Grb2 mutant blastocysts have epiblast characteristics (Feldman et al., 1995; Arman et al., 1998; Cheng et al., 1998; Chazaud et al., 2006). Moreover, recent studies have demonstrated that it is possible to shift the balance between epiblast and PE precursors through modulation of the levels of FGF/MAP kinase signaling in pre-implantation mouse embryos (Nichols et al., 2009b; Lanner et al., 2010; Yamanaka et al., 2010). MAP kinase signaling is also involved in the differentiation of mouse embryonic stem (ES) cells. It is possible to prevent mouse ES cells from differentiating through inhibition of MEK (Hamazaki et al., 2006; Ying et al., 2008). Moreover, by simultaneous inhibition of FGF/MAP kinase signaling and glycogen synthase kinase 3b (GSK3b), mouse ES cells can be captured in a ground Development 139, 871-882 (2012) doi:10.1242/dev.071688 © 2012. Published by The Company of Biologists Ltd
Fast reaction to different sensory modalities activates common fields in the motor areas, but the anterior cingulate cortex is involved in the speed of reaction.

We examined which motor areas would participate in the coding of a simple opposition of the thumb triggered by auditory, somatosensory and visual signals. We tested which motor areas might be active in response to all three modalities, which motor structures would be activated specifically in response to each modality, and which neural populations would be involved in the speed of the reaction. The subjects were required to press a button with their right thumb as soon as they detected a change in the sensory signal. The regional cerebral blood flow (rCBF) was measured quantitatively with (15)O-butanol and positron emission tomography (PET) in nine normal male subjects. Cytoarchitectural areas were delimited in 10 post mortem brains by objective and quantitative methods. The images of the post mortem brains subsequently were transformed into standard anatomic format. One PET scanning for each of the sensory modalities was done. The control condition was rest with the subjects having their eyes closed. The rCBF images were anatomically standardized, and clusters of significant changes in rCBF were identified. These were localized to motor areas delimited on a preliminary basis, such as supplementary motor area (SMA), dorsal premotor zone (PMD), rostral cingulate motor area (CMAr), and within areas delimited by using microstructural i.e., cytoarchitectonic criteria, such as areas 4a, 4p, 3a, 3b, and 1. Fields of activation observed as a main effect for all three modalities were located bilaterally in the SMA, CMAr, contralateral PMD, primary motor (M1), and primary somatosensory cortex (SI). The activation in M1 engaged areas 4a and 4p and expanded into area 6. The activation in SI engaged areas 3b, 1, and extended into somatosensory association areas and the supramarginal gyrus posteriorly. We identified significant activations that were specific for each modality in the respective sensory association cortices, though no modality specific regions were found in the motor areas. Fields in the anterior cingulate cortex, rostral to the CMAr, consistently showed significant negative correlation with mean reaction time (RT) in all three tasks. These results show that simple reaction time tasks activate many subdivisions of the motor cortices. The information from different sensory modalities converge onto the common structures: the contralateral areas 4a, 4p, 3b, 1, the PMD, and bilaterally on the SMA and the CMAr. The anterior cingulate cortex might be a key structure which determine the speed of reaction in simple RT tasks.
A comparison of native and non-urate Total Antioxidant Capacity of fasting plasma and saliva among middle-aged and older subjects

ABSTRACT Objectives: As plasma and salivary total antioxidant capacity (TAC) is mainly contributed by uric acid (UA), the present study measures non-urate TAC (Nu-TAC). The aim of the study was to correlate plasma native TAC, Nu-TAC and UA with their salivary analogues, and compare the UA contribution in both body fluids using two different methods. Methods: The study involved 55 middle-aged and older subjects (66.7 ± 4.5 years). TAC was determined simultaneously with two methods (ferric reducing ability of plasma – FRAP, 2.2-diphenyl-1-picryl-hydrazyl – DPPH and countertypes for saliva – FRAS and DPPHS test), with and without UA (native TAC and Nu-TAC, respectively). Plasma UA and salivary UA (SUA) were assessed. Results: Subjects with increased FRAP, DPPH and UA had higher FRAS, DPPHS and SUA, respectively (P < 0.05). Plasma Nu-TAC indices did not correlate with salivary Nu-TAC. The contribution of UA to the plasma and salivary DPPH tests was similar: 75.7 ± 10.3% and 75.2 ± 14.0%, respectively. However, the contribution of UA to FRAS was higher than that for FRAP (71.6 ± 13.9% vs. 64.0 ± 8.1%; P < 0.001). Discussion: Our findings suggest that saliva is a good predictor for native plasma TAC but not for Nu-TAC. UA level is comparably dominant in saliva and in plasma according to DPPH, but lower in plasma according to FRAP.
Perspective: An Extension of the STROBE Statement for Observational Studies in Nutritional Epidemiology (STROBE-nut): Explanation and Elaboration

Nutritional epidemiology is an inherently complex and multifaceted research area. Dietary intake is a complex exposure and is challenging to describe and assess, and links between diet, health, and disease are difficult to ascertain. Consequently, adequate reporting is necessary to facilitate comprehension, interpretation, and generalizability of results and conclusions. The STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) statement is an international and collaborative initiative aiming to enhance the quality of reporting of observational studies. We previously presented a checklist of 24 reporting recommendations for the field of nutritional epidemiology, called “the STROBE-nut. ” The STROBE-nut is an extension of the general STROBE statement, intended to complement the STROBE recommendations to improve and standardize the reporting in nutritional epidemiology. The aim of the present article is to explain the rationale for, and elaborate on, the STROBE-nut recommendations to enhance the clarity and to facilitate the understanding of the guidelines. Examples from the published literature are used as illustrations, and references are provided for further reading.
Impaired Long-Term Memory and NR2A-Type NMDA Receptor-Dependent Synaptic Plasticity in Mice Lacking c-Fos in the CNS

The immediate early gene c-fos is part of the activator protein-1 transcription factor and has been postulated to participate in the molecular mechanisms of learning and memory. To test this hypothesis in vivo, we generated mice with a nervous system-specific c-fos knock-out using the Cre-loxP system. Adult mice lacking c-Fos in the CNS (c-fosΔCNS) showed normal general and emotional behavior but were specifically impaired in hippocampus-dependent spatial and associative learning tasks. These learning deficits correlated with a reduction of long-term potentiation (LTP) in hippocampal CA3-CA1 synapses. The magnitude of LTP was restored by a repeated tetanization procedure, suggesting impaired LTP induction in c-fosΔCNS mice. This rescue was blocked by a selective inhibitor of NR2B-type NMDA receptors. This blockade was compensated in wild-type mice by NR2A-type NMDA receptor-activated signaling pathways, thus indicating that these pathways are compromised in c-fosΔCNS mice. In summary, our data suggest a role for c-Fos in hippocampus-dependent learning and memory as well as in NMDA receptor-dependent LTP formation.
Structure and Spatial Distribution of the Chironomidae Community in Mesohabitats in a First Order Stream at the Poço D'Anta Municipal Biological Reserve in Brazil

Abstract The Chironomidae occupy different habitats along the lotic system with their distribution determined by different factors such as the substrate characteristics and water speed. The input of vegetable material from the riparian forest allows a higher habitat diversity and food to the benthic fauna. The main aim of this paper is to verify the structure and spatial distribution of the Chironomidae fauna in different mesohabitats in a first order stream located at a Biological Reserve in the southeast of Brazil. In the months of July, August, and September 2007, and in January, February, and March 2008, samples were collected with a hand net (250 µm) in the following mesohabitats: litter from riffles, litter from pools, and sediment from pools. The community structure of each mesohabitat was analyzed through the abundance of organisms, taxa richness, Pielou's evenness, Shannon's diversity, and taxa dominance. Similarity among the mesohabitats was obtained by Cluster analysis, and Chironomidae larvae distribution through the Correspondence analysis. Indicator species analysis was used to identify possible taxa preference for a determined mesohabitat. The analyzed mesohabitats showed high species richness and diversity favored by the large environmental heterogeneity. Some taxa were indicators of the type of mesohabitat. The substrate was the main factor that determined taxa distribution in relation to water flow differences (riffle and pool). Stream characteristics such as low water speed and the presence of natural mechanisms of retention may have provided a higher faunistic similarity between the areas with different flows. The results showed that the physical characteristics of each environment presented a close relationship with the structure and spatial distribution of the Chironomidae fauna in lotic systems.
Insulins with built‐in glucose sensors for glucose responsive insulin release

Derivatization of insulin with phenylboronic acids is described, thereby equipping insulin with novel glucose sensing ability. It is furthermore demonstrated that such insulins are useful in glucose‐responsive polymer‐based release systems. The preferred phenylboronic acids are sulfonamide derivatives, which, contrary to naïve boronic acids, ensure glucose binding at physiological pH, and simultaneously operate as handles for insulin derivatization at LysB29. The glucose affinities of the novel insulins were evaluated by glucose titration in a competitive assay with alizarin. The affinities were in the range 15–31 mM (Kd), which match physiological glucose fluctuations. The dose‐responsive glucose‐mediated release of the novel insulins was demonstrated using glucamine‐derived polyethylene glycol polyacrylamide (PEGA) as a model, and it was shown that Zn(II) hexamer formulation of the boronated insulins resulted in steeper glucose sensitivity relative to monomeric insulin formulation. Notably, two of the boronated insulins displayed enhanced insulin receptor affinity relative to native insulin (113%–122%) which is unusual for insulin LysB29 derivatives. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.
Adaptive Modeling of Sound Transmission in the Respiratory System

In this study, adaptive filtering techniques have been used in an attempt to model the respiratory system. The respiratory system has been considered as a dynamic system for which input-output relationship is to be defined. Simultaneous measurement of the respiratory sounds over the trachea and posterior chest were made, with the signal from the trachea forming the input to a finite impulse response filter and the signal from the posterior chest forming the desired response of the filter. The chest cavity was stimulated with speech sounds. Least-mean square algorithm was used to update filter coefficients. The learning curves of the filter are presented in the paper. It can be concluded that adaptive filtering is a promising way to characterize transmission characteristics of the respiratory system and further improvement may be obtained if anatomical information is integrated in the modeling process.
Modeling Sources of Uncertainty in Spoken Word Learning

In order to successfully learn the meaning of novel words such as bin or pin, language learners must not only be able to perceive relevant differences in the speech signal but also learn mappings from words to referents. Prior work in native (Stager & Werker, 1997) and second (Pajak, Creel, & Levy, 2016) language acquisition has found that the ability to perceptually discriminate between words does not guarantee successful word learning. Put differently, learners fail to utilize knowledge that they can otherwise use in speech perception. To explore possible mechanisms accounting for this phenomenon, we present a probabilistic model capable of inferring a word’s phonetic form and of integrating the result with prior label/referent representations in memory. By analyzing the reasons for successes and failures when fitting different versions of the model to experimental results from Pajak et al. (2016), we argue that a mechanism for spoken word learning needs to incorporate both perceptual uncertainty as well as additional, task-related sources of uncertainty to successfully account for the data.
Image Filtering using All Neighbor Directional Weighted Pixels: Optimization using Particle Swarm Optimization

In this paper a novel approach for de noising images corrupted by random valued impulses has been proposed. Noise suppression is done in two steps. The detection of noisy pixels is done using all neighbor directional weighted pixels (ANDWP) in the 5 x 5 window. The filtering scheme is based on minimum variance of the four directional pixels. In this approach, relatively recent category of stochastic global optimization technique i.e., particle swarm optimization (PSO) has also been used for searching the parameters of detection and filtering operators required for optimal performance. Results obtained shows better de noising and preservation of fine details for highly corrupted images.