Miracle-dz/UniFAR-FTUs huggingface dataset:
Retinal ganglion cell death is induced by microglia derived pro‐inflammatory cytokines in the hypoxic neonatal retina

Hypoxic injury, including that resulting in the retinopathy of prematurity, may induce retinal ganglion cell (RGC) death in the neonatal retina. We hypothesized that this may be mediated by excess production of tumour necrosis factor‐α (TNF‐α) and interleukin‐1β (IL‐1β) by microglia. One‐day‐old Wistar rats were subjected to hypoxia for 2 h and the expression of TNF‐α and IL‐1β and their receptors was determined in the retina. The mRNA and protein expression of TNF‐α, IL‐1β, TNF‐receptor 1 (TNF‐R1), and IL‐1 receptor 1 (IL‐1R1) and the tissue concentration of TNF‐α and IL‐1β were up‐regulated significantly after the hypoxic exposure. TNF‐α and IL‐1β immunoreactivity was localized in microglial cells, whereas that of TNF‐R1 and IL‐1R1 was restricted to RGCs, as confirmed by double immunofluorescence labelling. Along with this, increased expression of monocyte chemoattractant protein‐1 and its receptor CCR2 was detected in the microglia. Primary cultured microglia subjected to hypoxia showed enhanced release of TNF‐α and IL‐1β. Primary cultured retinal ganglion cells (RGCs) treated with conditioned medium derived from hypoxic microglia showed enhanced apoptosis, which was significantly reduced when the cells were treated with microglia conditioned medium neutralized with TNF‐α/IL‐1β antibody. Our results suggest that activated microglial cells in hypoxic neonatal retina produce increased amounts of TNF‐α and IL‐1β that could induce RGC death. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Stability and stabilization of homogeneous stochastic systems

This study considers homogeneous stochastic systems and shows their stability and stabilization. We define a homogeneous stochastic system as an extension of a homogeneous deterministic system. We show that homogeneous systems can exhibit exponential stability or finite-time stability according to the degree of homogeneity. Further, we show a control law for the stabilization of homogeneous stochastic control systems. Numerical examples of stable homogeneous systems and the stabilization of a homogeneous control system are also presented.
Fasting decreases rates of noninsulin-mediated glucose uptake in man.

Although fasting decreases insulin-mediated glucose uptake (IMGU), its effect on noninsulin-mediated glucose uptake (NIMGU) is not known. To examine this issue we studied seven obese men [mean (+/- SD) age, 36 +/- 5 yr; weight, 91 +/- 13 kg] after an overnight fast (day 0) and 3 days (day 4) and 9 days (day 10) of total fasting and six normal weight men (age, 32 +/- 4 yr; weight, 73 +/- 6 kg) after an overnight and 3 days of fasting. To study NIMGU, somatostatin (0.16 micrograms/kg.min) was infused to create severe insulin deficiency and [3H]3-glucose to measure glucose disappearance (Rd), while serum glucose was sequentially clamped at a level of about 4.7 mmol/L for 180 min and about 11 mmol/L for an additional 100 min. The results from the last 60 min of each glycemic plateau were used for analysis. Under these conditions insulin action is absent and Rd = NIMGU. Since under conditions of euglycemic insulinopenia, NIMGU into noncentral nervous system tissues is negligible, and central nervous system (CNS) glucose uptake saturates at physiological glucose concentrations, it follows that at a glucose level of about 4.7 mmol/L, NIMGU reflects CNS glucose uptake and at about 11 mmol/L, NIMGU reflect CNS plus non-CNS tissues. Thus, non-CNS NIMGU = NIMGU at 11 mmol/L - NIMGU at about 4.7 mmol/L. The obese subjects' mean weight fell to 88 +/- 5 kg on day 4 and 85 +/- 5 kg on day 10 (P less than 0.001 between all values). The mean basal serum glucose level fell from 5.3 +/- 0.1 on day 0 to 4.2 +/- 0.2 and 3.8 +/- 0.2 mmol/L on days 4 and 10, respectively (P less than 0.01 between all values). During insulinopenia plasma FFA and serum beta-hydroxybutyrate levels on day 10 were 3- and 30-fold higher than the basal prefast levels, respectively. Noninsulin-mediated glucose clearance at about 4.7 mmol/L did not change during fasting [0.0016 +/- 0.0001 (day 0) vs. 0.0016 +/- 0.0001 (day 4) and 0.0014 +/- 0.0001 L/kg.min (day 10); P = NS between all values]; at about 11 mmol/L noninsulin-mediated glucose clearance fell from 0.0016 +/- 0.0001 on day 0 to 0.0001 +/- 0.0001 dL/kg.min on day 10 (P less than 0.001). Results in the lean group were similar to those in the obese group after a 3-day fast. (ABSTRACT TRUNCATED AT 400 WORDS)
SMEE: a tool to extract sorting motif data from PubMed Central abstracts and full text documents

Data from biological research experiments is being posted online at a phenomenal rate. Even in a fairly narrow topic, one can easily become overloaded trying to keep up with information relevant to a single researcher. An automated method for analyzing and presenting this data is the key to conducting efficient and fruitful research in any biological field. Before now, there has not been a freely available semi-automated protein sorting motif text mining solution. This paper details a current work in progress to create a novel procedure for text mining protein sorting motif data from both full text documents and abstracts retrieved from PubMed Central. A full set of processing stages are currently implemented and early results are promising. We expect further work to yield a valuable tool to be made freely available for the community.
A coalgebraic view on decorated traces

In the concurrency theory, various semantic equivalences on transition systems are based on traces decorated with some additional observations, generally referred to as decorated traces. Using the generalized powerset construction, recently introduced by a subset of the authors (Silva et al. 2010 FSTTCS. LIPIcs 8 272–283), we give a coalgebraic presentation of decorated trace semantics. The latter include ready, failure, (complete) trace, possible futures, ready trace and failure trace semantics for labelled transition systems, and ready, (maximal) failure and (maximal) trace semantics for generative probabilistic systems. This yields a uniform notion of minimal representatives for the various decorated trace equivalences, in terms of final Moore automata. As a consequence, proofs of decorated trace equivalence can be given by coinduction, using different types of (Moore-) bisimulation (up-to context).
Drought × CO2 interactions in trees: a test of the low-intercellular CO2 concentration (Ci ) mechanism.

Models of tree responses to climate typically project that elevated atmospheric CO2 concentration (eCa ) will reduce drought impacts on forests. We tested one of the mechanisms underlying this interaction, the 'low Ci effect', in which stomatal closure in drought conditions reduces the intercellular CO2 concentration (Ci ), resulting in a larger relative enhancement of photosynthesis with eCa , and, consequently, a larger relative biomass response. We grew two Eucalyptus species of contrasting drought tolerance at ambient and elevated Ca for 6-9 months in large pots maintained at 50% (drought) and 100% field capacity. Droughted plants did not have significantly lower Ci than well-watered plants, which we attributed to long-term changes in leaf area. Hence, there should not have been an interaction between eCa and water availability on biomass, and we did not detect one. The xeric species did have higher Ci than the mesic species, indicating lower water-use efficiency, but both species exhibited similar responses of photosynthesis and biomass to eCa , owing to compensatory differences in the photosynthetic response to Ci . Our results demonstrate that long-term acclimation to drought, and coordination among species traits may be important for predicting plant responses to eCa under low water availability.
Insulin Action in Cells Expressing Truncated or Kinase-Defective Insulin Receptors: Dissection of Multiple Hormone-Signaling Pathways

An attempt has been made to dissect insulin-signaling pathways by means of in vitro mutagenesis of the insulin receptor. Studies of two mutants are reviewed: a COOH-truncated receptor and a mutant of the ATPbinding site that is tyrosine kinase defective. The COOH-truncated receptor has normal insulin binding and normal endocytosis and undergoes autophosphorylation and activation as a kinase in vitro and in vivo. Loss of the COOH-terminal43 amino acids has, however, impaired the ability of the receptor to signal metabolic events while augmenting its ability to signal mitogenesis. Thus, domains have been partially identified that are separately involved in metabolic and mitogenic signaling, facilitating future studies of these pathways. The kinase-defective receptor is not only biologically inactive, but has a dominant inhibitory effect on the endogenous insulin receptors in the cell. That is, transfected Rat-1 cells carrying defective human receptors still have normally active rat insulin receptors but are incapable of signaling insulin action. The fact that metabolic signaling by insulinlike growth factor I (IGF-I) is intact in these cells allows definition of separate insulin and IGF-I pathways, leading to stimulation of glucose transport. Analysis of dose responsiveness for mitogenesis implies that mitogenic signaling pathways are shared by insulin and IGF-I, however. The utility of these cell lines in defining these pathways is discussed.
Displacements, strains, and tilts at teleseismic distances

The dislocation theory representation of faulting of Vvedenskaya, Steketee, Chinnery, and Maruyama is used to compute the residual displacement, strain, and tilt fields at intermediate and large distances from major earthquakes. It is shown that the distant fields are large enough to be detected by modern instruments. The vertical displacement field from the Alaskan earthquake of March 27, 1964, indicates that the primary fault extended to a depth of 150 to 200 km and that it probably came to within 15 km of the surface. The residual strain observed at Hawaii amounted to 10−8, a value which is reasonably consistent with the extent of faulting and the displacements near the source. The elastic strain energy release was about 1025 ergs. Other observations of residual strains and tilts are examined. In some cases nonfaulting sources are probably involved. In other cases the observations may be a spurious manifestation of instrumental hysteresis. The Mindlin-Cheng catalog of fields from various nuclei of strain in a half-space offers a convenient way to derive residual displacements from diverse sources, including those of Chinnery and Maruyama.
A Simple Algorithm for Bayesian Signal Analysis With Applications to Metrology

A Bayesian approach to spectrum analysis using approximations based on the posterior mode is applied here to waveform metrology. A simple algorithm for obtaining accurate estimates of signal parameters and their associated uncertainties is presented. It is assumed that the data can be modeled with trigonometric equations. The algorithm can be easily implemented with those commercial laboratory software packages routinely used by metrologists for controlling instrumentation and reporting measurement results. Its performance has been confirmed through several experimental setups.
Assessing the Role of Discourse References in Entailment Inference

Discourse references, notably coreference and bridging, play an important role in many text understanding applications, but their impact on textual entailment is yet to be systematically understood. On the basis of an in-depth analysis of entailment instances, we argue that discourse references have the potential of substantially improving textual entailment recognition, and identify a number of research directions towards this goal.
The hydrolysis of agro-industrial residues by holocellulose-degrading enzymes

Holocellulose structures from agro-industrial residues rely on main and side chain attacking enzymes with different specificities for complete hydrolysis. Combinations of crude enzymatic extracts from different fungal species, including Aspergillus terreus, Aspergillus oryzae, Aspergillus niger and Trichoderma longibrachiatum, were applied to sugar cane bagasse, banana stem and dirty cotton residue to investigate the hydrolysis of holocellulose structures. A. terreus and A. oryzae were the best producers of FPase and xylanase activities. A combination of A. terreus and A. oryzae extracts in a 50% proportion provided optimal hydrolysis of dirty cotton residue and banana stem. For the hydrolysis of sugar cane bagasse, the best results were obtained with samples only containing A. terreus crude extract.
Severe hemolytic anemia in a Vietnamese family, associated with novel mutations in the gene encoding for pyruvate kinase.

BACKGROUND AND OBJECTIVES Chronic hemolytic anemias are very frequent diseases in intertropical countries mainly caused by hemoglobin disorders. We studied a Vietnamese family in which a first child suffered from a severe transfusion-dependent anemia. The family requested an antenatal diagnosis during a second pregnancy. To characterize the molecular defect, we studied the family over three generations. DESIGN AND METHODS Blood from family members was sampled for a full hematologic evaluation, including enzymatic dosage, and DNA analysis was performed for patients displaying pyruvate kinase deficiency (PK-R). Mutation research on the 11 exons of the PKLR gene was done using a scanning method and sequencing. Deletion was evidenced by a Sybergreen based quantitative real time polymerase chain reaction (PCR) and mapped using quantitative multiplex PCR of short fluorescent fragments spread along the whole sequence of the PKLR gene. RESULTS Hematologic and molecular studies of this severe chronic anemia demonstrated the existence of two defects in the PKLR gene, a new mutation located on exon 7: c.948C->G (N316K) and a large deletion extending from exon 4 to exon 10. INTERPRETATION AND CONCLUSIONS We describe a family in a south-east Asian country; the proband had severe transfusion-dependent chronic anemia caused by the association between two PKLR gene mutations, PK Saigon (N316K) and PK Viet del 4-10. Severe chronic anemia could be induced by various molecular defects mainly affecting the globin genes. However, even in populations in which hemoglobin diseases are frequent, enzymatic diseases should be considered.
Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal

Background Microbial eukaryotes represent an important component of the human gut microbiome, with different beneficial or harmful roles; some species are commensal or mutualistic, whereas others are opportunistic or parasitic. The diversity of eukaryotes inhabiting humans remains relatively unexplored because of either the low abundance of these organisms in human gut or because they have received limited attention from a whole-community perspective. Methodology/Principal Finding In this study, a single fecal sample from a healthy African male was studied using both culture-dependent methods and extended molecular methods targeting the 18S rRNA and ITS sequences. Our results revealed that very few fungi, including Candida spp. , Galactomyces spp. , and Trichosporon asahii, could be isolated using culture-based methods. In contrast, a relatively a high number of eukaryotic species could be identified in this fecal sample when culture-independent methods based on various primer sets were used. A total of 27 species from one sample were found among the 977 analyzed clones. The clone libraries were dominated by fungi (716 clones/977, 73.3%), corresponding to 16 different species. In addition, 187 sequences out of 977 (19.2%) corresponded to 9 different species of plants; 59 sequences (6%) belonged to other micro-eukaryotes in the gut, including Entamoeba hartmanni and Blastocystis sp; and only 15 clones/977 (1.5%) were related to human 18S rRNA sequences. Conclusion Our results revealed a complex eukaryotic community in the volunteer’s gut, with fungi being the most abundant species in the stool sample. Larger investigations are needed to assess the generality of these results and to understand their roles in human health and disease.
Immunoparasitological Studies of Trypanosoma Cruzi Low Virulence Clones from Panama: Humoral Immune Responses and Antigenic Cross‐Reactions with Trypanosoma Rangeli in Experimentally Infected Mice

The kinetics of humoral immune responses were investigated in mice experimentally infected with five clones of Trypanosoma cruzi isolated from different sources in Panama. Sera were collected at different timepoints post‐infection. ELISA and IHA tests were used to detect antibodies against T. cruzi epimastigote antigens. The levels of T. cruzi specific antibodies increased during the course of infection; at day 90 post‐infection the range was between 1:5120 and 1: 10240. A high correlation was evident between ELISA and IHA results. Western blots revealed that these antibodies recognized polypeptides of 81, 76 and 71 KDa during the first weeks and 81, 76, 71, 50, 40, 28 and 12 KDa after 30–50 days. Only minor differences in antigen recognition patterns were demonstrated, suggesting that the major antigens may be represented in all clones. T. rangeli antigens were also recognized by T. cruzi seropositive sera. However, an ELISA test using antigens isolated from a genomic expression library of T. cruzi revealed that a hyperimmune rabbit serum against T. rangeli was unable to recognize the repeat sequence of SAPA (Shed Acute Phase Antigen) peptides but did recognize a number of other T. cruzi synthetic peptide antigens. The importance of these findings, in the context of Chagas' disease, is discussed.
Software Reliability Modeling with Test Coverage: Experimentation and Measurement with A Fault-Tolerant Software Project

As the key factor in software quality, software reliability quantifies software failures. Traditional software reliability growth models use the execution time during testing for reliability estimation. Although testing time is an important factor in reliability, it is likely that the prediction accuracy of such models can be further improved by adding other parameters which affect the final software quality. Meanwhile, in software testing, test coverage has been regarded as an indicator for testing completeness and effectiveness in the literature. In this paper, we propose a novel method to integrate time and test coverage measurements together to predict the reliability. The key idea is that failure detection is not only related to the time that the software experiences under testing, but also to what fraction of the code has been executed by the testing. This is the first time that execution time and test coverage are incorporated together into one single mathematical form to estimate the reliability achieved. We further extend this method to predict the reliability of fault- tolerant software systems. The experimental results with multi-version software show that our reliability model achieves a substantial estimation improvement compared with existing reliability models.
Autonomous Systems

INTRODUCTION . 260 I. PERSONHOOD. 260 A. What Is Legal Personhood? 260 B. Should A.I. Systems Have Legal Personhood? 262 II. DOES A.I. PERSONHOOD ALREADY EXIST? 264 A. New York . 265 1. LLC Members and Managers Must be Persons. 267 2. The Limitations on Operating Agreements Under New York Law . 269 3. Purpose of the LLC Statute . 270 4. Section 608 and the Real Meaning of § 701(a)(4) . 271 5. Conclusion . 272 B. The Revised Uniform Limited Liability Company Act (RULLCA) . 273 1. The Text of RULLCA . 274 2. Enacted Statutes Based on RULLCA . 276 C. Conclusion . 277 III. ALTERNATIVES TO A.I. PERSONHOOD: DIGITAL ANALOGUES . 279 A. Products . 280 B. Animals . 281 C. Children . 283 D. Agents . 285 CONCLUSION . 290
How motion verbs are spatial: The spatial foundations of intransitive motion verbs in French

This paper aims to bring out the spatial properties of motion eventualities by focusing on French intransitive motion verbs. After examining changes of posture and changes of placement, we introduce the concept of change of basic locative relation (J.-P. Boons 1987) in order to accurately grasp the telic processes usually characterized as changes of location. The complex combinatory possibilities as between changes of relation and changes of placement are then illustrated by pinpointing the factors that condition the use of predicates of change of placement in utterances denoting changes of relation and placement (the notion of tendenciality). Finally, a categorization of French intransitive verbs of change of relation and placement is proposed, which is based on the way these two notions interact in their semantics.
E proteins and Notch signaling cooperate to promote T cell lineage specification and commitment

The helix-loop-helix protein, E47, is essential for both B- and T-lineage development. Here we demonstrate that in vitro E47 and Notch signaling act in concert to promote T cell development from fetal hematopoieitic progenitors and to restrain development into the natural killer and myeloid cell lineages. The expression of an ensemble of genes associated with Notch signaling is activated by E47, and additionally, Notch signaling and E47 act in parallel pathways to induce a T lineage–specific program of gene expression. Enforced expression of the intracellular domain of Notch rescues the developmental arrest at the T cell commitment stage in E2A-deficient fetal thymocytes. Finally, we demonstrate that regulation of Hes1 expression by Notch signaling and E47 is strikingly similar to that observed during Drosophila melanogaster sensory development. Based on these observations, we propose that in developing fetal thymocytes E47 acts to induce the expression of an ensemble of genes involved in Notch signaling, and that subsequently E47 acts in parallel with Notch signaling to promote T-lineage maturation.
Power line carrier (PLC) signal analysis of smart meters for outlier detection

A method for identifying outliers among a set of smart meters by using the power line carrier (PLC) signal strength is presented in this paper. The broad goal is to use the PLC signal as a predictor of transmission problems to proactively avert local power outages. The proposed method uses the PLC signal strength measured between the communication node (transformer) and residential smart meters. The paper presents four metrics based on the distribution of signal strengths, with each metric identifying a class of outliers. After detecting the set of outliers using these metrics, we identify the set of representative good meters.
Submillimeter vibrationally excited water emission from the peculiar red supergiant VY Canis Majoris

Context. Vibrationally excited emission from the SiO and H2O molecules probes the innermost circumstellar envelopes of oxygenrich red giant and supergiant stars. VY CMa is the most prolific known emission source in these molecules. Aims. Observations were made to search for rotational lines in the lowest vibrationally excited state of H2O. Methods. The APEX telescope was used for observations of H2O lines at frequencies around 300 GHz. Results. Two vibrationally excited H2O lines were detected, a third one could not be found. In one of the lines we find evidence for weak maser action, similar to known (sub)millimeter ν2 = 1 lines. We find that the other line’s intensity is consistent with thermal excitation by the circumstellar infrared radiation field. Several SiO lines were detected together with the H2O lines.