Miracle-dz/UniFAR-FTUs huggingface dataset:
Polarization gating based on Mueller matrices

Abstract. We present mathematical formulas generalizing polarization gating (PG) techniques. PG refers to a collection of imaging methods based on the combination of different controlled polarization channels. In particular, we show how using the measured Mueller matrix (MM) of a sample, a widespread number of PG configurations can be evaluated just from analytical expressions based on the MM coefficients. We also show the interest of controlling the helicity of the states of polarization used for PG-based metrology, as this parameter has an impact in the image contrast of samples. In addition, we highlight the interest of combining PG techniques with tools of data analysis related to the MM formalism, such as the well-known MM decompositions. The method discussed in this work is illustrated with the results of polarimetric measurements done on artificial phantoms and real ex-vivo tissues.
Further Evaluation of Presentation Format of Competing Stimuli for Treatment of Automatically Maintained Challenging Behavior

Behavioral interventions have been effective in reducing automatically maintained skin picking for individuals with disabilities including autism spectrum disorder (ASD). A competing stimulus assessment (CSA) is typically utilized in behavioral intervention and assessment to identify potential stimuli which compete with the reinforcer for various forms of challenging behavior (CB). Treatment evaluations have validated the results of these assessments by demonstrating competing stimuli may reduce levels of CB. In Phase 1 of this study, we conducted a functional analysis (FA) to determine what variables were maintaining skin picking of an 11-year-old girl diagnosed with ASD. In Phase 2, we conducted a CSA to determine which stimulus competed the most with skin picking. In Phase 3, we utilized a multielement with reversal design to compare the effectiveness of three presentation formats: (a) single stimulus (single), (b) multiple stimuli (multiple), and (c) alternating stimuli (alternating) in reducing levels of automatically maintained CB. We found noncontingent access to a single item was the most effective intervention to decrease skin picking. This study adds to the literature on reducing CB in children with ASD by incorporating a CSA before the evaluation of different formats of delivering competing stimuli, across extended duration session times.
Dapoxetine and the treatment of premature ejaculation

Background Premature ejaculation (PE) is the most common male sexual complaint. Off-label oral selective serotonin reuptake inhibitors (SSRIs) are commonly prescribed for the treatment of PE. Dapoxetine is a short-acting SSRI specifically designed for on-demand use. The objective of this communication is to summarize the clinical and physiological evidence regarding the role of the serotonergic pathway and specifically dapoxetine in the treatment of PE. Methods A PubMed search was conducted on articles reporting data on dapoxetine for the treatment of PE. Articles describing the pathophysiology and treatment options for PE were additionally included for review. Results The etiology of PE is multi-factorial in nature. There are many treatment options for PE such as psychological/behavioral therapy, topical anesthetic agents, phosphodiesterase type 5 (PDE-5) inhibitors, and tramadol hydrochloride. SSRIs play a major role in PE treatment. Animal and clinical studies in addition to its pharmacokinetic document dapoxetine’s clinical efficacy and safety for on-demand treatment of PE. Conclusions Dapoxetine demonstrates clinical efficacy and a favorable side effect profile. Dapoxetine is currently the oral drug of choice for on-demand treatment of PE.
Particle Acceleration and the Production of Relativistic Outflows in Advection-dominated Accretion Disks with Shocks

Relativistic outflows (jets) of matter are commonly observed from systems containing black holes. The strongest outflows occur in the radio-loud systems, in which the accretion disk is likely to have an advection-dominated structure. In these systems, it is clear that the binding energy of the accreting gas is emitted primarily in the form of particles rather than radiation. However, no comprehensive model for the disk structure and the associated outflows has yet been produced. In particular, none of the existing models establish a direct physical connection between the presence of the outflows and the action of a microphysical acceleration mechanism operating in the disk. In this paper we explore the possibility that the relativistic protons powering the jet are accelerated at a standing, centrifugally supported shock in the underlying accretion disk via the first-order Fermi mechanism. The theoretical analysis employed here parallels the early studies of cosmic-ray acceleration in supernova shock waves, and the particle acceleration and disk structure are treated in a coupled, self-consistent manner based on a rigorous mathematical approach. We find that first-order Fermi acceleration at standing shocks in advection-dominated disks proves to be a very efficient means for accelerating the jet particles. Using physical parameters appropriate for M87 and Sgr A*, we verify that the jet kinetic luminosities computed using our model agree with estimates based on observations of the sources.
Low Testosterone and the Association With Type 2 Diabetes

Purpose The purpose of this article is to describe androgen deficiency in men, the consequences of this clinically underdiagnosed endocrine disorder, and its relationship to the metabolic syndrome and the association with type 2 diabetes. An overview of prevalence, screening, diagnosis, treatment, and monitoring of male hypogonadism is presented. Method Established guidelines were used to provide definition, diagnosis, treatment, and monitoring information for male hypogonadism. A literature review from 1990 to 2007 revealed study findings that identify the link between low testosterone in men and the development of type 2 diabetes. The following databases were used to review and analyze the current literature: CINAHL, PubMed, and MEDLINE. Results An analysis of 26 studies was completed. The key findings in all of these studies show that there is a link between low levels of testosterone and an adverse metabolic profile (ie, obesity and insulin resistance). There is evidence that hypogonadism is associated with metabolic syndrome and type 2 diabetes in men. Conclusion Male hypogonadism is a clinical condition that affects a significant number of men in the United States and can affect up to 50% of men diagnosed with type 2 diabetes. The implications for diabetes educators are two-fold: first, there is a high prevalence of low testosterone in men with type 2 diabetes, and second, educators need to have a better understanding of this disease state to provide instructional guidance for their patients and to coordinate care with other clinicians.
Quantification of cardiolipin molecular species in Escherichia coli lipid extracts using liquid chromatography/electrospray ionization mass spectrometry.

RATIONALE Cardiolipin (CL), a glycerophospholipid containing four acyl chains, is found in most organisms including Gram-negative bacteria such as Escherichia coli. While CL composes only a fraction of the total glycerophospholipids, the four acyl chains lead to a large number of possible molecular species as defined by the total number of carbons and unsaturations in the acyl chains. Understanding the molecular composition of CL, and how it changes under different growth conditions, will aid in understanding the complex role of CL in E. coli. METHODS Normal-phase liquid chromatography/electrospray ionization mass spectrometry was used to quantify the CL molecular species (as defined by the total number of carbons:unsaturations in the acyl chains) in lipid extracts prepared from E. coli grown at 15 °C, 30 °C, 37 °C and 42 °C. RESULTS Fifty-six different CL species were identified as [M-2H](2-) ions in E. coli lipid extracts ranging from 60:0 to 72:4. CL species with an increased total number of unsaturations were more abundant in lipid extracts prepared from cells grown at 15 °C as compared to higher temperatures. CONCLUSIONS This work characterizes the CL composition of E. coli cells grown at various temperatures. By quantifying CL species at a molecular level we have illuminated the molecular complexity of the CL in this relatively simple model organism. This data will be useful for understanding CL function in E. coli and other organisms.
Global routing based on Steiner min-max trees

Global routing of multiterminal nets is studied. A novel global router is proposed; each step consists of finding a tree, called a Steiner min-max tree, that is Steiner tree with maximum-weight edge minimized (real vertices represent channels containing terminals of a net, Steiner vertices represent intermediate channels, and weights correspond to densities). An O (min(e loglog e, n/sup 2/)) time algorithm is proposed for obtaining a Steiner min-max tree in a weighted graph with e edges and n vertices. (This result should be contrasted with the NP-completeness of the traditional minimum-length Steiner tree problem). Experimental results on difficult examples, on randomly generated data, on master slice chips, and on benchmark examples from the Physical Design Workshop are included. >
Changing Characteristics of Drug Use Between Two Older Adult Cohorts: Small Sample Speculations on Baby Boomer Trends to Come

ABSTRACT This retrospective chart review of 2 cohorts of individuals 55 years and older (n = 116) suggests that the aging population entering addiction treatment today may no longer be a homogenous group of mostly alcohol-dependent individuals. Whereas the 1992 cohort is primarily alcoholic, the 2002 cohort of baby boomers included individuals with illicit drug use, prescription drug abuse and dependence, and co-occurring disorders.
Physical Activity in Childhood Asthma: Friend or Foe?

Physical activity has been considered as a double-edged sword for children with asthma. Children with asthma are recommended to participate in physical activities like their healthy nonasthmatic peers because regular physical activity positively affects psychological functioning, quality of life, morbidity, and aerobic fitness in children with asthma. However, uncontrolled asthma with ongoing exercise-induced bronchoconstriction may limit participation in sports, free play, and daily living. Observations also suggest that high-intensity exercise performed in cold air, seasonal allergens, pollutants, or respiratory virus infections may increase the risk for asthma in the highly active child. In contrast, a sedentary lifestyle has been highlighted as the explanation for the increased prevalence of asthma in the past decades. However, there is no consensus on whether a low level of physical activity increases the severity or risk of asthma. Use of asthma medications and good asthma control can make the conditions favorable for a physically active lifestyle and influence physical activity level and the level of aerobic fitness.
In vitro modeling of the HIV‐macrophage reservoir

Macrophages are recognized as a putative reservoir for HIV‐1, but whether HIV can establish latent infection in this cell type is not known. An in vitro model using long‐term cultured primary human monocyte‐derived macrophages (MDM) infected with an M‐tropic, enhanced green fluorescent protein (EGFP) tagged reporter virus was developed to test the hypothesis that HIV can establish a latent infection of this cell type. The EGFP‐IRES‐Nef cassette allowed detection of early gene transcription. The expression of GFP+ MDM was followed with time and the GFP‐ population was purified and analyzed for evidence of latent infection. Interestingly, in MDM cultures propagated for over two months, distinct subpopulations of infected GFP+ cells were observed and quantitated. In particular, infected MDM that displayed a high level of transcription, characterized as the GFP hi group, yet produced low levels of the late viral gene product, p24, increased with time and represented 10% of the GFP+ population in long‐term cultures. The high level production of early genes such as Nef, a protein that can facilitate viral immune escape, but low level of structural proteins such as p24 in the GFP hi population suggests that a subset of infected MDM can exhibit an alternative mode of replication. The GFP‐ MDM population obtained by a two‐step purification protocol using flow cytometry and laser ablation contained integrated provirus as assessed by Alu‐LTR real‐time PCR analyses. A subset of these, were replication competent as shown by their ability to express GFP and/or p24 antigen after reactivation with IL‐4.
Development of a Treatment Algorithm for Staphylococcal Pyoderma in the Emergency Department

The incidence of culture-confirmed methicillin-resistant Staphylococcus aureus (MRSA) has been increasingly reported in the community. The number of patients presenting with pyoderma that were not responding to first-line agents with a corresponding increase of MRSA isolates was seen in our Emergency Department (ED). After evaluation of the literature and review of recent cases, the infectious diseases team developed a treatment algorithm for use by ED personnel in order to identify patients that are more likely to have an MRSA infection and to facilitate the provision of effective therapy with the initial visit. Three months after the algorithm implementation, 12 of 13 patients seen in the ED with MRSA pyoderma had cultures done, and 10 were appropriately treated with non-beta-lactam agents on initial visit. Monitoring of infections seen in the ED can help clinicians identify trends in resistance that warrant a change in treatment guideline recommendations with the ultimate aim of improving patient care outcomes.
Diffuse optical tomography guided adaptive reconstruction in fluorescence molecular tomography

The adaptive finite element method (AFEM) is an effective way to retain enough resolution in selected regions while improving computational efficiency for reconstruction in fluorescent molecular tomography (FMT). In addition, background optical properties acquired by diffuse optical tomography (DOT) will improve the quality of reconstructed images. In this work, a DOT-guided adaptive reconstruction method (DGARM) is proposed, in which DOT is introduced into an adaptive reconstruction framework of FMT. Besides being used as functional a priori information in the forward modeling, the reconstructed local absorption coefficients in DOT are also used to form internal structural a priori information, which is further used to identify regions of interest (ROIs) in the mesh refinement of the adaptive procedure. Because optical properties are recovered before the formulation of FMT, a linear relationship is established between the fluorescent field and boundary measurements. We implemented numerical simulations and physical experiments to evaluate the performance of the algorithm. Compared with the strategies of uniform meshing with DOT and AFEM without DOT, DGAM improves localization accuracy of the reconstruction of fluorescence inclusion.
A Markov chain-based yield formula for VLSI fault-tolerant chips

A yield calculation method for the yield formula of fault-tolerant VLSI chips that improves existing methods and combines generalities, ease of computation, and predictability in approximation levels is presented. The method is concerned with the evaluation of the probability that a chip is acceptable given n defects. This is accomplished by introducing a Markov chain model in which each state represents an operating chip configuration, and the state transitions take place in the presence of manufacturing defects. Results from the comparison of this method to a method for memory chip yield evaluation, a method for the M-out-of-N yield problem evaluation, and a method for the square grid chip yield evaluation are presented. >
Obesity And Hyperbolic Discounting: An Experimental Analysis

Behavioral economists maintain that addictions such as alcoholism, smoking and over-eating represent examples of present-bias in decision making that is fundamentally irrational. In this article, we develop a model of present bias and apparently hyperbolic discounting that is fully consistent with rational behavior. We construct an experiment to test our hypothesis and to determine whether discount rates differ for individuals who engage in behaviors that could endanger their health. Our results show that discount functions are quasi-hyperbolic in shape, and that obesity and drinking are positively related to the discount rate. Anti-obesity policy, therefore, would be best directed to informing individuals as to the long-term implications of short-term gratification, rather than taxing foods directly.
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains.

RATIONALE The hypothesis that dissociation energies can serve as a predictor of observability of b- and y-peaks is tested for seven hexapeptides. If the hypothesis holds true for large classes of peptides, one would be able to improve the scoring accuracy of peptide identification tools by excluding theoretical peaks that cannot be observed in practical product ion spectra due to various physical, chemical or thermodynamic considerations. METHODS Product ion m/z spectra of hexapeptides AAAAAA, AAAFAA, AAAVAA, AAFAAA, AAVAAA, AAFFAA and AAVVAA have been acquired on a Finnigan LTQ XL mass spectrometer in the collision-induced dissociation (CID) activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35%. Dissociation energies were calculated for all fragmentation channels leading to b- and y-fragments at the TPSS/6-31G(d,p) level of the density functional theory. RESULTS It was demonstrated that the m/z peaks observed in the product ion spectra correspond to the fragmentation channels with dissociation energies below a certain threshold value. However, there is no direct correlation between the most intense m/z peaks and the lowest dissociation energies. Using the dissociation energies, it was predicted that out of 63 theoretically possible peaks in the b- and y-series of the seven hexapeptides, 19 should not be observable in practical spectra. In the experiments, 24 peaks were not observed, including all 19 predicted. CONCLUSIONS Dissociation energies alone are not sufficient for predicting ion intensity relationships in product ion m/z spectra. Nevertheless, the present data suggest that dissociation energies appear to be good predictors of observability of b- and y-peaks and potentially very useful for filtering theoretical peaks of each candidate peptide in peptide identification tools. Published 2012. This article is a US Government work and is in the public domain in the USA.
Parents of Children Newly Diagnosed With Type 1 Diabetes: Experiences With Social Support and Family Management

Purpose The purpose of this mixed-methods descriptive study with parents of children newly diagnosed with type 1 diabetes was to explore their experiences with peer social support following the Social Support to Empower Parents (STEP) intervention and the usefulness of the Family Management Measure (FaMM) in this population. Methods Parents who were in the experimental arm of STEP were recruited. Qualitative interviews were conducted (n = 21), and 11 parents completed the FaMM, a quantitative family-functioning measure. Qualitative content data analysis was conducted and compared to the descriptive measure analysis. Findings Three themes were identified: availability, practical tips, and common ground. Five FaMM subscales were reliable (α > .80) in this small sample. Conclusions The findings illustrate that the STEP intervention is helpful, providing the participants with emotional, affirmational, and informational social support. The use of the FaMM is a first step in assessing family management in families with children with type 1 diabetes.
Properties of isotope patterns and their utility for peptide identification in large-scale proteomic experiments.

RATIONALE In proteomic experiments, isotope patterns are routinely generated for all detected peptides. While this pattern is determined by peptide composition, it has not been evaluated as a parameter that can help in the process of peptide identification. METHODS First, we investigated how the relative isotope abundance (RIA) accuracy in proteomic data sets depends on the spectral intensity, resolution, and the number of mass spectrometry (MS) 1 scans, using an Orbitrap Velos mass spectrometer. Next, we explored the discriminatory power of isotope patterns in the context of proteome analyses of various complexities, either alone or in combination with a Mascot database search. Finally, we provide a theoretical framework for the required accuracies of both peptide mass and RIA for peptide identification. RESULTS We demonstrate that the RIA error obtained in routine proteome analyses is 4-5%, and that this is only modestly influenced by spectral intensity, resolution, and the number of MS1 scans. While RIA alone has no discriminatory power, in a Mascot search isotope patterns can distinguish top scoring hits from runner-up hits in 70-95% of cases. Our theoretical approach shows that RIA accuracy needs to be ~0.2% in order to uniquely identify peptides in full proteomes. CONCLUSIONS Our results demonstrate that isotope patterns can have discriminatory power when used in combination with a classical database search. Inclusion of this parameter in proteomic workflows may help to increase confidence in peptide identification, but in practical terms this will be limited to small proteomes.
Numerical study of the influence of the shell structure of the crystalline lens on the refractive properties of the human eye

In this paper, the numerical model of the refractive properties of the human eye is given. A special account is given of the laminated structure of the crystalline lens. The crystalline lens is presented in the form of hundreds of shells with rotational symmetry, and with the refractive index constant within each shell. The shells have the form of two semi‐ellipsoids joined along the equator. The refractive index increases from the cortical shell to the inner one, according to the exponential dependency. The cornea, approximated by two ellipsoidal surfaces, is added in front of the crystalline lens. A ray‐tracing procedure is applied to study the refractive properties of such a system: refractive power, spherical aberration and energy distribution. The optical properties of the given model are analysed by changing some parameters such as refractive index profile and number of shells. Calculations show that the gradient of the refractive index inside the crystalline lens results in the generation of many focal planes in such an optical system.