Miracle-dz/UniFAR-FTUs huggingface dataset:
Domain Mapping of Human PEX5 Reveals Functional and Structural Similarities to Saccharomyces cerevisiae Pex18p and Pex21p*

PEX5 functions as an import receptor for proteins with the type-1 peroxisomal targeting signal (PTS1). Although PEX5 is not involved in the import of PTS2-targeted proteins in yeast, it is essential for PTS2 protein import in mammalian cells. Human cells generate two isoforms of PEX5 through alternative splicing, PEX5S and PEX5L, and PEX5L contains an additional insert 37 amino acids long. Only one isoform, PEX5L, is involved in PTS2 protein import, and PEX5L physically interacts with PEX7, the import receptor for PTS2-containing proteins. In this report we map the regions of human PEX5L involved in PTS2 protein import, PEX7 interaction, and targeting to peroxisomes. These studies revealed that amino acids 1–230 of PEX5L are required for PTS2 protein import, amino acids 191–222 are sufficient for PEX7 interaction, and amino acids 1–214 are sufficient for targeting to peroxisomes. We also identified a 21-amino acid-long peptide motif of PEX5L, amino acids 209–229, that overlaps the regions sufficient for full PTS2 rescue activity and PEX7 interaction and is shared bySaccharomyces cerevisiae Pex18p and Pex21p, two yeast peroxins that act only in PTS2 protein import in yeast. A mutation in PEX5 that changes a conserved serine of this motif abrogates PTS2 protein import in mammalian cells and reduces the interaction of PEX5L and PEX7 in vitro. This peptide motif also lies within regions of Pex18p and Pex21p that interact with yeast PEX7. Based on these and other results, we propose that mammalian PEX5L may have acquired some of the functions that yeast Pex18p and/or Pex21p perform in PTS2 protein import. This hypothesis may explain the essential role of PEX5L in PTS2 protein import in mammalian cells and its lack of importance for PTS2 protein import in yeast.
Physics-based modeling of FinFET RF variability under Shorted- and Independent-Gates bias

FinFETs operated with varying bias, and in particular with Short-circuited Gates (SG) or Independent Gates (IG), are actively investigated for RF analog applications. The device process variability is known to vary, at least for DC performances, according to the FINFET bias. This paper presents a novel, comprehensive physics-based variability analysis focused on AC parameters for a double-gate (DG) MOSFET (FinFET) both in SG and IG conditions. The analysis is carried out with a numerically efficient Green's Function technique [1], [2], that exploits a nonlinear variability analysis tool in quasi-linear condition. The AC variability analysis of the FinFET includes selected geometrical and physical parameters, such as the fin width, the source/drain-gate distance and the doping level, whose role is especially relevant for the extraction of the device parasitics' variations. We demonstrate that the sensitivity of the AC parameters differs in the IG and SG case, especially concerning gate capacitances.
Timing of Sonic hedgehog and Gli1 expression segregates midbrain dopamine neurons

The ventral midbrain (vMb) is organized into distinct anatomical domains and contains cohorts of functionally distinct subtypes of midbrain dopamine (mDA) neurons. We tested the hypothesis that genetic history and timing of gene expression within mDA neuron progenitors impart spatial diversity. Using genetic inducible fate mapping to mark the Sonic hedgehog (Shh) and Gli1 lineages at varying embryonic stages, we performed a quantitative and qualitative comparison of the two lineages' contribution to the mDA neuron domains. Dynamic changes in Shh and Gli1 expression in the vMb primordia delineated their spatial contribution to the embryonic day 12.5 vMb: Both lineages first contributed to the medial domain, but subsequently the Gli1 lineage exclusively contributed to the lateral vMb while the Shh lineage expanded more broadly across the vMb. The contribution of both lineages to the differentiated mDA neuron domain was initially biased anteriorly and became more uniform across the anterior/posterior vMb throughout development. Our findings demonstrate that the early Shh and Gli1 lineages specify mDA neurons of the substantia nigra pars compacta while the late Shh and Gli1 lineages maintain their progenitor state longer in the posterior vMb to extend the production of mDA neurons in the ventral tegmental area. Together, our study demonstrates that the timing of gene expression along with the genetic lineage (Shh or Gli1) within the neural progenitors segregate mDA neurons into distinct spatial domains. J. Comp. Neurol. 519:3001–3018, 2011. © 2011 Wiley‐Liss, Inc.
Attribution, Accountability, and Institutional Design in Bureaucratic Politics

Attribution, Accountability, and Institutional Design in Bureaucratic Politics is a collection of three essays about news coverage of regulatory agencies. In a democracy, the news is a crucial source of information about public affairs for voters. The news enables accountability for elected officials such as the president and members of Congress. I ask how news coverage enables political accountability of powerful federal agencies, whose leaders are unelected and only accountable to the public only through the executive, legislative, and judicial branches. In particular, voters rely on the news to connect agency regulations and enforcements to the elected officials with formal responsibility for those agencies. If the news provides poor information, by blaming the wrong official, mischaracterizing the authorities of the president and Congress, or biasing the news to favor a particular ideology, accountability is undermined. In Chapter II, I examine how agency institutional design moderates attributions of responsibility to the president. A lack of direct electoral checks on government bureaucrats challenges norms of democratic accountability. One proposed solution is to increase the president’s control over federal agencies. It is, however, an open question as to whether voters will attribute responsibility to the president even when in charge of agencies. A key empirical challenge has been that presidential control is not randomly assigned across agencies. To overcome this issue, I compare two agencies that enforce the same policy but differ in insulation from presidential control. I examine a large, original dataset of news coverage, showing that news coverage of the presidentially-controlled agency features more politicized content that ties the agency to the president. I then demonstrate that this political content increases attribution of control to the president. The results support theories that claim agency design moderates voter attribution of responsibility to the president. In Chapter III, I investigate whether formal presidential authority over agencies moderates attributions of responsibility for agency scandals. Using a survey experiment that manipulates news coverage of a major agency scandal. I find that providing details about
Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing

ABSTRACT Nonhemolytic variants of Haemophilus haemolyticus are difficult to differentiate from Haemophilus influenzae despite a wide difference in pathogenic potential. A previous investigation characterized a challenging set of 60 clinical strains using multiple PCRs for marker genes and described strains that could not be unequivocally identified as either species. We have analyzed the same set of strains by multilocus sequence analysis (MLSA) and near-full-length 16S rRNA gene sequencing. MLSA unambiguously allocated all study strains to either of the two species, while identification by 16S rRNA sequence was inconclusive for three strains. Notably, the two methods yielded conflicting identifications for two strains. Most of the “fuzzy species” strains were identified as H. influenzae that had undergone complete deletion of the fucose operon. Such strains, which are untypeable by the H. influenzae multilocus sequence type (MLST) scheme, have sporadically been reported and predominantly belong to a single branch of H. influenzae MLSA phylogenetic group II. We also found evidence of interspecies recombination between H. influenzae and H. haemolyticus within the 16S rRNA genes. Establishing an accurate method for rapid and inexpensive identification of H. influenzae is important for disease surveillance and treatment.
Different Primary Target Cells Are Important for Fiber Lamination in the Fascia Dentata: A Lesson from Reeler Mutant Mice

The factors determining the lamina-specific termination of entorhinal and commissural afferents to the fascia dentata are poorly understood. Recently it was shown that early generated Cajal-Retzius (CR) cells in the outer molecular layer and reelin, synthesized by CR cells, play a role in the lamina-specific termination of entorhinal fibers which form transient synapses with CR cells before establishing their definite contacts with granule cell dendrites (J. A. del Rio et al., 1997, Nature 385, 70-74). By using anterograde tracing with Phaseolus vulgaris leukoagglutinin we show that the normal, sharply delineated entorhinal projection to the outer molecular layer is retained in reeler mutant mice lacking reelin. This coincides with the regular presence of CR cells, the primary, transient target cells of entorhinal fibers. In contrast, the commissural fibers were found to terminate in an abnormal broad, not clearly defined area. This widespread projection coincides with the distribution of granule cells which in the mutant do not form a dense cell layer but are scattered all over the hilus due to a migration defect. Unlike the entorhinal fibers, the commissural fibers arrive in their target layer late in development, when granule cell dendrites are already there. We hypothesize from these results that the presence of the adequate postsynaptic element at the time of fiber ingrowth, CR cells for the early ingrowing entorhinal fibers and granule cells for the late-arriving commissural fibers, is crucial for the normal formation of these layer-specific projections.
Resynthesis and retiming of synchronous sequential circuits

Retiming is a technique used in synchronous sequential circuits to move the registers across the circuit in order to minimize the cycle time or the number of registers used. Peripheral retiming is extended retiming in which all registers are moved (if possible) to the peripheral edges, where combinational logic optimization techniques can be used. A generalization of this method is proposed. It consists in moving the maximum number of registers to the peripheral edges. This approach may then also be applied to all sequential circuits for which the usual peripheral retiming concept does not hold. The authors' model of the circuit is a bipartite graph, and it is proved that the resynthesizing problem is equivalent to a linear optimization problem in this graph. A new algorithm for the optimization of sequential circuits is proposed. <<ETX>>
Equity Return Modeling and Prediction Using Hybrid ARIMA-GARCH Model

In this paper, a hybrid ARIMA-GARCH model is proposed to model and predict the equity returns for three US benchmark indices: Dow Transportation, S&P 500 and VIX. Equity returns are univariate time series data sets, one of the methods to predict them is using the Auto-Regressive Integrated Moving Average (ARIMA) models. Despite the fact that the ARIMA models are powerful and flexible, they are not be able to handle the volatility and nonlinearity that are present in the time series data. However, the Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models are designed to capture volatility clustering behavior in time series. In this paper, we provide motivations and descriptions of the hybrid ARIMA-GARCH model. A complete data analysis procedure that involves a series of hypothesis testings and a model fitting procedure using the Akaike Information Criterion (AIC) is provided in this paper as well. Simulation results of out of sample predictions are also provided in this paper as a reference.
Cultured astrocytes express toll‐like receptors for bacterial products

It has become apparent that astrocytes may be important contributors to inflammatory immune responses within the brain in response to microbial challenges. To date, the mechanisms that underlie activation of this major glial cell type by such challenges have not been investigated. In the present study, we present evidence for members of a recently discovered family of receptors for highly conserved microbial components, the Toll‐like receptors (TLRs), in isolated cultures of primary murine astrocytes. We describe the low‐level constitutive expression of messenger RNA‐encoding TLR2, TLR4, TLR5, and TLR9 in resting cultures of these cells. Importantly, the level of expression of messenger RNA for each of these receptors is markedly elevated following exposure to specific bacteria‐derived ligands for these receptors. The functional expression of these receptor proteins is further supported by the ability of known ligands for each TLR to induce both message expression and protein secretion of the proinflammatory cytokine, interleukin‐6. In addition, the recent availability of antibodies to TLR2 and TLR4 has enabled us to demonstrate directly the presence of these receptors on astrocytes by Western blot and immunofluorescence analysis, respectively. Furthermore, we have confirmed the sensitivity of such receptor expression to ligand stimulation. The present demonstration of Toll‐like microbial pattern‐recognition receptors on primary astrocytes provides a mechanistic link between bacterial challenge and inflammatory immune responses that may be an important component of the pathologies of bacterially induced inflammatory CNS disorders. © 2003 Wiley‐Liss, Inc.
Prognostic microRNAs in upper tract urothelial carcinoma: multicenter and international validation study.

OBJECTIVE To validate previously discovered miRNAs (miR-31-5p and miR-149-5p) as prognostic factors for UTUC in an independent cohort of UTUC patients. PATIENTS AND METHODS Multicenter, international and retrospective study of formalin-fixed paraffin-embedded tissue samples from 103 UTUC patients (45 progressing and 58 non-progressing) who underwent radical nephroureterectomy. Total RNA was isolated and reverse transcribed. The expression of target miRNAs (miR-31-5p and miR-149-5p) and the endogenous control miR-218-5p was evaluated in all samples by reverse transcription quantitative PCR. Normalized miRNA expression values were evaluated by multivariate forward stepwise Cox regression analysis. Kaplan Meier curves were used to discriminate between two groups of patients with a different probability of tumour progression. RESULTS The mean age (range) of the series was 67 (33-94) years. Overall, 45 patients (43.7%) developed tumour progression and 32 patients (31.2%) died, 20 of these (62.5%) due to their UTUC, after a median follow-up of 36 months. The mean time for tumour progression and cancer-specific survival were 15 and 20 months, respectively. Five year tumour progression free survival and cancer-specific survival were 58% for ≤ pT2, 36% for pT3 and 0% for pT4 and 67.8% for ≤ pT2, 50.6% for pT3 and 0% for pT4, respectively. In the multivariate analysis, expression of miR-31-5p was found to be an independent prognostic factor of tumour progression (HR 1.1; 95% CI 1.039-1.273; p=0.02). Kaplan Meier curve shows that miR-31-5p expression values are able to discriminate between two groups of UTUC patients with a different probability of tumour progression (p=0.007). CONCLUSIONS We have been able to validate our previous results in an independent multicentre international cohort of UTUC patients, suggesting that miRNA-31-5p could be a useful prognostic marker of UTUC progression. The application of miRNA expression values to clinical practice could refine the currently used clinicopathological-based approach for predicting UTUC patients' outcome.
A novel strategy for the isolation of luxl homologues: evidence for the widespread distribution of a LuxR:Luxl superfamily in enteric bacteria

The pheromone N‐(3‐oxohexanoyl)‐L‐homoserine lactone (OHHL) regulates expression of bioluminescence in the marine bacterium Vibrio fischeri, the production of carbapenem antibiotic in Erwinia carotovora and exoenzymes in both E. carotovora and Pseudomonas aeruginosa. A characteristic feature of this regulatory mechanism in V. fischeri is that it is cell density‐dependent, reflecting the need to accumulate sufficient pheromone to trigger the induction of gene expression. Using a lux plasmid‐based bioluminescent sensor for OHHL, pheromone production by E. carotovora, Enterobacter agglomerans, Hafnia alvei, Rahnella aquatilis and Serratia marcescens has been demonstrated and shown also to be cell density‐dependent. Production of OHHL implies the presence in these bacteria of a gene equivalent to luxl. Chromosomal banks from all five enteric bacteria have yielded clones capable of eliciting OHHL production when expressed in Escherichia coli. The luxl homologue from both E. carotovora (carl) and E. agglomerans (eagl) were characterized at the DNA sequence level and the deduced protein sequences have only 25% identity with the V. fischeri Luxl. Despite this, carl, eagl and luxl are shown to be biologically equivalent. An insertion mutant of eagl demonstrates that this gene is essential for OHHL production in E. agglomerans.
The Behavioral Intention of Citizen of Nigeria on E-Government Service by Utilization of The Unified Theory of Acceptance and Use of Technology (UTAUT)

The government around the world is now using the electronic government as the modern way of providing service for their citizen. Hence, a number of studies have been investigated and explored the importance of information technology to transform delivery service by the government to their citizen, However, e-government implementation in Nigeria still lacking due to some reasons, such as inadequate of infrastructure and the participation of the citizen to use the e-government service. This is call for change and further study is needed to investigate the behavioral intention of a citizen to use e-government service in Nigeria. Furthermore, the Unified Theory of acceptance and Use of Technology (UTAUT) model is used in this paper as its best model to explore the behavioral intention and usage, and it is combined with eight theories and models of technology adoption or acceptance toward a unified view. Thus the current paper is conceptualized that citizens' behavioral intention to use e-government is expected to be influenced by the citizen. This paper contributes in two folds; practically and theoretically. Citizen is the main role of using e-government service, thus require attention. The social influence, facilitating condition, performance expectancy and Effort expectancy are expected to influence the behavioral intention to use the e-government service. Therefore, the findings will help the government to formulate policies that consider the citizen's intention to use e-government service. The conceptual paper compares only on the fundamental concepts and findings, thus calls for an empirical validation of the proposed framework.
Immunohistochemical localization of angiotensin II receptor types 1 and 2 in the mesenteric artery from spontaneously hypertensive rats

Angiotensin II plays a crucial role in the control of blood pressure, acting at AT1 or AT2 receptors, and can act as a potent vasoconstrictor of the peripheral vasculature inducing hypertrophy, hyperplasia, or both, in resistance arteries. The aim of the present study was to investigate whether the pattern of distribution of angiotensin AT1 and AT2 receptors on mesenteric artery sections differs in spontaneously hypertensive rats (SHR) versus their respective controls (Wistar–Kyoto [WKY] rats). Immunohistochemistry using anti‐AT1 or anti‐AT2 antibodies was performed on perfused‐fixed/paraffin‐embedded mesenteric arteries from SHR and WKY rats. 3,3′‐Diaminobenzidine tetrahydrochloride (DAB; activated by hydrogen peroxide) staining revealed distinct AT1 and AT2 labeling of all artery layers (adventitia, media and intima) from WKY rats, whereas in SHR an abundant AT1 labeling was found in both intima and adventitia and a sparser labeling in the media. There was a vast reduction of AT2 labeling throughout all layers. These results suggest a crucial role for AT2 receptors in the pathogenesis of hypertension. Microsc. Res. Tech., 2007. © 2007 Wiley‐Liss, Inc.
Correlation of observed fold frequency with the occurrence of local structural motifs.

It is well known that some protein folds (superfolds) occur very frequently. We show that compared to other folds, most superfold structures have a higher proportion of their alpha-helical or beta-strand residues in one of three basic units of supersecondary structure (alpha-hairpin, beta-hairpin or betaalphabeta-unit). Furthermore, by taking into consideration two more complex motifs, the four-stranded Greek-key (beta4) and the betaalpha-Greek key (betaalphabetabeta), we demonstrate that the remaining superfold structures contain many of these higher order units of three-dimensional packing. The implications of these results for folding are discussed.
Efficiency-driven complex transit network model

To design an urban public transport network which has the maximum transport efficiency and optimal robustness, it defined the transport efficiency function of transit network and applied complex network theory to propose complex transit network model driven by transport efficiency. This model took into account the restriction coefficient of road network, passenger congestion, travel demand, station impedance, arc section impedance etc. It was applied to a real case of Meihekou city in Jilin province, China. It analyzed node degree and robustness of the transit network. The results are consistent with the anticipation. So the model got a higher practical value.
Educational software system for reasoning and decision making using Bayesian networks

Artificial intelligence represents important area in the field of Computer Science and Engineering. The paper describes Bayesian thinking and the software system for learning Bayesian networks which has been realized at the University of Belgrade - School of Electrical Engineering. This software has been developed as visual interactive educational system for students and will be used within undergraduate studies, within the course subject ‘Intelligent Systems. ’ In this system it is possible to create arbitrary Bayesian network and demonstrate the process of reasoning and decision making, through detailed monitoring of the process. The main objectives of using the system are: to simplify the learning process, and make it efficient and easily integrated into the course.