Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Sensitive Electrochemical Biosensor Based on Polyaniline and Gold Nanoparticles for DNA Detection

In recent years, development of sensitive, selective, and rapid detection of deoxyribonucleic acid (DNA) is very important in various fields of science and technology. DNA biosensors present an alternate approach for detecting DNA sequence in a faster, simpler, and less expensive manner as compared with conventional hybridization methods. In this paper, an electrochemical biosensor was developed based on the sandwich hybridization strategy for the highly specific detection of target DNA molecules without amplification. The surface of screen-printed carbon electrode (SPCE) was first modified using polyaniline (PANI). Then, gold nanoparticles were electrodeposited on the surface of working electrode. Next, the biotinylated nucleic acid capture probe sequence was immobilized onto the avidin-modified SPCE surface via biotin/avidin interaction. After the addition of the target sequence and digoxigenin-labeled detector probe, anti-digoxigenin antibody conjugated to horseradish peroxidase (HRP) was dropped onto the electrode prior to electrochemical analysis. The accomplishment of these steps of biosensor fabrication was carefully studied and approved by scanning electron microscopy and cyclic voltammetry. The results showed that our biosensor has offered a stable sensitive platform with a linear range from 1000 to 0.001 pM and a limit of detection of 0.01 fM. Hence, it is believed that by taking advantage of unique properties of PANI, AuNPs, and HRP enzyme, the proposed biosensor can facilitate the detection and quantification of desired DNA sequences in various biological samples.
Specification of an access control system with a formalism combining CCS and CASL

Multi-formalism specifications are essential for the modelling of complex systems including different aspects such as data or concurrency. We advocate a formalism which combines the CCS process algebra with the CASL algebraic specification language. Formal foundations of this combination are presented following two steps, the syntax and the semantics. Our proposal is illustrated with a real size case study: an access control system to a set of buildings. With this concrete example, we aim at showing how our formalism proposal could be used to specify a comprehensive application.
A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection

We propose an integrative, mechanistic model that integrates in vitro virology data, pharmacokinetics, and viral response to a combination regimen of a direct-acting antiviral (telaprevir, an HCV NS3-4A protease inhibitor) and peginterferon alfa-2a/ribavirin (PR) in patients with genotype 1 chronic hepatitis C (CHC). This model, which was parameterized with on-treatment data from early phase clinical studies in treatment-naïve patients, prospectively predicted sustained virologic response (SVR) rates that were comparable to observed rates in subsequent clinical trials of regimens with different treatment durations in treatment-naïve and treatment-experienced populations. The model explains the clinically-observed responses, taking into account the IC50, fitness, and prevalence prior to treatment of viral resistant variants and patient diversity in treatment responses, which result in different eradication times of each variant. The proposed model provides a framework to optimize treatment strategies and to integrate multifaceted mechanistic information and give insight into novel CHC treatments that include direct-acting antiviral agents.
A Reduction in Age-Enhanced Gluconeogenesis Extends Lifespan

The regulation of energy metabolism, such as calorie restriction (CR), is a major determinant of cellular longevity. Although augmented gluconeogenesis is known to occur in aged yeast cells, the role of enhanced gluconeogenesis in aged cells remains undefined. Here, we show that age-enhanced gluconeogenesis is suppressed by the deletion of the tdh2 gene, which encodes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a protein that is involved in both glycolysis and gluconeogenesis in yeast cells. The deletion of TDH2 restores the chronological lifespan of cells with deletions of both the HST3 and HST4 genes, which encode yeast sirtuins, and represses the activation of gluconeogenesis. Furthermore, the tdh2 gene deletion can extend the replicative lifespan in a CR pathway-dependent manner. These findings demonstrate that the repression of enhanced gluconeogenesis effectively extends the cellular lifespan.
CEP11004, a novel inhibitor of the mixed lineage kinases, suppresses apoptotic death in dopamine neurons of the substantia nigra induced by 6‐hydroxydopamine

There is much evidence that the kinase cascade which leads to the phosphorylation of c‐jun plays an important signaling role in the mediation of programmed cell death. We have previously shown that c‐jun is phosphorylated in a model of induced apoptotic death in dopamine neurons of the substantia nigra in vivo. To determine the generality and functional significance of this response, we have examined c‐jun phosphorylation and the effect on cell death of a novel mixed lineage kinase inhibitor, CEP11004, in the 6‐hydroxydopamine model of induced apoptotic death in dopamine neurons. We found that expression of total c‐jun and Ser73‐phosphorylated c‐jun is increased in this model and both colocalize with apoptotic morphology. CEP11004 suppresses apoptotic death to levels of 44 and 58% of control values at doses of 1.0 and 3.0 mg/kg, respectively. It also suppresses, to approximately equal levels, the number of profiles positive for the activated form of capase 9. CEP11004 markedly suppresses striatal dopaminergic fiber loss in these models, to only 22% of control levels. We conclude that c‐jun phosphorylation is a general feature of apoptosis in living dopamine neurons and that the mixed lineage kinases play a functional role as up‐stream mediators of cell death in these neurons.
Investigation of the Efficacy of Micafungin in the Treatment of Histoplasmosis Using Two North American Strains of Histoplasma capsulatum

ABSTRACT Micafungin alone and combined with liposomal amphotericin B was evaluated against two strains of Histoplasma capsulatum. Micafungin was active in vitro against the mold but not the yeast form but was ineffective in vivo. Micafungin appears to be ineffective in treatment of histoplasmosis.
On the Smallest Minimal Blocking Sets in Projective Space Generating the Whole Space

It was conjectured that the smallest minimal point sets of PG(2s,q), q a square, that meet every s-subspace and that generate the whole space are Baer subgeometries PG(2s, p q). This was shown in 1971 by Bruen for s = 1, and by Metsch and Storme (5) for s = 2. Our main interest in this paper is to prepare a possible proof of this conjecture by proving a strong theorem on line-blocking sets in projective spaces (see Theorem 1.1). We apply this theorem to prove the conjecture in the case s = 3. The general case will be handled in a forthcoming paper by the first author.
Handbook of Materials Selection

This comprehensive organization of the materials selection process includes analytical approaches to materials selection and extensive information about materials available in the marketplace, sources of properties data, procurement and data management, properties testing procedures and equipment, analysis of failure modes, manufacturing processes and assembly techniques, and applications. Throughout the handbook, an international roster of contributors with a broad range of experience conveys practical knowledge about materials and illustrates in detail how they are used in a wide variety of industries.
Analysis of a Study of the Users, Uses, and Future Agenda of the UMLS

OBJECTIVES The UMLS constitutes the largest existing collection of medical terms. However, little has been published about the users and uses of the UMLS. This study sheds light on these issues. DESIGN We designed a questionnaire consisting of 26 questions and distributed it to the UMLS user mailing list. Participants were assured complete confidentiality of their replies. To further encourage list members to respond, we promised to provide them with early results prior to publication. Sector analysis of the responses, according to employment organizations is used to obtain insights into some responses. RESULTS We received 70 responses. The study confirms two intended uses of the UMLS: access to source terminologies (75%), and mapping among them (44%). However, most access is just to a few sources, led by SNOMED, MeSH, and ICD. Out of 119 reported purposes of use, terminology research (37), information retrieval (19), and terminology translation (14) lead. Four important observations are that the UMLS is widely used as a terminology (77%), even though it was not designed as one; many users (73%) want the NLM to mark concepts with multiple parents in an indented hierarchy and to derive a terminology from the UMLS (73%). Finally, auditing the UMLS is a top budget priority (35%) for users. CONCLUSIONS The study reports many uses of the UMLS in a variety of subjects from terminology research to decision support and phenotyping. The study confirms that the UMLS is used to access its source terminologies and to map among them. Two primary concerns of the existing user base are auditing the UMLS and the design of a UMLS-based derived terminology.
Multicomponent Phase Diagrams: Applications for Commercial Aluminum Alloys

Chapter 1: Alloys of the Al-Fe-Mn-Si System Chapter 2: Alloys of the Al-Mg-Si-Fe System Chapter 3: Alloys of the Al-Cu-Si-(Mg, Fe)System Chapter 4: Alloys of the Al-Mg-Mn-Si-Fe System Chapter 5: Alloys of the Al-Cu-Mn (Mg, Fe, Si) System Chapter 6: Alloys with a High Content of Zinc Chapter 7: Alloys with Nickel Chapter 8: Alloys with Lithium Chapter 9: Alloys with Transition Metals Chapter 10: Composite Materials with SiC, Al2O3 and SiO2 Appendix 1: Main Characteristics of Binary Phase Diagrams Appendix 2: Visualization of Quaternary Phase Diagrams Appendix 3: Visualization of Quinary Phase Diagrams Appendix 4: Mathematical Approximation of Phase Diagrams Appendix 5: Summary of some calculated multicomponent phase diagrams of Al-based systems Appendix 2: Visualization of Quaternary Phase Diagrams Appendix 3: Visualization of Quinary Phase Diagrams Appendix 4: Mathematical Approximation of Phase Diagrams Appendix 5: Summary of some calculated multicomponent phase diagrams of Al-based systems
High-fructose feeding impacts on the adrenergic control of renal haemodynamics in the rat

The present study explored the hypothesis that a prolonged 8 weeks exposure to a high fructose intake suppresses adrenergic and angiotensin II (Ang II)-mediated vasoconstriction and is associated with a higher contribution of α1D-adrenoceptors. A total of thirty-two Sprague–Dawley rats received either 20 % fructose solution (FFR) or tap water (control, C) to drink ad libitum for 8 weeks. Metabolic and haemodynamic parameters were assessed weekly. The renal cortical vasoconstrictor responses to noradrenaline (NA), phenylephrine (PE), methoxamine (ME) and Ang II were determined in the presence and absence of BMY7378 (α1D-adrenoceptor antagonist). FFR had increased blood pressure, plasma levels of glucose, TAG and insulin. FFR expressed reduced renal vascular responses to adrenergic agonists and Ang II (NA: 50 %, PE: 50 %, ME, 65 %, Ang II: 54 %). Furthermore in the C group, the magnitude of the renal cortical vasoconstriction to all agonists was blunted in the presence of the low or high dose of BMY7378 (NA: 30 and 31 %, PE: 23 and 33 %, ME: 19 and 44 %, Ang II: 53 and 77 %), respectively, while in the FFR, vasoconstriction was enhanced to adrenergic agonists and reduced to Ang II (NA: 8 and 83 %, PE: 55 %, ME, 2 and 177 %, Ang II: 61 and 31 %). Chronic high fructose intake blunts vascular sensitivity to adrenergic agonists and Ang II. Moreover, blocking of the α1D-adrenoceptor subtype results in enhancement of renal vasoconstriction to adrenergic agonists, suggesting an inhibitory action of α1D-adrenoceptors in the FFR. α1D-Adrenoceptors buffer the AT1-receptor response in the renal vasculature of normal rats and fructose feeding suppressed this interaction.
Magnetodielectric and magnetoelastic properties of spinel Mn3O4

The magnetodielectric and magnetoelastic properties of spinel Mn3O4 with the orbital degree of freedom in the eg state of the Mn3+ site were investigated. We found that strain (ΔL/L) shows anomalies at the magnetic phase transition temperatures and is anisotropic against the crystallographic axis. We also found that this compound exhibits large magnetic field (H) dependences of ΔL/L, details of which are different at three different magnetic phases. Similar anomalies and H dependence are observed in dielectric measurements. These behaviors can be explained by the inverse effect of single-ion spin anisotropy.
OrthoCluster: a new tool for mining synteny blocks and applications in comparative genomics

By comparing genomes among both closely and distally related species, comparative genomics analysis characterizes structures and functions of different genomes in both conserved and divergent regions. Synteny blocks, which are conserved blocks of genes on chromosomes of related species, play important roles in comparative genomics analysis. Although a few tools have been designed to identify synteny blocks, most of them cannot handle some challenging application requirements, particularly the strandedness of genes, gene inversions, gene duplications, and comparison of more than two genomes. We developed a data mining tool, Ortho-Cluster, which can handle all those challenges. It is publicly available at http://genome.sfu. ca/projects/orthocluster. OrthoCluster takes the annotated gene sets of candidate genomes and pairwise orthologous relationships as input and efficiently identifies the complete set of synteny blocks. In addition, OrthoCluster identifies four types of genome rearrangement events namely inversion, transposition, insertion/deletion, and reciprocal translocation. To be fleexible in various application scenarios, OrthoCluster comes with a systematic set of parameters such as the synteny block size, number of mismatches allowed, whether the strandedness is enforced, whether gene ordering is preserved. Furthermore, OrthoCluster can be used to identify segmental duplication in a genome. In this paper, we introduce the major technical ideas, and present some interesting findings using OrthoCluster.
Dopamine-Independent Locomotor Actions of Amphetamines in a Novel Acute Mouse Model of Parkinson Disease

Brain dopamine is critically involved in movement control, and its deficiency is the primary cause of motor symptoms in Parkinson disease. Here we report development of an animal model of acute severe dopamine deficiency by using mice lacking the dopamine transporter. In the absence of transporter-mediated recycling mechanisms, dopamine levels become entirely dependent on de novo synthesis. Acute pharmacological inhibition of dopamine synthesis in these mice induces transient elimination of striatal dopamine accompanied by the development of a striking behavioral phenotype manifested as severe akinesia, rigidity, tremor, and ptosis. This phenotype can be reversed by administration of the dopamine precursor, L-DOPA, or by nonselective dopamine agonists. Surprisingly, several amphetamine derivatives were also effective in reversing these behavioral abnormalities in a dopamine-independent manner. Identification of dopamine transporter- and dopamine-independent locomotor actions of amphetamines suggests a novel paradigm in the search for prospective anti-Parkinsonian drugs.
Effectiveness of Acupressure on Pruritus and Lichenification Associated with Atopic Dermatitis: A Pilot Trial

Background Pruritus is a debilitating aspect of atopic dermatitis (AD). Acupuncture has been reported to diminish pruritus, but self-administered acupressure has not been previously evaluated. Objectives To evaluate the effectiveness of acupressure on the severity of eczema in a pilot trial. Methods Adult patients with AD were randomised to an intervention group (acupressure with standard of care) or a control group (standard of care alone). Subjects in the intervention group performed acupressure using a 1.2 mm acupellet at the LI11 point, applying pressure for 3 min three times per week for 4 weeks. The severity of itching and AD at baseline and at 4 weeks were measured on a visual analogue scale (VAS), the Investigator's Global Assessment (IGA) and the Eczema Area and Severity Index (EASI). Results Fifteen subjects were enrolled, 12 of whom completed the study between November 2009 and May 2011. There was no significant change between baseline and follow-up survey scores within the control group. In the investigation group there was a decrease in the VAS score (p=0.05) and EASI lichenification (p=0.03), although without significant change in the overall EASI score. Comparison of the scores between groups showed a greater decrease in VAS in the experimental group than in the control group (p=0.04), and a decrease in the IGA (p=0.03) and EASI lichenification score (p=0.03). The overall EASI scores were unchanged. Conclusion Subjects using acupressure at LI11 for 4 weeks had improvement in pruritus and lichenification. Acupressure may prove to be an easily administered alternative treatment, but larger-scale studies are needed to confirm these preliminary findings.
Brain activity underlying emotional valence and arousal: A response‐related fMRI study

Emotional behavior is organized along two psychophysiologic dimensions: (1) valence, varying from negative to positive, and (2) arousal, varying from low to high. Behavioral responses along these dimensions are assumed to be mediated by different brain circuits. We recorded startle reflex modulation and skin conductance responses in healthy volunteers during functional magnetic resonance imaging (fMRI) while they viewed a set of emotional pictures and took verbal ratings of the emotional valence and arousal of each picture after scanning. Response‐related multiple correlation analysis revealed differential brain activity in five brain regions. Startle reflex changes, associated with the valence of a stimulus, correlated with activity in the amygdala, while verbal reports of negative emotional valence varied with insular activity. Peripheral physiologic and verbal responses along the arousal dimension varied with thalamic and frontomedial activity. Peripheral physiologic responses along both dimensions correlated with activity in somatosensory association areas in the anterior parietal cortex. In the valence dimension, activity in the left anterior parietal cortex was associated with highly correlating peripheral physiologic and verbal responses, suggesting that verbal reports of emotional valence might depend partly on brain circuits representing peripheral physiologic changes. Our data provide direct evidence for a functional segregation of brain structures underlying peripheral physiologic responses and verbal ratings along the emotional dimensions of valence and arousal. Hum. Brain Mapp. 23:200–209, 2004. © 2004 Wiley‐Liss, Inc.
The de novo centriole assembly pathway in HeLa cells

It has been reported that nontransformed mammalian cells become arrested during G1 in the absence of centrioles (Hinchcliffe, E., F. Miller, M. Cham, A. Khodjakov, and G. Sluder. 2001. Science. 291:1547–1550). Here, we show that removal of resident centrioles (by laser ablation or needle microsurgery) does not impede cell cycle progression in HeLa cells. HeLa cells born without centrosomes, later, assemble a variable number of centrioles de novo. Centriole assembly begins with the formation of small centrin aggregates that appear during the S phase. These, initially amorphous “precentrioles” become morphologically recognizable centrioles before mitosis. De novo–assembled centrioles mature (i.e., gain abilities to organize microtubules and replicate) in the next cell cycle. This maturation is not simply a time-dependent phenomenon, because de novo–formed centrioles do not mature if they are assembled in S phase–arrested cells. By selectively ablating only one centriole at a time, we find that the presence of a single centriole inhibits the assembly of additional centrioles, indicating that centrioles have an activity that suppresses the de novo pathway.
Channel Capacity Limits of Cognitive Radio in Asymmetric Fading Environments

Cognitive radio technology is an innovative radio design concept which aims to increase spectrum utilization by exploiting unused spectrum in dynamically changing environments. By extending previous results, we investigate the capacity gains achievable with this dynamic spectrum approach in asymmetric fading channels. More specifically, we allow the secondary-to- primary and secondary-to-secondary user channels to undergo Rayleigh or Rician fading, with arbitrary link power. In order to compute the capacity, we derive the distributions of ratios of Rayleigh and Rician variables. Compared to the symmetric fading scenario, our results indicate several interesting features of the capacity behaviour under both average and peak received power constraints. Finally, the impact of multiple primary users on the capacity under asymmetric fading has also been studied.
Urinary Metabolites of Prostanoids and Risk of Recurrent Colorectal Adenomas in the Aspirin/Folate Polyp Prevention Study (AFPPS)

Aspirin has been shown to protect against colorectal neoplasms; however, the optimal chemopreventive dose and underlying mechanisms are unclear. We aimed to study the relationship between prostanoid metabolites and aspirin's effect on adenoma occurrence. We used data from the Aspirin/Folate Polyp Prevention Study, in which 1,121 participants with a recent adenoma were randomized to placebo or two doses of aspirin (81 or 325 mg/d) to be taken until the next surveillance colonoscopy, anticipated about 3 years later. Urinary metabolites of prostanoids (PGE-M, PGI-M, and dTxB2) were measured using liquid chromatography/mass spectrometry or GC/NICI-MS in 876 participants near the end of treatment follow-up. Poisson regression with a robust error variance was used to calculate relative risks and 95% confidence intervals. PGE-M, PGI-M, and dTxB2 levels were 28%, 37%, and 60% proportionately lower, respectively, in individuals who took 325 mg of aspirin compared with individuals who took placebo (all P < 0.001). Similarly, among individuals who took 81 mg of aspirin, PGE-M, PGI-M, and dTxB2 were, respectively, 18%, 30%, and 57% proportionally lower compared with placebo (all P < 0.005). None of the metabolites or their ratios were statistically significantly associated with the risk of adenoma occurrence. The effect of aspirin in reducing adenoma risk was independent of prostanoid levels. Aspirin use is associated with lower levels of urinary prostanoid metabolites. However, our findings do not support the hypothesis that these metabolites are associated with adenoma occurrence, suggesting that COX-dependent mechanisms may not completely explain the chemopreventive effect of aspirin on colorectal neoplasms. Cancer Prev Res; 8(11); 1061–8. ©2015 AACR.