Miracle-dz/UniFAR-FTUs huggingface dataset:
NG2 cell response in the CNP‐EGFP mouse after contusive spinal cord injury

NG2+ cells in the adult CNS are a heterogeneous population. The extent to which the subpopulation of NG2+ cells that function as oligodendrocyte progenitor cells (OPCs) respond to spinal cord injury (SCI) and recapitulate their normal developmental progression remains unclear. We used the CNP‐EGFP mouse, in which oligodendrocyte lineage cells express EGFP, to study NG2+ cells in the normal and injured spinal cord. In white matter of uninjured mice, bipolar EGFP+NG2+ cells and multipolar EGFPnegNG2+ cells were identified. After SCI, EGFP+NG2+ cell proliferation in residual white matter peaked at 3 days post injury (DPI) rostral to the epicenter, while EGFPnegNG2+ cell proliferation peaked at 7 DPI at the epicenter. The expression of transcription factors, Olig2, Sox10, and Sox17, and the basic electrophysiological membrane parameters and potassium current phenotype of the EGFP+NG2+ population after injury were consistent with those of proliferative OPCs during development. EGFPnegNG2+ cells did not express transcription factors involved in oligodendrogenesis. EGFP+CC1+ oligodendrocytes at 6 weeks included cells that incorporated BrdU during the peak of EGFP+NG2+ cell proliferation. EGFPnegCC1+ oligodendrocytes were never observed. Treatment with glial growth factor 2 and fibroblast growth factor 2 enhanced oligodendrogenesis and increased the number of EGFPnegNG2+ cells. Therefore, based on EGFP and transcription factor expression, spatiotemporal proliferation patterns, and response to growth factors, two populations of NG2+ cells can be identified that react to SCI. The EGFP+NG2+ cells undergo cellular and physiological changes in response to SCI that are similar to those that occur in early postnatal NG2+ cells during developmental oligodendrogenesis. © 2008 Wiley‐Liss, Inc.
Self Control , Risk Aversion , and the Allais Paradox

This paper develops a dual-self model that is compatible with modern dynamic macroeconomic theory and evidence, and shows how it leads to a wide range of behavioral anomalies concerning risk, including the Allais paradox. We calibrate the model to obtain a quantitative fit, by extending the simpler “nightclub” model of Fudenberg and Levine [2006] by introducing consumption commitment. We find that most of the data can be explained with subjective interest rates in the range of 1-7%, short-run relative risk aversion of about 2, and a time horizon of one day for the short-run self.
Solvent Stress Response of the Denitrifying Bacterium “Aromatoleum aromaticum” Strain EbN1

ABSTRACT The denitrifying betaproteobacterium “Aromatoleum aromaticum” strain EbN1 degrades several aromatic compounds, including ethylbenzene, toluene, p-cresol, and phenol, under anoxic conditions. The hydrophobicity of these aromatic solvents determines their toxic properties. Here, we investigated the response of strain EbN1 to aromatic substrates at semi-inhibitory (about 50% growth inhibition) concentrations under two different conditions: first, during anaerobic growth with ethylbenzene (0.32 mM) or toluene (0.74 mM); and second, when anaerobic succinate-utilizing cultures were shocked with ethylbenzene (0.5 mM), toluene (1.2 mM), p-cresol (3.0 mM), and phenol (6.5 mM) as single stressors or as a mixture (total solvent concentration, 2.7 mM). Under all tested conditions impaired growth was paralleled by decelerated nitrate-nitrite consumption. Additionally, alkylbenzene-utilizing cultures accumulated poly(3-hydroxybutyrate) (PHB) up to 10% of the cell dry weight. These physiological responses were also reflected on the proteomic level (as determined by two-dimensional difference gel electrophoresis), e.g., up-regulation of PHB granule-associated phasins, cytochrome cd1 nitrite reductase of denitrification, and several proteins involved in oxidative (e.g., SodB) and general (e.g., ClpB) stress responses.
Airway wall thickness in cigarette smokers: quantitative thin-section CT assessment.

PURPOSE To design and validate a dedicated software tool to measure airway dimensions on thin-section computed tomographic (CT) images and to use the tool to prospectively compare airway wall thickness in nonsmokers with normal lung function with that in smokers with and without chronic obstructive pulmonary disease (COPD). MATERIALS AND METHODS All subjects gave written informed consent. The study was approved by local ethics committee. With Laplacian of Gaussian algorithm, software was tested in phantom and excised sheep lung fixed in inflation and validated with Bland-Altman analysis. Study prospectively included nine nonsmokers (six women, three men; mean age, 53 years +/- 5.6 [standard error of the mean]) with normal lung function (group 1), seven smokers (three women, four men; mean age, 56 years +/- 5.6) with normal lung function (group 2), and eight smokers (zero women, eight men; mean age, 65 years +/- 4.0) with COPD. Calculations were determined with spirometrically gated CT: For each selected bronchus, the wall area (WA), internal area (IA), airway caliber (sum of IA and WA), and WA/IA ratio were calculated. For each patient, summation of WA to summation of IA (SigmaWA/SigmaIA) ratio, which reflected normalized airway wall thickness, was calculated. Groups were compared by using analysis of variance with generalized linear model and unpaired t test. Pearson correlation coefficient was used to assess correlation between software measurements and pulmonary function test results. RESULTS Comparison of measurements in phantom and excised sheep lung with algorithm measurements revealed that the latter were reliable and repeatable. In clinical study, SigmaWA/SigmaIA ratio was significantly different among three groups (P < .001). Normalized airway wall thickness and IA were significantly related to lung function test data, including forced expiratory volume in 1 second (r = -0.54, P = .006), specific airway conductance (r = -0.45, P = .03), and forced expiratory flow between 25% and 75% of vital capacity (r = -0.65, P < .001). CONCLUSION This software provides accurate and reproducible measurements of IA and WA of bronchi on thin-section CT images and demonstrates that in vivo normalized airway wall thickness was larger in smokers with COPD than it was in smokers or nonsmokers without COPD.
Efficacy and Temporal Stability of Reduced Safety Margins for Ventricular Defibrillation: Primary Results From the Low Energy Safety Study (LESS)

Background—Traditionally, a safety margin of at least 10 J between the maximum output of the pulse generator and the energy needed for ventricular defibrillation has been used because lower safety margins were associated with unacceptably high rates of failed defibrillation and sudden cardiac death. The Low Energy Safety Study (LESS) was a prospective, randomized assessment of the safety margin requirements for modern implantable cardioverter-defibrillator (ICD) systems. Methods and Results—A total of 636 patients undergoing initial ICD implantation with a dual-coil lead and active pulse generator were evaluated. The defibrillation threshold (DFT) and enhanced DFT (DFT+ and DFT++) were measured using a modified step-down protocol. Conversion testing of induced ventricular fibrillation before discharge, at 3 months, and at 12 months was performed, as was randomization to chronic programming at either 2 steps above DFT++ or maximal output. The induced ventricular fibrillation data had conversion success rates of 91.4%, 97.9%, 99.1%, 99.6%, and 99.8% for safety margins of 0, 1, 2, 3, and 4 steps above the DFT++, respectively. A margin of 4 to 6 J was adequate to maintain high conversion success over time (98.9% before discharge versus 99.2% at 12 months;P =NS). Over a mean follow-up of 24±13 months, conversion of spontaneously occurring ventricular tachyarrhythmias >200 bpm was identical (97.3%), despite a safety margin difference of 5.2±1.1 J for the 2-step group versus 20.8±4.2 J for maximal output. Conclusions—With a rigorous implantation algorithm, a safety margin of about 5 J is adequate for safe implantation of modern ICD systems.
A routing scheme for optimizing multiple classes in a DiffServ network

Recent study shows that high-priority class traffic may significantly degrade the performance of low-priority class traffic in a DiffServ network, which is called the inter-class effect. The effect is mainly due to the fact that low-priority traffic can hardly avoid traffic congestion caused by high-priority traffic when all traffic is routed through same routes. In this paper we present a simple but effective routing scheme called multi-class routing (MCR) to relieve the effect. The essence of the scheme is to route low-priority traffic through routes lightly loaded with high-priority traffic by applying a specific routing for each class. In comparison with the MCR, we call traditional routing that routes all traffic through same routes single-class routing (SCR). We also define the optimization problem of low-priority class and model the MCR scheme. We compare the performance of MCR with SCR through simulation study. Our results show that choosing a suitable set of routing for MCR can largely improve the performance of low-priority class.
Association of DRD4 with attention problems in normal childhood development

Several previous studies found an association of clinically diagnosed attention deficit hyperactivity disorder with long alleles of a variation in the DRD4 dopamine receptor gene exon III coding sequence. We evaluated the DRD4 polymorphism in a non‐clinically selected sample of children for whom maternal reports of attention problems were available at 4 and 7 years of age. There was a significant elevation in attention problem scores in children carrying DRD4 long alleles that accounted for 3–4% of total variation at each age and for 5–7% of the temporally stable component of the phenotype. Our results show that the DRD4 gene influences normal as well as pathological attention processes, and the results highlight the utility of longitudinal measurements in psychiatric genetics.
PERSONALITY PROCESSES AND INDIVIDUAL DIFFERENCES Microbes , Mating , and Morality : Individual Differences in Three Functional Domains of Disgust

What is the function of disgust? Whereas traditional models have suggested that disgust serves to protect the self or neutralize reminders of our animal nature, an evolutionary perspective suggests that disgust functions to solve 3 qualitatively different adaptive problems related to pathogen avoidance, mate choice, and social interaction. The authors investigated this 3-domain model of disgust across 4 studies and examined how sensitivity to these functional domains relates to individual differences in other psychological constructs. Consistent with their predictions, factor analyses demonstrated that disgust sensitivity partitions into domains related to pathogens, sexuality, and morality. Further, sensitivity to the 3 domains showed predictable differentiation based on sex, perceived vulnerability to disease, psychopathic tendencies, and Big 5 personality traits. In exploring these 3 domains of disgust, the authors introduce a new measure of disgust sensitivity. Appreciation of the functional heterogeneity of disgust has important implications for research on individual differences in disgust sensitivity, emotion, clinical impairments, and neuroscience.
OntoRama: Browsing RDF ontologies using a hyperbolic-style browser

This paper presents a Java-based hyperbolic-style browser designed to render RDF files as structured ontological maps. The program was motivated by the need to browse the content of a web-accessible ontology server: WEB KB-2. The ontology server contains descriptions of over 74,500 object types derived from the WordNet 1.7 lexical database and can be accessed using RDF syntax. Such a structure creates complications for hyperbolic-style displays. In WEB KB-2 there are 140 stable ontology link types and a hyperbolic display needs to filter and iconify the view so different link relations can be distinguished in multi-link views. Our browsing tool, OntoRama, is therefore motivated by two possibly interfering aims: the first to display up to 10 times the number of nodes in a hyperbolic-style view than using a conventional graphics display; secondly, to render the ontology with multiple links comprehensible in that view.
Hearing Differently: The Impact of Hearing Impairment on Family Life

Part I: Introduction. The nature of the study. Part II: Ways of looking at hearing loss and relationships. Hearing loss. Relationships. Part III: Hearing loss and families. Hearing loss and initiating serious relationships. Hearing loss and established couples: attachment/caregiving. Hearing loss and established couples: mutuality. Hearing loss and children. Part IV: Hearing loss and social networks. Hearing loss and kinship networks. Hearing loss and wider networks. Hearing loss and bereavement. Part V: Social policy issues and conclusions. Provisions for people with acquired hearing loss: how adequate? An overview. Conclusions
Lateral Intra-Articular Transposition of the Anterior Tibialis Tendon for the Treatment of Relapsed Clubfoot in Toddlers: A Previously Unreported Surgical Technique

Dynamic supination of the foot is a common residual deformity in children with clubfeet treated with the Ponseti method. Transfer of the anterior tibialis tendon (ATT) to the lateral cuneiform is an effective method for correcting this deformity when the cuneiform is ossified in children who are 3 to 5 years of age. We describe two cases of a previously unreported method of ATT transposition for correction of bilateral residual dynamic supination in a 26-month-old and a 19-month-old patient. Both patients presented shortly after birth with bilateral congenital idiopathic clubfoot and were initially treated with the Ponseti method. Both had residual deformity following initial treatment that included posterior contracture and metatarsus adductus with dynamic forefoot supination. This was surgically corrected with a posterior release and medial release of the 1st metatarsal/1st cuneiform joint. To correct dynamic supination, the ATT was transplanted laterally into the released midfoot joint. These two patients were followed post-operatively for 7.5 years and have correction of their residual deformity in both feet based on subjective functioning, appearance, range of motion, strength, and gait. Both have excellent lateral pull of their ATT, which functions as a strong foot dorsiflexor. No residual supination is present. This is the first report of lateral transposition of the ATT as an interposition graft at the released 1st metatarsal/1st cuneiform joint in patients with relapsed clubfoot. We suggest that this method should provide a high level of functioning in children with relapsed supination deformity and whose 3rd cuneiform has not yet ossified.
Modification of Cɛ mRNA Expression by EBV-Encoded Latent Membrane Protein 1

To evaluate the effect of expression of latent membrane protein (LMP) 1 encoded by Epstein-Barr virus (EBV) on Cɛ mRNA expression, mRNA levels were examined by RT-PCR or Northern blot analysis upon transient transfection of LMP1 in the splenocytes derived from Brown-Norway rats with or without immunization with 2,4-dinitrophenyl-conjugated Ascaris suum antigen. Splenocytes were transfected with LMP1 expression vector, pSG5-LMP1, using lipofection method. Cɛ mRNA levels were considerably increased by transfection with pSG5-LMP1 in the splenocytes derived from the nonimmunized rats; however, Cɛ mRNA levels were decreased in the splenocytes derived from the immunized rats. Cɛ mRNA expression in IgE-producing cells are modulated by LMP1, which might depend on the differentiation status of B cells upon exposure to allergen.
Arabidopsis thaliana VOZ (Vascular plant One-Zinc finger) transcription factors are required for proper regulation of flowering time

Summary Transition to flowering in plants is tightly controlled by environmental cues, which regulate the photoperiod and vernalization pathways, and endogenous signals, which mediate the autonomous and gibberellin pathways. In this work, we investigated the role of two Zn2+-finger transcription factors, the paralogues AtVOZ1 and AtVOZ2, in Arabidopsis thaliana flowering. Single atvoz1-1 and atvoz2-1 mutants showed no significant phenotypes as compared to wild type. However, atvoz1-1 atvoz2-1 double mutant plants exhibited several phenotypes characteristic of flowering-time mutants. The double mutant displayed a severe delay in flowering, together with additional pleiotropic phenotypes. Late flowering correlated with elevated expression of FLOWERING LOCUS C (FLC), which encodes a potent floral repressor, and decreased expression of its target, the floral promoter FD. Vernalization rescued delayed flowering of atvoz1-1 atvoz2-1 and reversed elevated FLC levels. Accumulation of FLC transcripts in atvoz1-1 atvoz2-1 correlated with increased expression of several FLC activators, including components of the PAF1 and SWR1 chromatin-modifying complexes. Additionally, AtVOZs were shown to bind the promoter of MOS3/SAR3 and directly regulate expression of this nuclear pore protein, which is known to participate in the regulation of flowering time, suggesting that AtVOZs exert at least some of their flowering regulation by influencing the nuclear pore function. Complementation of atvoz1-1 atvoz2-1 with AtVOZ2 reversed all double mutant phenotypes, confirming that the observed morphological and molecular changes arise from the absence of functional AtVOZ proteins, and validating the functional redundancy between AtVOZ1 and AtVOZ2.
Endogenous GLP-1 as a key self-defense molecule against lipotoxicity in pancreatic islets

The number of pro-α cells is known to increase in response to β cell injury and these cells then generate glucagon-like peptide-1 (GLP-1), thus attenuating the development of diabetes. The aim of the present study was to further examine the role and the mechanisms responsible for intra-islet GLP-1 production as a self-protective response against lipotoxicity. The levels of the key enzyme, prohormone convertase 1/3 (PC1/3), as well as the synthesis and release of GLP-1 in models of lipotoxicity were measured. Furthermore, islet viability, apoptosis, oxidative stress and inflammation, as well as islet structure were assessed after altering GLP-1 receptor signaling. Both prolonged exposure to palmitate and a high-fat diet facilitated PC1/3 expression, as well as the synthesis and release of GLP-1 induced by β cell injury and the generation of pro-α cells. Prolonged exposure to palmitate increased reactive oxygen species (ROS) production, and the antioxidant, N-acetylcysteine (NAC), partially prevented the detrimental effects induced by palmitate on β cells, resulting in decreased GLP-1 levels. Furthermore, the inhibition of GLP-1 receptor (GLP-1R) signaling by treatment with exendin-(9-39) further decreased cell viability, increased cell apoptosis and caused a stronger inhibition of the β cell-specific transcription factor, pancreatic duodenal homeobox 1 (PDX1). Moreover, treatment with the GLP-1R agonist, liraglutide, normalized islet structure and function, resulting in a decrease in cell death and in the amelioration of β cell marker expression. Importantly, liraglutide maintained the oxidative balance and decreased inflammatory factor and p65 expression. Overall, our data demonstrate that an increase in the number of pro-α cells and the activation of the intra-islet GLP-1 system comprise a self-defense mechanism for enhancing β cell survival to combat lipid overload, which is in part mediated by oxidative stress and inflammation.
The More Antecedents, the Merrier: Resolving Multi-Antecedent Anaphors

Anaphor resolution is an important task in NLP with many applications. Despite much research effort, it remains an open problem. The difficulty of the problem varies substantially across different sub-problems. One sub-problem, in particular, has been largely untouched by prior work despite occurring frequently throughout corpora: the anaphor that has multiple antecedents, which here we call multi-antecedent anaphors or manaphors. Current coreference resolvers restrict anaphors to at most a single antecedent. As we show in this paper, relaxing this constraint poses serious problems in coreference chain-building, where each chain is intended to refer to a single entity. This work provides a formalization of the new task with preliminary insights into multi-antecedent noun-phrase anaphors, and offers a method for resolving such cases that outperforms a number of baseline methods by a significant margin. Our system uses local agglomerative clustering on candidate antecedents and an existing coreference system to score clusters to determine which cluster of mentions is antecedent for a given anaphor. When we augment an existing coreference system with our proposed method, we observe a substantial increase in performance (0.6 absolute CoNLL F1) on an annotated
Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design

Significance Hepatitis C virus is a major public health concern, infecting approximately 3% of the world’s population, with no vaccine currently available. To enable rational vaccine design for this highly diverse and dynamic virus, we performed alanine scanning of nearly all positions of the E2 envelope protein, which is the primary target of the antibody response, using a panel of 16 human monoclonal antibodies that target a broad range of epitopes. This approach provided an unprecedented global view of the determinants of E2 stability, residue connectivity, and neutralizing antibody recognition. These insights and mapping data provide a framework to engineer E2 to modulate antibody recognition and optimize its capacity to induce broadly neutralizing antibodies in the context of a vaccine. The E2 envelope glycoprotein is the primary target of human neutralizing antibody response against hepatitis C virus (HCV), and is thus a major focus of vaccine and immunotherapeutics efforts. There is emerging evidence that E2 is a highly complex, dynamic protein with residues across the protein that are modulating antibody recognition, local and global E2 stability, and viral escape. To comprehensively map these determinants, we performed global E2 alanine scanning with a panel of 16 human monoclonal antibodies (hmAbs), resulting in an unprecedented dataset of the effects of individual alanine substitutions across the E2 protein (355 positions) on antibody recognition. Analysis of shared energetic effects across the antibody panel identified networks of E2 residues involved in antibody recognition and local and global E2 stability, as well as predicted contacts between residues across the entire E2 protein. Further analysis of antibody binding hotspot residues defined groups of residues essential for E2 conformation and recognition for all 14 conformationally dependent E2 antibodies and subsets thereof, as well as residues that enhance antibody recognition when mutated to alanine, providing a potential route to engineer E2 vaccine immunogens. By incorporating E2 sequence variability, we found a number of E2 polymorphic sites that are responsible for loss of neutralizing antibody binding. These data and analyses provide fundamental insights into antibody recognition of E2, highlighting the dynamic and complex nature of this viral envelope glycoprotein, and can serve as a reference for development and rational design of E2-targeting vaccines and immunotherapeutics.