Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Ammonia and β‐Methylene‐dl‐Aspartate on the Oxidation of Glucose and Pyruvate by Neurons and Astrocytes in Primary Culture

Abstract: Both ammonia and β‐methylene‐dl‐aspartate (β‐MA), an irreversible inhibitor of aspartate aminotransferase activity and thus of the malate‐aspartate shuttle, were found previously to decrease oxidative metabolism in cerebral cortex slices. In the present work, the possibility that ammonia and β‐MA affect energy metabolism by a common mechanism (i.e., via inhibition of the malate‐aspartate shuttle) was investigated using primary cultures of neurons and astrocytes. Incubation of astrocytes for 30 min with 5 mMβ‐MA resulted in a decreased production of 14CO2 from [U‐14Clglucose, but did not affect 14CO2 production from [2–14C] pyruvate. Conversely, incubation of astrocytes with 3 mM ammonium chloride resulted in decreased 14CO2 production from [2–14C] pyruvate, but 14CO2 production from [U‐14C] glucose was not significantly affected. Ammonium chloride had no significant effect on 14CO2 production from either [U‐14C] glucose or [2–14]pyruvate by neurons. However, incubation of neurons with β‐MA or β‐MA plus ammonium chloride resulted in a 45% decrease of 14CO2 production from both [U‐14C] glucose and [2–14C] pyruvate. A 2‐h incubation of astrocytes with β‐MA resulted in no change in ATP levels, but a 35% decrease in phosphocreatine. Similar treatment of neurons resulted in >50% decrease in ATP, but had little effect on phosphocreatine. β‐MA also caused a decrease in glutamate and aspartate content of neurons, but not of astrocytes. The different metabolic responses of neurons and astrocytes towards β‐MA were probably not due to a differential inhibition of aspartate aminotransferase which was inhibited by ∼45% in astrocytes and by ∼55% in neurons.
PCorral—interactive mining of protein interactions from MEDLINE

The extraction of information from the scientific literature is a complex task—for researchers doing manual curation and for automatic text processing solutions. The identification of protein–protein interactions (PPIs) requires the extraction of protein named entities and their relations. Semi-automatic interactive support is one approach to combine both solutions for efficient working processes to generate reliable database content. In principle, the extraction of PPIs can be achieved with different methods that can be combined to deliver high precision and/or high recall results in different combinations at the same time. Interactive use can be achieved, if the analytical methods are fast enough to process the retrieved documents. PCorral provides interactive mining of PPIs from the scientific literature allowing curators to skim MEDLINE for PPIs at low overheads. The keyword query to PCorral steers the selection of documents, and the subsequent text analysis generates high recall and high precision results for the curator. The underlying components of PCorral process the documents on-the-fly and are available, as well, as web service from the Whatizit infrastructure. The human interface summarizes the identified PPI results, and the involved entities are linked to relevant resources and databases. Altogether, PCorral serves curator at both the beginning and the end of the curation workflow for information retrieval and information extraction. Database URL: http://www.ebi. ac.uk/Rebholz-srv/pcorral.
Approximate Message-Passing Decoder and Capacity Achieving Sparse Superposition Codes

We study the approximate message-passing decoder for sparse superposition coding on the additive white Gaussian noise channel and extend our preliminary work. We use heuristic statistical-physics-based tools, such as the cavity and the replica methods, for the statistical analysis of the scheme. While superposition codes asymptotically reach the Shannon capacity, we show that our iterative decoder is limited by a phase transition similar to the one that happens in low density parity check codes. We consider two solutions to this problem, that both allow to reach the Shannon capacity: 1) a power allocation strategy and 2) the use of spatial coupling, a novelty for these codes that appears to be promising. We present, in particular, simulations, suggesting that spatial coupling is more robust and allows for better reconstruction at finite code lengths. Finally, we show empirically that the use of a fast Hadamard-based operator allows for an efficient reconstruction, both in terms of computational time and memory, and the ability to deal with very large messages.
On Tests for Hypothetical ReasoningSheila McIlraith

Suppose that HY P is a set of hypotheses which we currently entertain about some state of aaairs represented by a propositional sentence. In a diagnostic setting, HY P might consist of all the diagnoses of some device whose description is given by , although our analysis is not restricted to diagnosis. Our concern is with tests { how they can be designed, and what conclusions can be drawn about the hypotheses in HY P as a result of performing tests. Speciically, we deene the concept of a test and the concept of the outcome of a test. We characterize those tests whose outcomes refute or con-rm an hypothesis, and discriminate between competing hypotheses. These characterizations are in terms of the prime implicates of , and hence are implementable using assumption-based truth maintenance systems. In addition, we characterize the impact of a test outcome on consistency-based and abductive hypothesis spaces. Finally, we provide a characterization of diierential diagnosis for consistency-based and abductive reasoning.
Condensation of actin filaments pushing against a barrier

We develop a model to describe the force generated by the polymerization of an array of parallel biofilaments. The filaments are assumed to be coupled only through mechanical contact with a movable barrier. We calculate the filament density distribution and the force–velocity relation with a mean-field approach combined with simulations. We identify two regimes: a non-condensed regime at low force in which filaments are spread out spatially and a condensed regime at high force in which filaments accumulate near the barrier. We confirm a result previously known from other related studies, namely that the stall force is equal to N times the stall force of a single filament. In the model studied here, the approach to stalling is very slow, and the velocity is practically zero at forces significantly lower than the stall force.
Radiative return method as a tool in hadronic physics

A short review of both theoretical and experimental aspects of the radiative return method is presented. It is emphasised that the method gives not only possibility of the independent from the scan method measurement of the hadronic cross section, but also can provide information concerning details of the hadronic interactions. New developments in the PHOKHARA event generator are also reviewed. The 3 pion and kaon pair production is implemented within the version 5.0 of the program, together with contributions of the radiative phi decays to the 2 pion final states. Missing NLO radiative corrections to the e+e- -> mu+ mu- gamma process will be implemented in the forthcoming version of the generator.
Animal models of enteroaggregative Escherichia coli infection

Enteroaggregative Escherichia coli (EAEC) has been acknowledged as an emerging cause of gastroenteritis worldwide for over two decades. Epidemiologists are revealing the role of EAEC in diarrheal outbreaks as a more common occurrence than ever suggested before. EAEC induced diarrhea is most commonly associated with travelers, children and immunocompromised individuals however its afflictions are not limited to any particular demographic. Many attributes have been discovered and characterized surrounding the capability of EAEC to provoke a potent pro-inflammatory immune response, however cellular and molecular mechanisms underlying initiation, progression and outcomes are largely unknown. This limited understanding can be attributed to heterogeneity in strains and the lack of adequate animal models. This review aims to summarize current knowledge about EAEC etiology, pathogenesis and clinical manifestation. Additionally, current animal models and their limitations will be discussed along with the value of applying systems-wide approaches such as computational modeling to study host-EAEC interactions.
Random-Edge Is Slower Than Random-Facet on Abstract Cubes

Random-Edge and Random-Facet are two very natural randomized pivoting rules for the simplex algorithm. The behavior of Random-Facet is fairly well understood. It performs an expected sub-exponential number of pivoting steps on any linear program, or more generally, on any Acyclic Unique Sink Orientation (AUSO) of an arbitrary polytope, making it the fastest known pivoting rule for the simplex algorithm. The behavior of Random-Edge is much less understood. We show that in the AUSO setting, Random-Edge is slower than Random-Facet. To do that, we construct AUSOs of the n-dimensional hypercube on which Random-Edge performs an expected number of 2^{Omega(sqrt(n*log(n)))} steps. This improves on a 2^{Omega(sqrt^3(n))} lower bound of Matousek and Szabo. As Random-Facet performs an expected number of 2^{O(sqrt(n)} steps on any n-dimensional AUSO, this established our result. Improving our 2^{Omega(sqrt(n*log(n)))} lower bound seems to require radically new techniques.
Is Systematic Downside Beta Risk Really Priced? Evidence in Emerging Market Data

Several studies advocating safety first as a major concern to investors propose downside beta risk as an alternative to the traditional systematic risk-beta. Downside measures are concerned with a subset of the data and therefore the results in the studies that consider the downside beta only may be biased. This study addresses this issue by including downside co-skewness risk in addition to the downside beta risk in the pricing model. In a sample of 27 emerging markets two-stage rolling regression analysis fails to support pricing models with downside risk measures. In a cross-sectional analysis inclusion of downside co-skewness improves model fit. When considered together, downside beta is potential and downside co-skewness is a risk to the rational investor. Even though our results are inconclusive the evidence strongly suggests a need for further investigation of co-skewness risk in pricing models that adopt a downside risk framework.
Predicting carbon isotope discrimination in Eelgrass (Zostera marina L.) from the environmental parameters—light, flow, and [DIC]

Isotopic discrimination against 13C during photosynthesis is determined by a combination of environmental conditions and physiological mechanisms that control delivery of CO2 to RUBISCO. This study investigated the effects of light, flow, dissolved inorganic carbon (DIC) concentration, and its speciation, on photosynthetic carbon assimilation of Zostera marina L. (eelgrass) using a combination of laboratory experiments and theoretical calculations leading to a mechanistic understanding of environmental conditions that influence leaf carbon uptake and determine leaf stable carbon isotope signatures (δ13C). Photosynthesis was saturated with respect to flow at low velocity (∼ 3 cm s−1), but was strongly influenced by [DIC], and particularly aqueous CO2 (CO2(aq)) under all flow conditions. The non‐linear responses of light‐ and flow‐saturated photosynthesis to [DIC] were used to quantify the maximum physiological capacity for photosynthesis, and to determine the degree of photosynthetic carbon limitation for light‐saturated photosynthesis, which provided a mechanistic pathway for modeling regulation of carbon uptake and 13C discrimination. Model predictions of δ13C spanned the typical range of values reported for a variety of seagrass taxa, and were most sensitive to [DIC] (predominantly [CO2(aq)]) and flow, but less sensitive to DIC source [CO2(aq) vs. HCO3− ]. These results provide a predictive understanding of the role of key environmental parameters (light, flow, and DIC availability) can have in driving δ13C of seagrasses, which will become increasingly important for predicting the response of these ecosystem engineers to local processes that affect light availability and flow, as well as global impacts of climate warming and ocean acidification in the Anthropocene.
Rendering SU-8 hydrophilic to facilitate use in micro channel fabrication

A simple method is presented to reduce the contact angle of the photo-resist SU-8. A low contact angle is valuable in micro total analysis systems for the fabrication of micro channels where the capillary pressure is linearly related to the cosine of the contact angle, θ. If the surface of the channel is hydrophilic, the capillary pressure can be used as the only means to direct the liquid through the channels and the need for external pumps can be avoided. This is very useful, especially in the fabrication of devices for 'lab-on-a-chip' where it is important to keep the design as simple as possible. A commonly used technique for releasing structures fabricated on Si wafers is to use a sacrificial Cr layer. It is shown that the contact angle of SU-8 decreases by 40° after etching this layer. A further reduction in contact angle is desirable and can be achieved by treating the sample with ethanolamine at 50 °C for only 10 min. The resulting contact angle is 23° ± 7°. Using a wet chemical treatment, a selective change in contact angle between different areas of a micro channel system can be achieved, without the need to involve different materials in the fabrication process.
10 years later: Assessing the impact of public health efforts on the collection of family health history

In 2004, a nationwide survey found that the majority (96.3%) of Americans believed their family health history (FHx) was important for their own health; however, only a third (29.8%) of respondents had ever actively collected this information. Over the past decade, government agencies, advocacy groups, professional societies, and healthcare provider organizations have aimed to improve the collection rates and utilization of FHx. This study assesses the current attitudes, knowledge, and practices of Americans regarding their FHx and whether the interventions over the past 10 years have led to any FHx‐related changes. We conducted a nationwide survey of 5,258 respondents using the same measures used in the 2004 survey. Overall, there was little change in Americans knowledge and use of FHx information. While there was a statistically significant increase in respondents who have actively collected their FHx (36.9%), respondents know roughly the same or less about his or her FHx today. Furthermore, only a small fraction (2.6%) had ever collected their FHx using a web‐based FHx tool. Several factors were identified which influence whether an individual actively collects his or her FHx. New FHx tools and approaches may be necessary to promote clinically meaningful improvement in FHx collection among patients. © 2015 Wiley Periodicals, Inc.
Methods for Smoothing the Optimizer Instability in SMT

In SMT, the instability of MERT, the commonly used optimizer, is an acknowledged problem. This paper presents two methods for smoothing the MERT instability. Both exploit a set of different realizations of the same system obtained by running the optimization stage multiple times. One method averages the sets of different optimal weights; the other combines the translations generated by the various realizations. Experiments conducted on two different sized tasks involving four different language pairs show that both methods are effective in smoothing instability, but also that the average system well competes with the more expensive system combination.
Abnormal Cardiac Autonomic Regulation in Mice Lacking ASIC3

Integration of sympathetic and parasympathetic outflow is essential in maintaining normal cardiac autonomic function. Recent studies demonstrate that acid-sensing ion channel 3 (ASIC3) is a sensitive acid sensor for cardiac ischemia and prolonged mild acidification can open ASIC3 and evoke a sustained inward current that fires action potentials in cardiac sensory neurons. However, the physiological role of ASIC3 in cardiac autonomic regulation is not known. In this study, we elucidate the role of ASIC3 in cardiac autonomic function using Asic3 −/− mice. Asic3 −/− mice showed normal baseline heart rate and lower blood pressure as compared with their wild-type littermates. Heart rate variability analyses revealed imbalanced autonomic regulation, with decreased sympathetic function. Furthermore, Asic3 −/− mice demonstrated a blunted response to isoproterenol-induced cardiac tachycardia and prolonged duration to recover to baseline heart rate. Moreover, quantitative RT-PCR analysis of gene expression in sensory ganglia and heart revealed that no gene compensation for muscarinic acetylcholines receptors and beta-adrenalin receptors were found in Asic3 −/− mice. In summary, we unraveled an important role of ASIC3 in regulating cardiac autonomic function, whereby loss of ASIC3 alters the normal physiological response to ischemic stimuli, which reveals new implications for therapy in autonomic nervous system-related cardiovascular diseases.
Non radial motions and the shapes and the abundance of clusters of galaxies

We study the effect of non-radial motions on the mass function, the velocity dispersion function (hereafter VDF) and on the shape of clusters of galaxies using the model introduced in Del Popolo & Gambera (1998a,b; 1999). The mass function of clusters, obtained using the quoted model, is compared with the statistical data by Bahcall & Cen (1992a,b) and Girardi et al. (1998), while the VDF is compared with the Center for Astrophysics (hereafter CfA) data by Zabludoff et al. (1993) for local clusters and those of Mazure et al. (1996) and Fadda et al. (1996). In both cases the model predictions are in good agreement with the observational data showing once more how non-radial motions can reduce many of the discrepancies between Cold Dark Matter (hereafter CDM) model predictions and observational data. Finally we study the effect of non-radial motions on the intrinsic shape of clusters of galaxies showing that non-radial motions produce clusters less elongated with respect to CDM model in agreement with de Theije et al. (1995, 1997) results.
Identification of a Pre-BCR Lacking Surrogate Light Chain

SLP-65−/− pre-B cells show a high proliferation rate in vitro. We have shown previously that λ5 expression and consequently a conventional pre-B cell receptor (pre-BCR) are essential for this proliferation. Here, we show that pre-B cells express a novel receptor complex that contains a μ heavy chain (μHC) but lacks any surrogate (SL) or conventional light chain (LC). This SL-deficient pre-BCR (SL−pre-BCR) requires Ig-α for expression on the cell surface. Anti-μ treatment of pre-B cells expressing the SL−pre-BCR induces tyrosine phosphorylation of substrate proteins and a strong calcium (Ca2+) release. Further, the expression of the SL−pre-BCR is associated with a high differentiation rate toward κLC-positive cells. Given that B cell development is only partially blocked and allelic exclusion is unaffected in SL-deficient mice, we propose that the SL−pre-BCR is involved in these processes and therefore shares important functions with the conventional pre-BCR.
Poverty Impedes Cognitive Function

Burden of Poverty Lacking money or time can lead one to make poorer decisions, possibly because poverty imposes a cognitive load that saps attention and reduces effort. Mani et al. (p. 976; see the Perspective by Vohs) gathered evidence from shoppers in a New Jersey mall and from farmers in Tamil Nadu, India. They found that considering a projected financial decision, such as how to pay for a car repair, affects people's performance on unrelated spatial and reasoning tasks. Lower-income individuals performed poorly if the repairs were expensive but did fine if the cost was low, whereas higher-income individuals performed well in both conditions, as if the projected financial burden imposed no cognitive pressure. Similarly, the sugarcane farmers from Tamil Nadu performed these tasks better after harvest than before. Being poor is a state of mind. [Also see Perspective by Vohs] The poor often behave in less capable ways, which can further perpetuate poverty. We hypothesize that poverty directly impedes cognitive function and present two studies that test this hypothesis. First, we experimentally induced thoughts about finances and found that this reduces cognitive performance among poor but not in well-off participants. Second, we examined the cognitive function of farmers over the planting cycle. We found that the same farmer shows diminished cognitive performance before harvest, when poor, as compared with after harvest, when rich. This cannot be explained by differences in time available, nutrition, or work effort. Nor can it be explained with stress: Although farmers do show more stress before harvest, that does not account for diminished cognitive performance. Instead, it appears that poverty itself reduces cognitive capacity. We suggest that this is because poverty-related concerns consume mental resources, leaving less for other tasks. These data provide a previously unexamined perspective and help explain a spectrum of behaviors among the poor. We discuss some implications for poverty policy.
Prevalence of Undiagnosed Celiac Disease in the Parents of Preterm and/or Small for Gestational Age Infants

OBJECTIVES:The aim of this study was to estimate the prevalence of undiagnosed celiac disease (CD) in the parents of preterm and/or small for gestational age (SGA) infants.METHODS:A sample of 1,714 parents (868 women, 846 men) of 905 preterm (<37 wk of gestational age) and/or SGA (<10th percentile of birthweight) infants consecutively born in Lombardy, Northern Italy, and not diagnosed with CD prior to pregnancy, were tested for CD. Diagnosis was based on antitissue transglutaminase and anti-endomysial antibodies and confirmed by duodenal biopsy.RESULTS:The overall prevalence of undiagnosed CD was 0.64% (95% confidence interval [CI] 0.32–1.15%), 0.92% (0.40–1.81%) in women and 0.35% (0.07–1.03%) in men. In the mothers of preterm infants prevalence of CD was 0.39% (0.05–1.39%). In the mothers of SGA infants prevalence of CD was 1.60% (0.64–3.27%), and the observed number of mothers with CD was 2.25 times higher than the expected one in the Italian female population (P = 0.039). Undiagnosed CD in mothers was associated with an increased risk of SGA birth (odds ratio 6.97, 95% CI 1.11–43.55%). CONCLUSIONS:While additional powered studies are needed, the present results suggest that the prevalence of undiagnosed CD in the mothers of SGA infants is higher than in the general female population.