Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual microtubules in the axon consist of domains that differ in both composition and stability

We have explored the composition and stability properties of individual microtubules (MTs) in the axons of cultured sympathetic neurons. Using morphometric means to quantify the MT mass remaining in axons after various times in 2 micrograms/ml nocodazole, we observed that approximately 48% of the MT mass in the axon is labile, depolymerizing with a t1/2 of approximately 5 min, whereas the remaining 52% of the MT mass is stable, depolymerizing with a t1/2 of approximately 240 min. Immunofluorescence analyses show that the labile MTs in the axon are rich in tyrosinated alpha-tubulin, whereas the stable MTs contain little or no tyrosinated alpha-tubulin and are instead rich in posttranslationally detyrosinated and acetylated alpha-tubulin. These results were confirmed quantitatively by immunoelectron microscopic analyses of the distribution of tyrosinated alpha-tubulin among axonal MTs. Individual MT profiles were typically either uniformly labeled for tyrosinated alpha-tubulin all along their length, or were completely unlabeled. Roughly 48% of the MT mass was tyrosinated, approximately 52% was detyrosinated, and approximately 85% of the tyrosinated MTs were depleted within 15 min of nocodazole treatment. Thus, the proportion of MT profiles that were either tyrosinated or detyrosinated corresponded precisely with the proportion of MTs that were either labile or stable respectively. We also observed MT profiles that were densely labeled for tyrosinated alpha-tubulin at one end but completely unlabeled at the other end. In all of these latter cases, the tyrosinated, and therefore labile domain, was situated at the plus end of the MT, whereas the detyrosinated, and therefore stable domain was situated at the minus end of the MT, and in each case there was an abrupt transition between the two domains. Based on the frequency with which these latter MT profiles were observed, we estimate that minimally 40% of the MTs in the axon are composite, consisting of a stable detyrosinated domain in direct continuity with a labile tyrosinated domain. The extreme drug sensitivity of the labile domains suggests that they are very dynamic, turning over rapidly within the axon. The direct continuity between the labile and stable domains indicates that labile MTs assemble directly from stable MTs. We propose that stable MTs act as MT nucleating structures that spatially regulate MT dynamics in the axon.
The Early Expression of HLA-DR and CD64 Myeloid Markers Is Specifically Compartmentalized in the Blood and Lungs of Patients with Septic Shock

Identification of reliable biomarkers is key to guide targeted therapies in septic patients. Expression monitoring of monocyte HLA-DR and neutrophil CD64 could fulfill the above need. However, it is unknown whether their expression on circulating cells reflects the status of tissue resident cells. We compared expressions of HLA-DR and CD64 markers in the circulation and airways of septic shock patients and evaluated their outcome prognostic value. The expression of CD64 on neutrophils and HLA-DR on monocytes was analyzed in the peripheral blood and mini-bronchoalveolar lavage fluid cells by flow cytometry. Twenty-seven patients with septic shock were enrolled into the study. The fluorescence intensity of HLA-DR on circulating monocytes was 3.5-fold lower than on the pulmonary monocytes (p = 0.01). The expression of CD64 on circulating and airway neutrophils was similar (p = 0.47). Only the expression of CD64 on circulating neutrophils was higher in nonsurvivors versus survivors (2.8-fold; p = 0.031). Pulmonary monocytes display a higher level of HLA-DR activation compared to peripheral blood monocytes but the expression of neutrophil CD64 is similar on lung and circulating cells. Death in septic patients was effectively predicted by neutrophil CD64 but not monocytic HLA-DR. Prognostic value of cellular activation markers in septic shock appears to strongly depend on their level of compartmentalization.
Multi-stage Analysis of Gene Expression and Transcription Regulation in C57/b6 Mouse Liver Development

a r t i c l e i n f o The liver performs a number of essential functions for life. The development of such a complex organ relies on finely regulated gene expression profiles which change over time in the development and determine the phenotype and function of the liver. We used high-density oligonucleotide microarrays to study the gene expression and transcription regulation at 14 time points across the C57/B6 mouse liver development, which include E11. and normal adult liver. With these data, we made a comprehensive analysis on gene expression patterns, functional preferences and transcriptional regulations during the liver development. A group of uncharacterized genes which might be involved in the fetal hematopoiesis were detected. Background The liver is one of the largest organs in the body and performs a number of complex functions essential to life. Functions of the liver range from converting glucose to glycogen, producing bile acids, to forming plasma proteins and filtering harmful substances from the blood. In mouse, liver ontogeny begins around E9 (embryonic day 9). At E10.5 to E12.5, liver becomes a major site of fetal hematopoiesis [1]. Around E14.5, both hepatocytes and bile-duct epithelial cells develop from the bipotential hepatoblast [1]. As these hepatoblasts gradually become mature hepatocytes the main function of liver switches from hematopoiesis to metabolism [1,2]. During liver development, gene expression profiles change over time and determine the phenotypes and functions of liver [3]. Elucidating molecular regulations in this developmental process is important for understanding liver functions and also useful for exploring liver diseases. High-throughput gene expression profiling techniques are well suited to reveal the expression changes in the developmental process. We used high-density oligonucleotide microarrays to investigate gene expression profiles and studied the transcriptional regulation in mouse liver development. The gene expression data in this study were sampled from fetal mouse liver tissue at E11. Day21, and from a normal adult liver tissue. Hierarchical clustering on genes whose expressions changed by more than 1.5-fold during liver development uncovered two groups of genes with distinct temporal expression patterns. Genes in the first group have high expression mainly in the late stage of liver development and genes in the other group are mostly activated in the early stage. GO biological function analyses on the elevated and inhibited genes at each time point reveal that in early embryo development, cell-cycle-related genes are highly expressed; around the birth, defence-related genes are …
RSS based localization by using lognormal mixture shadowing model

Performance of received signal strength (RSS) based localization techniques are directly related to the employed RSS model. Hence, localization performance can be enhanced by improving the accuracy of the RSS model. Lognormal mixture shadowing model for wireless channels, generated by taking distinct scattering clusters into account, characterizes RSS variable more accurately than classical lognormal shadowing model. In this paper, lognormal mixture is applied to localization techniques by means of the derived maximum likelihood estimator. Through simulations performed making use of an exemplary microcellular network structure, it is demonstrated that the mixture model significantly increases the performance of RSS based localization systems compared to the classical model.
On blind beamforming for multiple non-Gaussian signals and the constant-modulus algorithm

A new method for blindly separating multiple cochannel non-Gaussian signals received by a sensor array is presented. The method is based on a cumulant-based least-squares criterion that, for identically distributed negative-kurtosis signals, is proven to be identical to the "2-2" constant-modulus (CM) cost function commonly used by CM algorithms. A computationally simple algorithm is proposed to minimize the criterion. The algorithm performs well even when the number of samples is small, thus allowing its application in dynamic environments (e.g., moving emitters). For the special case of two signals only, the minimization is obtained analytically. Simulation results are included.
Channel Characterization and Performance Evaluation of Mobile Communication Employing Stratospheric Platforms

Stratospheric platforms have been recently proposed as a new wireless infrastructure for realizing the next generation of communication systems. To provide high quality services, an investigation of the wireless stratospheric platform channel is essential. This paper proposes a definition and describes an analysis of the wireless channel for the link between stratospheric platforms and terrestrial mobile users based on an experiment in a semi-urban environment. Narrowband channel characteristics are presented in terms of Ricean factor (K factor) and local mean received power over a wide range of elevation angles ranging from 10° to 90°. Finally, we evaluated average bit error probability based on the proposed channel model to examine the channel, performance. For the environment in which the measurements were conducted, we find that elevation angles greater than 40° yield better performance.
Effect of two prophylaxis methods on adherence of Streptococcus mutans to microfilled composite resin and giomer surfaces.

OBJECTIVES Surface attributes of a restoration play an important role in adherence of plaque bacteria. Prophylaxis methods may be involved in modification of or damaging the restoration surface. The aim of the present study was to evaluate the effect of two prophylaxis methods on adherence of Streptococcus mutans to the surface of two restorative materials. STUDY DESIGN A total of 60 specimens were prepared from each material; a microfilled composite resin (HelioProgress) and a giomer (Beautifil II). For each material, the specimens were randomly divided into three groups (n=20). Group 1: no prophylaxis treatment (control); Group 2: prophylaxis with pumice and rubber cup; Group 3: prophylaxis with air-powder polishing device (APD). The surfaces of selected specimens from each group were evaluated under a scanning electron microscope (SEM), and the surface topography formed by the two prophylaxis methods was determined by atomic force microscopy (AFM). Adherence of Streptococcus mutans to the surface of specimens was determined by the plate counting method following immersion in a bacterial innoculum for 4 hours, rinsing and sonication. Data were analyzed by two-way ANOVA and post hoc Tukey test for multiple comparisons. Statistical significance was set at P<0.05. RESULTS Bacterial adherence was significantly affected by both factors: restorative material type and prophylaxis method (P<0.0005). Mean bacterial adhesion was significantly higher in composite groups compared to corresponding giomer groups. Within each material, bacterial adherence was significantly lower in the control group compared to prophylaxis groups. Prophylaxis with pumice and rubber cup resulted in a significantly lower bacterial adherence compared to prophylaxis with APD. CONCLUSIONS Based on the results of the present study, giomer specimens demonstrated lower bacterial adherence compared to composite resin specimens. In both materials, the highest bacterial adherence was observed with prophylaxis with APD, pumice and rubber cup and the control group, respectively.
Bayesian approach to potency estimation for aquatic toxicology experiments when a toxicant affects both fecundity and survival

Chemicals in aquatic systems may impact a variety of endpoints including mortality, growth, or reproduction. Clearly, growth or reproduction will only be observed in organisms that survive. Because it is common to observe mortality in studies focusing on the reproduction of organisms, especially in higher concentration conditions, the resulting observed numbers of young become a mixture of zeroes and positive counts. Zeroes are recorded for organisms that die before having any young and living organisms with no offspring. Positive counts are recorded for living organisms with offspring. Thus, responses reflect both fecundity and mortality of the organisms used in such tests. In the present study, the authors propose the estimation of the concentration associated with a specified level of reproductive inhibition (RIp) using a Bayesian zero‐inflated Poisson (ZIP) regression model. This approach allows any prior information and expert knowledge about the model parameters to be incorporated into the regression coefficients or RIp estimation. Simulation studies are conducted to compare the Bayesian ZIP regression model and classical methods. The Bayesian estimator outperforms the frequentist alternative by producing more precise point estimates with smaller mean square differences between RIp estimates and true values, narrower interval estimates with better coverage probabilities. The authors also applied their proposed model to a study of Ceriodaphnia dubia exposed to a test toxicant. Environ. Toxicol. Chem. 2012; 31: 1920–1930. © 2012 SETAC
Piaget's stage IV object concept error: evidence of forgetting or object conception?

GRATCH, GERALD; APPEL, KENNETH J.; EVANS, WILSON F. ; LECOMPTE, GUiNEY K. ; and WRIGHT, NANCY A. Piaget's Stage IV Object Concept Error: Evidence of Forgetting or Object Conception? CHILD DEVELOPMENT, 1974, 45, 71-77. Piaget explains the Stage IV error as a failure to assimilate the new place of hiding rather than a forgetting of it. His hypothesis predicts that the likelihood of error should not vary with the length of the delay interval. 9month-old infants were delayed 0, 1, 3, or 7 sec before having the opportunity to search. Infants in all conditions, save 0 sec, were likely to err. While Piaget's hypothesis was not supported by the results of the 0-sec condition, subsequent analyses of the data provided some support for Piaget's hypothesis.
Extension Rules or What Would the Sage Do

Quite often, decision makers face choices that involve new aspects and alternatives never considered before. Scenarios of this sort may arise, for instance, as a result of technological progress or from individual circumstances such as growing awareness. In such situations, simple inference rules, past experience, and knowledge about historic choice problems may prove helpful in determining what would be a reasonable action to take vis-a-vis a new problem. In the context of decision making under uncertainty, we introduce and study an extension rule that enables the decision maker to extend a preference order defined on a restricted domain.
Computing top-k Closeness Centrality Faster in Unweighted Graphs

Given a connected graph G=(V,E), where V denotes the set of nodes and E the set of edges of the graph, the length (that is, the number of edges) of the shortest path between two nodes v and w is denoted by d(v,w). The closeness centrality of a vertex v is then defined as n=1/Σw ∈ V d(v,w), where n=|V|. This measure is widely used in the analysis of real-world complex networks, and the problem of selecting the k most central vertices has been deeply analyzed in the last decade. However, this problem is computationally not easy, especially for large networks: in the first part of the article, we prove that it is not solvable in time O(|E|2=ϵ) on directed graphs, for any constant ϵ > 0, under reasonable complexity assumptions. Furthermore, we propose a new algorithm for selecting the k most central nodes in a graph: we experimentally show that this algorithm improves significantly both the textbook algorithm, which is based on computing the distance between all pairs of vertices, and the state of the art. For example, we are able to compute the top k nodes in few dozens of seconds in real-world networks with millions of nodes and edges. Finally, as a case study, we compute the 10 most central actors in the Internet Movie Database (IMDB) collaboration network, where two actors are linked if they played together in a movie, and in the Wikipedia citation network, which contains a directed edge from a page p to a page q if p contains a link to q.
ICU-Onset Clostridium difficile Infection in a University Hospital in China: A Prospective Cohort Study

A prospective study was conducted to investigate the incidence, clinical profiles and outcome of ICU-onset CDI in a 50-bed medical ICU at a university hospital in China. Stools were collected from patients who developed ICU-onset diarrhea and was screened for tcdA (toxin A gene) and tcdB (toxin B gene) by PCR. CDI cases were compared with the ICU-onset non-CDI diarrhea cases for demographics, comorbidities, potential risk factors, major laboratory findings and outcomes. Stool samples from CDI cases were subjected to C. difficile culture and C. difficile isolates were screened for tcdA, tcdB and the binary toxin genes (cdtA and cdtB) using multiplex PCR. Strain typing of toxigenic C. difficile isolates was performed using multilocus sequence typing. There were 1,277 patients in the ICU during the study period and 124 (9.7%) developed ICU-onset diarrhea, of which 31 patients had CDI. The incidence of ICU-onset CDI was 25.2 cases per 10,000 ICU days. ICU-onset CDI cases had similar features with ICU-onset non-CDI diarrhea cases including the use of proton pump inhibitors and antibacterial agents. The crude mortality rate of ICU-onset CDI was 22.6%, but the attributable mortality rate of ICU-onset CDI was only 3.2% here. Toxigenic C. difficile isolates were recovered from 28 out of the 31 patients with CDI. cdtA and cdtB were found in two strains. Seventeen STs including 11 new STs were identified. All of the 11 new STs were single-locus variants of known STs and the 17 STs identified here could be clustered into 3 clades. The incidence of ICU-onset CDI here is similar to those in Europe and North America, suggesting that CDI is likely to be a common problem in China. Toxigenic C. difficile here belonged to a variety of STs, which may represent a significant clonal expansion rather than the true clonal diversity.
Interventions Targeting Deep Tissue Lymph Nodes May Not Effectively Reduce the Risk of Salmonellosis from Ground Pork Consumption: A Quantitative Microbial Risk Assessment

The inclusion of deep tissue lymph nodes (DTLNs) or nonvisceral lymph nodes contaminated with Salmonella in wholesale fresh ground pork (WFGP) production may pose risks to public health. To assess the relative contribution of DTLNs to human salmonellosis occurrence associated with ground pork consumption and to investigate potential critical control points in the slaughter‐to‐table continuum for the control of human salmonellosis in the United States, a quantitative microbial risk assessment (QMRA) model was established. The model predicted an average of 45 cases of salmonellosis (95% CI = [19, 71]) per 100,000 Americans annually due to WFGP consumption. Sensitivity analysis of all stochastic input variables showed that cooking temperature was the most influential parameter for reducing salmonellosis cases associated with WFGP meals, followed by storage temperature and Salmonella concentration on contaminated carcass surface before fabrication. The input variables were grouped to represent three main factors along the slaughter‐to‐table chain influencing Salmonella doses ingested via WFGP meals: DTLN‐related factors, factors at processing other than DTLNs, and consumer‐related factors. The evaluation of the impact of each group of factors by second‐order Monte Carlo simulation showed that DTLN‐related factors had the lowest impact on the risk estimate among the three groups of factors. These findings indicate that interventions to reduce Salmonella contamination in DTLNs or to remove DTLNs from WFGP products may be less critical for reducing human infections attributable to ground pork than improving consumers’ cooking habits or interventions of carcass decontamination at processing.
IL1 Receptor Antagonist Inhibits Pancreatic Cancer Growth by Abrogating NF-κB Activation

Purpose: Constitutive NF-κB activation is identified in about 70% of pancreatic ductal adenocarcinoma (PDAC) cases and is required for oncogenic KRAS-induced PDAC development in mouse models. We sought to determine whether targeting IL-1α pathway would inhibit NF-κB activity and thus suppress PDAC cell growth. Experimental Design: We determined whether anakinra, a human IL-1 receptor (rhIL-1R) antagonist, inhibited NF-κB activation. Assays for cell proliferation, migration, and invasion were performed with rhIL-1R antagonist using the human PDAC cell lines AsPc1, Colo357, MiaPaCa-2, and HPNE/K-rasG12V/p16sh. In vivo NF-κB activation–dependent tumorigenesis was assayed using an orthotopic nude mouse model (n = 20, 5 per group) treated with a combination of gemcitabine and rhIL-1RA. Results: rhIL-1R antagonist treatment led to a significant decrease in NF-κB activity. PDAC cells treated with rhIL-1R antagonist plus gemcitabine reduced proliferation, migration, and invasion as compared with single gemcitabine treatment. In nude mice, rhIL-1R antagonist plus gemcitabine significantly reduced the tumor burden (gemcitabine plus rhIL-1RA vs. control, P = 0.014). Conclusions: We found that anakinra, an FDA-approved drug that inhibits IL-1 receptor (IL-1R), when given with or without gemcitabine, can reduce tumor growth by inhibiting IL1α-induced NF-κB activity; this result suggests that it is a useful therapeutic approach for PDAC. Clin Cancer Res; 22(6); 1432–44. ©2015 AACR.
D M ] 2 3 M ay 2 01 7 Perfect Edge Domination : Hard and Solvable Cases

Let G be an undirected graph. An edge of G dominates itself and all edges adjacent to it. A subset E of edges of G is an edge dominating set of G, if every edge of the graph is dominated by some edge of E. We say that E is a perfect edge dominating set of G, if every edge not in E is dominated by exactly one edge of E. The perfect edge dominating problem is to determine a least cardinality perfect edge dominating set of G. For this problem, we describe two NP-completeness proofs, for the classes of claw-free graphs of degree at most 3, and for bounded degree graphs, of maximum degree at most d ≥ 3 and large girth. In contrast, we prove that the problem admits an O(n) time solution, for cubic claw-free graphs. In addition, we prove a complexity dichotomy theorem for the perfect edge domination problem, based on the results described in the paper. Finally, we describe a linear time algorithm for finding a minimum weight perfect edge dominating set of a P5-free graph. The algorithm is robust, in the sense that, given an arbitrary graph G, either it computes a minimum weight perfect edge dominating set of G, or it exhibits an induced subgraph of G, isomorphic to a P5.