Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectroscopy, Manipulation and Trapping of Neutral Atoms, Molecules, and Other Particles Using Optical Nanofibers: A Review

The use of tapered optical fibers, i.e., optical nanofibers, for spectroscopy and the detection of small numbers of particles, such as neutral atoms or molecules, has been gaining interest in recent years. In this review, we briefly introduce the optical nanofiber, its fabrication, and optical mode propagation within. We discuss recent progress on the integration of optical nanofibers into laser-cooled atom and vapor systems, paying particular attention to spectroscopy, cold atom cloud characterization, and optical trapping schemes. Next, a natural extension of this work to molecules is introduced. Finally, we consider several alternatives to optical nanofibers that display some advantages for specific applications.
A Role of Sp1 Binding Motifs in Basal and Large T-Antigen-Induced Promoter Activities of Human Polyomavirus HPyV9 and Its Variant UF-1

Human polyomavirus 9 (HPyV9) was originally detected in the serum of a renal transplant patient. Seroepidemiological studies showed that ~20–50% of the human population have antibodies against this virus. HPyV9 has not yet been associated with any disease and little is known about the route of infection, transmission, host cell tropism, and genomic variability in circulating strains. Recently, the HPyV9 variant UF-1 with an eight base-pair deletion, a thirteen base-pair insertion and with point mutations, creating three putative Sp1 binding sites in the late promoter was isolated from an AIDS patient. Transient transfection studies with a luciferase reporter plasmid driven by HPyV9 or UF1 promoter demonstrated that UF1 early and late promoters were stronger than HPyV9 promoters in most cell lines, and that the UF1 late promoter was more potently activated by HPyV9 large T-antigen (LTAg). Mutation of two Sp1 motifs strongly reduced trans-activation of the late UF1 promoter by HPyV9 LTAg in HeLa cells. In conclusion, the mutations in the UF1 late promoter seem to strengthen its activity and its response to stimulation by HPyV9 LTAg in certain cells. It remains to be investigated whether these promoter changes have an influence on virus replication and affect the possible pathogenic properties of the virus.
[Cognitive impairment and quality of life in multiple sclerosis patients].

INTRODUCTION Cognitive disorders may bias perception of quality-of-life in patients with multiple sclerosis (MS). METHODS Neuropsychological tests (WAIS-vocabulary, Gröber and Buschke, Stroop, WCST, WAIS-similitude, fluency, Hamilton's depression scale) along with a French health-related quality of life self questionnaire for MS patients (the SEP59) were performed by 117 MS patients with a minor cognitive impairment (Mini Mental State over 24) in order to explore the links between quality of life perception and cognitive functioning. RESULTS Main Component Analysis and correlation analysis showed that cognitive impairment produced an overrating of the self perception of quality of life. Threshold analysis, splitting patients between the most and the less cognitively impaired, confirmed this relationship. CONCLUSION The level of cognitive functioning must be considered with caution when analyzing health-related quality of MS patients.
Isolation, purification and characterisation of transglutaminase from rosemary (Rosmarinus officinalis L.) leaves.

BACKGROUND Rosemary (Rosmarinus officinalis L.) is a spice and medicinal herb widely used around the world of the natural antioxidants, and it has been widely accepted as one of the spices with the highest antioxidant activity. Transglutaminase (EC 2.3.2.13: TGase) is an enzyme capable of catalysing acyl transfer reactions by introducing covalent cross-links between proteins, as well as peptides and various primary amines. TGase activity in plants was first observed in pea seedlings, and subsequently found in organs of both lower and higher plants. Recently. TGase has captured researchers' interest due to its attractive potential application in food industries. Therefore, the objectives of this study are isolation and purification of TGase from new plant source rosemary (Rosmarinus officinalis L.) leaves at the laboratory scale. Moreover, investigation of the biochemical properties of the purified TGase to provide a suitable TGase enzyme for food industry applications are in focus. MATERIAL AND METHODS Rosemary (Rosmarinus officinalis L.) leaves was used as a new plant source to TGase. The biochemical characteristics of the crude and purified enzyme were determined. RESULTS Rosemary (Rosmarinus officinalis L.) TGase was purified to homogeneity by successive three purification steps including ammonium sulfate precipitatation, ion exchange chromatography on DEAE-Sephadex A-50 column and Size exclusion column chromatography on Sephadex G-100 column. Under experimental conditions. 20-30% of ammonium sulfate saturation in the enzyme solution had a high yield of enzyme activity could be obtained. The purified enzyme from the Sephadex G-100 column had 21.35% yield with increased about 7.31 in purification fold. Rosemary TGase exhibited optimum activity at pH 7.0 and 55°C for the catalytic reaction of hydroxylarnine and Z-Gln-Gly. The purified TGase almost maintained full activity after incubation for 15 ruin up to 60°C and it was completely inactivated at 85°C. The rosemary TGase was stimulated at 2-6 rnM CaCl2 concentrations while it lost about 5-20% from its activity by increasing CaCl2 concentration. Sodium chloride (2-14%) shows no noticeable inhibition of the purified TGase activity. Mg+2, Ba+2 were acivited by the purified TGase while it was str ongly inhibited by Fe+2, moderately by Cir2 and Mn+2. CONCLUSION This paper reports on the purification and characterisation of TGase from newly isolated plant, rosemary (Rosmarinus officinalis L.) leaves. Finding results of the TGase properties make this enzyme a good candidate for application in the food industry. However, additional work is required to increase activity yield during extraction and purification for commercial scale of TGase from this plant.
Unitary Events in Multiple Single-Neuron Spiking Activity: I. Detection and Significance

It has been proposed that cortical neurons organize dynamically into functional groups (cell assemblies) by the temporal structure of their joint spiking activity. Here, we describe a novel method to detect conspicuous patterns of coincident joint spike activity among simultaneously recorded single neurons. The statistical significance of these unitary events of coincident joint spike activity is evaluated by the joint-surprise. The method is tested and calibrated on the basis of simulated, stationary spike trains of independently firing neurons, into which coincident joint spike events were inserted under controlled conditions. The sensitivity and specificity of the method are investigated for their dependence on physiological parameters (firing rate, coincidence precision, coincidence pattern complexity) and temporal resolution of the analysis. In the companion article in this issue, we describe an extension of the method, designed to deal with nonstationary firing rates.
Superior control of HIV-1 replication by CD8+ T cells is reflected by their avidity, polyfunctionality, and clonal turnover

The key attributes of CD8+ T cell protective immunity in human immunodeficiency virus (HIV) infection remain unclear. We report that CD8+ T cell responses specific for Gag and, in particular, the immunodominant p24 epitope KK10 correlate with control of HIV-1 replication in human histocompatibility leukocyte antigen (HLA)–B27 patients. To understand further the nature of CD8+ T cell–mediated antiviral efficacy, we performed a comprehensive study of CD8+ T cells specific for the HLA-B27–restricted epitope KK10 in chronic HIV-1 infection based on the use of multiparametric flow cytometry together with molecular clonotypic analysis and viral sequencing. We show that B27-KK10–specific CD8+ T cells are characterized by polyfunctional capabilities, increased clonal turnover, and superior functional avidity. Such attributes are interlinked and constitute the basis for effective control of HIV-1 replication. These data on the features of effective CD8+ T cells in HIV infection may aid in the development of successful T cell vaccines.
The generalized minimum spanning tree problem

We consider the Generalized Minimum Spanning Tree Problem denoted by GMSTP. It is known that GMSTP is NP-hard and even finding a near optimal solution is NP-hard. We introduce a new mixed integer programming formulation of the problem which contains a polynomial number of constraints and a polynomial number of variables. Based on this formulation we give an heuristic solution, a lower bound procedure and an upper bound procedure and present the advantages of our approach in comparison with an earlier method. We present a solution procedure for solving GMST problem using cutting planes.
Creencias de tres profesores italianos de E/LE: estrategias de enseñanza, importancia de la formación y autoridad sociocultural del profesor no nativo

La reflexion sobre la actividad docente es una de las cuestiones mas trascendentales en la formacion del profesorado (Williams y Burden, 1999). El siguiente estudio presta especial atencion a las reflexiones de un colectivo cada vez mas visible en E/LE: el de profesores no nativos. A traves de las entrevistas y de los cuestionarios realizados a tres profesores italianos, se intentara analizar el sistema de creencias de estos, poniendo el foco de atencion en su propia percepcion como profesores no nativos y las ventajas e inconvenientes que ello pueda conllevar. Asi mismo, se analizara la relacion que los profesores entrevistados puedan establecer entre su naturaleza y los diferentes aspectos de su actividad docente: la reflexion sobre sus propias estrategias de ensenanza teniendo en cuenta su condicion de aprendices antes y profesores de E/LE despues, el papel que desempena la formacion en su labor y la autoridad sociocultural de la que estan dotados, es decir, la credibilidad que creen que los aprendices les otorgan cuando transmiten sus saberes culturales y socioculturales en un contexto de no inmersion linguistica y en el que comparten lengua y cultura con su alumnado.
Prognosis of neutrophil-to-lymphocyte ratio in clinical early-stage tongue (cT1/T2N0) cancer

Background Inflammation plays a role in the development of cancer. This study aims to analyze the prognostic value of the neutrophil-to-lymphocyte ratio (NLR) and other clinicopathological determinants in early-stage (cT1/T2N0) tongue cancer. Materials and methods A total of 262 patients were selected from our institute’s cancer database between 2004 and 2011. Optimal cutoff value of NLR and lymph node density (LND) were determined statistically using receiver operating characteristic curve analysis for survival prediction. The 5-year overall survival (OS), disease-specific survival (DSS), and disease-free survival (DFS) rates were estimated using the Kaplan–Meier method. Results The results showed that, in this cohort, the optimal cutoff value of NLR was 2.95 and for LND, it was 0.031. Patients with NLR ≥2.95 correlated significantly with positive N classification (P=0.011), T2 classification (P=0.007), positive perineural invasion (P<0.001), and a tumor thickness of >5 mm (P=0.005). The 5-year OS among patients with NLR <2.95 was much higher than that in patients with NLR ≥2.95 (P<0.001). Similarly, the 5-year DSS among patients with NLR <2.95 was much higher than that in patients with NLR ≥2.95 (P=0.002). The 5-year DFS among patients with NLR <2.95 was much higher than that in patients with NLR ≥2.95 (P=0.004). The 5-year OS, DSS, and DFS were significantly reduced among patients with LND >0.031 compared to those with LND <0.031, respectively. In multivariate analysis, NLR, LND, and tumor thickness were independent prognostic factors for OS. Conclusion Pretreatment NLR ≥2.95 is significantly correlated with a larger tumor, positive neck lymph node metastasis, and positive perineural invasion. Importantly, it indicates reduced survival rate. Therefore, if the NLR ≥2.95 in early-stage (cT1/T2N0) tongue cancer is noted preoperatively, it reveals more invasive tumor behavior clinically. Then, aggressive treatments, including elective neck dissection, become necessary.
Model predictive control for stochastic max-min-plus-scaling systems - an approximation approach

A large class of discrete-event and hybrid systems can be described by a max-min-plus-scaling (MMPS) model, i.e., a model in which the main operations are maximization, minimization, addition, and scalar multiplication. Further, Model Predictive Control (MPC), which is one of the most widely used advanced control design methods in the process industry due to its ability to handle constraints on both inputs and outputs, has already been extended to both deterministic and stochastic MMPS systems. However, in order to compute an MPC controller for a general MMPS system, a nonlinear, nonconvex optimization problem has to be solved. In addition, for stochastic MMPS systems, the problem is computationally highly complex since the cost function is defined as the expected value of an MMPS function and its evaluation leads to a complex numerical integration. The aim of this paper is to decrease this computational complexity by applying an approximation method that is based on the raw moments of a random variable, to a stochastic MMPS system with a Gaussian noise. In this way, the problem can be transformed into a sequence of convex optimization problems, providing that linear or convex MPC input constraints are considered.
Phospholipid Flip-Flop and Phospholipid Scramblase 1 (PLSCR1) Co-localize to Uropod Rafts in Formylated Met-Leu-Phe-stimulated Neutrophils*

Movement of phosphatidylserine (PS) to the plasma membrane outer leaflet is a nearly universal marker of apoptosis and occurs during activation of many cells. Neutrophils stimulated with the chemotactic peptide formylated Met-Leu-Phe (fMLP) demonstrated transient PS exposure. Stimulated outward movement of PS was accompanied by enhanced inward movement of several phosphorylcholine lipid probes and was associated with enhanced FM 1-43 staining indicative of phospholipid packing changes. Unlike apoptosis, inward movement of exogenously added fluorescent PS did not decline, and DNA was not cleaved during fMLP stimulation. Movement of phospholipids occurred within minutes following stimulation, was independent of endocytosis/pinocytosis, and was consistent with bidirectional, transbilayer phospholipid flip-flop. While the role of phospholipid scramblase 1 (PLSCR1) is controversial in flip-flop, we sought evidence for its role in enhanced phospholipid movements during fMLP stimulation. Using antibodies to the carboxyl-terminal domain of PLSCR1, its presence in the plasma membranes of non-permeabilized neutrophils was confirmed by flow cytometry. Additionally subcellular fractionation demonstrated that PLSCR1 was also located in secretory vesicles and tertiary and secondary granules. Activation of neutrophils with fMLP, however, did not significantly alter surface labeling suggesting that stimulated phospholipid flip-flop does not require additional mobilization of PLSCR1 to the plasma membrane. As expected for palmitoylated proteins, PLSCR1 was enriched in detergent-insoluble membranes and co-localized with raft markers at the neutrophil uropod after stimulation. Of note, PS exposure, phospholipid uptake, and FM 1-43 staining also localized to the uropod following stimulation demonstrating that both PLSCR1 and phospholipid flip-flop characterize this specialized domain of polarized neutrophils.
Annual Report Graphic Use

Corporate annual reports typically include a narrative section and a financial section. The narrative section is not scrutinized by auditors as the financial section is, yet many readers rely heavily on its graphs to estimate the firm's financial situation. However, the graphs often misrepresent the financial data. To better understand annual report graphs' important role, this article examines more than 25 years of literature related to these four areas: (a) the ways financial graphs are prepared, used, and misinterpreted; (b) differences by country; (c) regulatory influences for accountants; and (d) the parts formatting and media selection decisions play in communication interpretation and persuasion. Across the literature, the author notes consensus that annual report graphs are widely used in many countries and that there is rampant disregard for the guidelines for their accurate, non-misleading presentation. The article concludes with seven proposed directions for future research.
On the toric algebra of graphical models

We formulate necessary and sufficient conditions for an arbitrary discrete probability distribution to factor according to an undirected graphical model, or a log-linear model, or other more general exponential models. For decomposable graphical models these conditions are equivalent to a set of conditional independence statements similar to the Hammersley-Clifford theorem; however, we show that for nondecomposable graphical models they are not. We also show that nondecomposable models can have nonrational maximum likelihood estimates. These results are used to give several novel characterizations of decomposable graphical models.
Optical Coherence Tomography: An Adjunctive Tool for Differentiating between Choroidal Melanoma and Metastasis

Purpose. To investigate the value of optical coherence tomography (OCT) for differentiation between choroidal melanoma and metastasis based on characteristics of the anterior choroidal surface and the chorioretinal interface. Methods. This retrospective observational case series included 29 patients with untreated choroidal melanomas and 21 patients with untreated choroidal metastases. Regularity and lobularity characteristics of the anterior choroidal surface were evaluated in a masked manner. Retinal and retinal pigment epithelium (RPE) findings were documented as well. Results. OCT demonstrated a regular and smooth anterior choroidal surface in 89.7% of the eyes with melanoma and in 47.6% of the eyes with metastasis (p = 0.002; sensitivity = 89.7%; specificity = 52.4%). The anterior choroidal contour was lobulated in 81.0% of the eyes with metastasis versus 17.2% of the eyes with melanoma (p < 0.001; sensitivity = 82.8%; specificity = 81.0%). RPE thickness and neuroretinal characteristics (e.g., retinal thickness, the presence of cysts, and the presence of subretinal fluid) were similar in both choroidal tumors. Conclusion. OCT may serve as a noninvasive adjunctive tool for the differential diagnosis of choroidal tumors. Choroidal melanomas usually demonstrate regular surfaces on OCT, while choroidal metastases usually have an irregular and lobulated surface.
Tests of a dual-system model of speech category learning*

In the visual domain, more than two decades of work has argued for the existence of dual category learning systems. The reflective system uses working memory in an explicit fashion to develop and test rules for classifying. The reflexive system operates by implicitly associating perception with actions that lead to reinforcement. Dual-system models posit that in learning natural categories, learners initially use the reflective system and with practice, transfer control to the reflexive system. The role of reflective and reflexive systems in second language (L2) speech learning has not been systematically examined. In the study reported in this paper, monolingual native speakers of American English were trained to categorize Mandarin tones produced by multiple speakers. Our computational modeling approach demonstrates that learners use reflective and reflexive strategies during tone category learning. Successful learners use speaker-dependent, reflective analysis early in training and reflexive strategies by the end of training. Our results demonstrate that dual-learning systems are operative in L2 speech learning. Critically, learner strategies directly relate to individual differences in successful category learning.
Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability

Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such genetic correlations should strongly influence evolutionary dynamics. We explore and quantify these intuitions by comparing three GP maps—a model for RNA secondary structure, the HP model for protein tertiary structure, and the Polyomino model for protein quaternary structure—to a simple random null model that maintains the number of genotypes mapping to each phenotype, but assigns genotypes randomly. The mutational neighbourhood of a genotype in these GP maps is much more likely to contain genotypes mapping to the same phenotype than in the random null model. Such neutral correlations can be quantified by the robustness to mutations, which can be many orders of magnitude larger than that of the null model, and crucially, above the critical threshold for the formation of large neutral networks of mutationally connected genotypes which enhance the capacity for the exploration of phenotypic novelty. Thus neutral correlations increase evolvability. We also study non-neutral correlations: Compared to the null model, i) If a particular (non-neutral) phenotype is found once in the 1-mutation neighbourhood of a genotype, then the chance of finding that phenotype multiple times in this neighbourhood is larger than expected; ii) If two genotypes are connected by a single neutral mutation, then their respective non-neutral 1-mutation neighbourhoods are more likely to be similar; iii) If a genotype maps to a folding or self-assembling phenotype, then its non-neutral neighbours are less likely to be a potentially deleterious non-folding or non-assembling phenotype. Non-neutral correlations of type i) and ii) reduce the rate at which new phenotypes can be found by neutral exploration, and so may diminish evolvability, while non-neutral correlations of type iii) may instead facilitate evolutionary exploration and so increase evolvability.
Oral contraceptives combined with interferon β in multiple sclerosis

Objective: To test the effect of oral contraceptives (OCs) in combination with interferon β (IFN-β) on disease activity in patients with relapsing-remitting multiple sclerosis (RRMS). Methods: One hundred fifty women with RRMS were randomized in a 1:1:1 ratio to receive IFN-β-1a subcutaneously (SC) only (group 1), IFN-β-1a SC plus ethinylstradiol 20 μg and desogestrel 150 μg (group 2), or IFN-β-1a SC plus ethinylestradiol 40 μg and desogestrel 125 μg (group 3). The primary endpoint was the cumulative number of combined unique active (CUA) lesions on brain MRI at week 96. Secondary endpoints included MRI and clinical and safety measures. Results: The estimated number of cumulative CUA lesions at week 96 was 0.98 (95% confidence interval [CI] 0.81–1.14) in group 1, 0.84 (95% CI 0.66–1.02) in group 2, and 0.72 (95% CI 0.53–0.91) in group 3, with a decrease of 14.1% (p = 0.24) and 26.5% (p = 0.04) when comparing group 1 with groups 2 and 3, respectively. The number of patients with no gadolinium-enhancing lesions was greater in group 3 than in group 1 (p = 0.03). No significant differences were detected in other secondary endpoints. IFN-β or OC discontinuations were equally distributed across groups. Conclusions: Our results translate the observations derived from experimental models to patients, supporting the anti-inflammatory effects of OCs with high-dose estrogens, and suggest possible directions for future research. Classification of evidence: This study provides Class II evidence that in women with RRMS, IFN-β plus ethinylstradiol and desogestrel decreases the cumulative number of active brain MRI lesions compared with IFN-β alone.