Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid density functional theory for π‐stacking interactions: Application to benzenes, pyridines, and DNA bases

The suitability of a hybrid density functional to qualitatively reproduce geometric and energetic details of parallel π‐stacked aromatic complexes is presented. The hybrid functional includes an ad hoc mixture of half the exact (HF) exchange with half of the uniform electron gas exchange, plus Lee, Yang, and Parr's expression for correlation energy. This functional, in combination with polarized, diffuse basis sets, gives a binding energy for the parallel‐displaced benzene dimer in good agreement with the best available high‐level calculations reported in the literature, and qualitatively reproduces the local MP2 potential energy surface of the parallel‐displaced benzene dimer. This method was further critically compared to high‐level calculations recently reported in the literature for a range of π‐stacked complexes, including monosubstituted benzene–benzene dimers, along with DNA and RNA bases, and generally agrees with MP2 and/or CCSD(T) results to within ±2 kJ mol−1. We also show that the resulting BH&H binding energy is closely related to the electron density in the intermolecular region. The net result is that the BH&H functional, presumably due to fortuitous cancellation of errors, provides a pragmatic, computationally efficient quantum mechanical tool for the study of large π‐stacked systems such as DNA. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 491–504, 2006
Analysis of Recurrent Networks of Pulse-Coupled Noisy Neural Oscillators

Synchronization of neural oscillators has been well studied by both theorists and experimentalists. However, realistic details are often disregarded for tractability. Here, we consider a recurrent network of pulse-coupled neural oscillators since synaptic communication is often mediated by spikes. Neurons receive many stochastic inputs that have effects depending on the state of the neuron; thus, we incorporate phase-dependent (multiplicative) noise. Previous analysis of neural oscillators with additive noise (not necessarily weak) cannot be directly applied here because this results in analytically intractable equations that possibly have singularities. However, assuming weak coupling and weak noise, we accurately and analytically characterize various phenomena by a linear stability analysis around an asymptotic steady-state density approximation. Depending on the phase resetting curve, the system can undergo a supercritical Andronov-Hopf bifurcation as the recurrent coupling strength of the oscillator is increased, leading to synchronous and oscillatory population activity. The analysis is extended to include recurrent input through synapses with kinetics—it generally stabilizes the incoherent state. Moreover, input via synapses can uncover a bifurcation that does not exist with instantaneous recurrent input. The analysis is further generalized to recurrent input that is a smooth function of the population firing rate. The results are applied to a closed-loop system of neural oscillators that receive feedback mediated by a noisy population of excitable integrate-and-fire neurons. Our results extend the power of perturbation methods for dealing with equations that, a priori, appear intractable.
Nanostructured Metal Aggregate-Assisted Lasing in Rhodamine 6G Solutions

We report on the experimental demonstration of considerable lowering of stimulated luminescence (lasing) threshold in R6G laser dye solution doped with metal agglomerates (Ag, Al, Ni) upon second harmonic of Nd:YAG-laser illumination. Due to strong structural coupling between individual nanoparticles, they may form fractal agglomerates providing an extreme optical pump-field enhancement near their complicated surface. For the first time, we have observed more than twofold increase in lasing efficiency of metal aggregated dye solution as compared to non-agglomerated monomeric metal nanocolloids. No random laser manifestation or surface plasmon-polariton resonances excitations were observed.
Thrombocytosis in adults: analysis of 777 patients

Abstract. A total of 777 patients with thrombocytosis, defined as a platelet count of > 500 × 109 l−1, seen in a University hospital over a 1‐year period, were studied prospectively for aetiology. The most frequent causes of thrombocytosis were infection (21.9%), rebound thrombocytosis (19.4%), tissue damage (17.9%), chronic inflammatory disorders (13.1%) and malignancy (5.9%). Thrombocytosis associated with multiple causative factors, occurring simultaneously, was seen in 6.1 % of cases. Thrombocytosis of ≥ 1 million × 109 l−1 was found most frequently in patients with multiple aetiological factors occurring at the same time, in myeloproliferative disorders, or in postsplenectomy patients.
Hope Theory: A Framework for Understanding Suicidal Action

This article examines C. R. Snyder's (1994 2000a) theory of hope and its application for understanding suicide. Strengths, weaknesses, and gaps in the suicide literature are outlined, and A. T. Beck's theory of hopelessness is compared with Snyder's hope theory. Hope theory constructs are used to examine the relationship of suicide to hope/hopelessness, goals, pathways thinking, and agency thinking. This critical review is intended to broaden our theoretical understanding of suicide and is meant to form the basis for future empirical investigation of suicide-related behavior using the framework of hope theory. Implications for suicide prevention programs and approaches to treating suicidal individuals are outlined.
Predictive Value of Plasma Prolactin Level in the Differential Diagnosis between Limbic Seizures and Psychotic Behavioral Disorders

This study evaluates the usefulness of serum prolactin (PRL) levels in predicting the disturbed behavior related to either epileptic or psychotic disorders. Data were collected from 112 patients consecutively admitted to Neurology and Psychiatric Departments, in a 12-month period. Those patients included 53 epileptic patients (3 1 had grand ma1 epilepsy “GM” and 22 had complex partial seizures “CPS”) and 59psychotic patients (1 9 had Electro convulsive therapy “ECT” and 40 had no ECT). Plasma PRL concentration (Pl) was assessed 20 minutes after the seizures or the abnormal behavior episodes and a second PRL level (P2) was 24 hours after (Pl) as a baseline level. Using the criteria of two-fold elevation of PRL levels above the baseline value correctly differentiated behavioral disorders due to either epilepsy or psychotic disorders. The criteria was positive in 2 1(67.7%) of 3 1 patients had GME, in 1 1 (50%) of 22 patients had CPS of temporal lobe origin (Limbic epilepsy), in 19(100%) of 19 psychotic patients received ECT, and in only 4 (10%) of 40 psychotic patients received no ECT. It could be concluded that two-fold increase of PRL level above the baseline has a highly predictive value in differentiating behavioral disorder due to epilepsy versus psychotic disorders. Also, this study suggests to perform further studies using one fold epileptic and psychotic behavioral disorders.
CD30: expression and function in health and disease.

CD30 was originally described as a marker of Hodgkin's and Reed-Sternberg cells in Hodgkin's lymphoma. Cloning and characterization of cDNAs encoding CD30 and its ligand (CD30L) established these proteins as members of the tumor necrosis factor receptor (TNFR) and tumor necrosis factor (TNF) superfamilies, respectively. Expression of CD30 is mostly restricted to virus-infected lymphocytes, neoplasms of lymphoid origin and a subset of activated T cells which produce Th2-type cytokines. The ligand is present on activated T cells, resting B cells, granulocytes, and the medulla of the thymus (epithelial cells and Hassal's corpuscles) as well as in various leukemia cells. The biological function of CD30 is pleiotropic but has come to be understood in the context of co-stimulatory signals. Signal transduction of CD30 utilizes signal transducers, TNFR-associated factors (TRAF1, 2, 3 and 5), which are shared by other TNFR family members. Mechanisms of signal transduction leading to diverse biological functions remain to be elucidated.
Antigen Binding Properties of Purified Immunoglobulin A and Reconstituted Secretory Immunoglobulin A Antibodies*

The hybridoma cell line ZAC3 expresses Vibrio cholerae lipopolysaccharide (LPS)-specific mouse IgA molecules as a heterogeneous population of monomeric (IgAm), dimeric (IgAd), and polymeric (IgAp) forms. We describe a gentle method combining ultrafiltration, ion-exchange chromatography, and size exclusion chromatography for the simultaneous and qualitative separation of the three molecular forms. Milligram quantities of purified IgA molecules were recovered allowing for direct comparison of the biological properties of the three forms. LPS binding specificity was tested after purification; IgAd and IgAp were found to bind strongly to LPS whereas IgAm did not. Secretory IgA (sIgA) could be reconstituted in vitro by combining recombinant secretory component (rSC) and purified IgAd or IgAp, but not IgAm. Surface plasmon resonance-based binding experiments using LPS monolayers indicated that purified reconstituted sIgA and IgA molecules recognize LPS with identical affinity (KA 1.0 × 108 M−1). Thus, this very sensitive assay provides the first evidence that the function of SC in sIgA complex is not to modify the affinity for the antigen. KA falls to 6.6 × 105 M−1 when measured by calorimetry using detergent-solubilized LPS and IgA, suggesting that the LPS environment is critical for recognition by the antibody.
A retrospective analysis of reported errata in five leading medical journals in 2012

Background Although medical publications are frequently used as the source of information, the prevalence of errata remains unclear. The objective of this study was to examine peer-review and publication processes of medical journals as well as to determine the occurrence of reported errata in medical journals and timeliness in identifying and correcting errata. Methods Five medical journals, New England Journal of Medicine, Annals of Internal Medicine, British Medical Journal, Journal of American Medical Association, and Lancet, were evaluated. The characteristics of these journals were obtained from editors’ survey. All these journals report errata noted in their prior publications. We retrospectively analyzed all errata reported from January 1, 2012, to December 31, 2012. The mean number of reported errata per issue, the most common errata, and the mean time to report errata were calculated. Results The journals had high impact factors (14–51), received 3,200 to more than 15,000 submissions in 2012, and utilized two or more external reviewers and usually two or more editors for any accepted articles. All the journals edited the accepted articles, including references, figures, and tables for style. A mean of 1.3 articles with ≥1 errata was reported per issue (a total of 306 articles with errata in 226 issues). Errata in author's information, numeric errata, and errata in the figures and tables were the most common errata. The mean time to report the errata was 122 days. Conclusion The high-impact journals, with extensive pre-publication review, reported relatively few errata per issue. The delay in reporting errata needs further exploration.
Neutron scattering by rough surfaces at grazing incidence.

There are a number of calculations in the literature of the effect of statistical surface roughness on the specular and diffuse scattering of neutrons and x rays which impinge on surfaces at grazing incidence. These calculations do not agree with one another and in some cases lack internal consistency. In this paper I show that these discrepancies can be resolved within the distorted-wave Born approximation. The result I obtain for the specular reflectivity is the widely used version of Nevot and Croce, while that for the diffuse scattering is the same as a recent calculation by Sinha, Sirota, Garoff, and Stanley. The approximations made by Nevot and Croce are clearly revealed by the distorted-wave Born approximation. A simple numerical algorithm is proposed for the calculation of diffuse scattering from a surface whose roughness is self-affine, and the form of the scattering is calculated for a range of parameters within this model. The calculation of diffusion scattering is extended in this paper to the case of films with rough surfaces. Correlation between roughness at the two film surfaces is considered and shown to be important for the description of neutron reflectivity data obtained with a thin film of titanium deposited onmore » a sapphire substrate. « less
Embedding the Rendezvous Point (RP) Address in an IPv6 Multicast Address

This memo defines an address allocation policy in which the address of the Rendezvous Point (RP) is encoded in an IPv6 multicast group address. For Protocol Independent Multicast - Sparse Mode (PIM-SM), this can be seen as a specification of a group-to-RP mapping mechanism. This allows an easy deployment of scalable inter-domain multicast and simplifies the intra-domain multicast configuration as well. This memo updates the addressing format presented in RFC 3306. [STANDARDS-TRACK]
IGF-1 Induces Foam Cell Formation in Rat Glomerular Mesangial Cells

When rat glomerular mesangial cells (MCs) are cultured with IGF-1 they accumulate intracellular lipid and take on foam cell morphology. These changes were characterized by electron microscopy and Nile red staining. To define the mechanism responsible for IGF-1-mediated lipid uptake, MCs were evaluated for endocytosis, scavenger receptor activity, and receptor-mediated uptake by the LDL receptor. Lipid accumulation was markedly increased when MCs were cultured with IGF. The primary route of uptake was through enhanced en-docytosis. Lipid-laden MCs have decreased phagocytic capacity and disrupted cytoskeletons. These data show that IGF-1 induces MC to take on a foam cell morphology and that lipid-laden MCs have impaired phagocytic function.
The syndrome of lung hemorrhage and nephritis is usually an ANCA-associated condition.

BACKGROUND In the absence of evidence of arteritis or Wegener's granulomatosis, the syndrome of lung hemorrhage and nephritis has been commonly associated with anti-glomerular basement membrane (GBM) antibodies. However, it has been increasingly recognized that many cases are associated with antineutrophil cytoplasmic antibodies (ANCAs). OBJECTIVE To review available clinical and pathologic findings to determine the diseases accounting for lung hemorrhage and nephritis. METHODS We studied the records of 750 patients from whom serum samples were sent to our laboratory for anti-GBM antibody assays between 1981 and 1993 and found 88 patients with evidence of lung hemorrhage and nephritis. Serum samples were retested, using current methods, for anti-GBM antibodies (against noncollagenous 1 domain of the alpha 3 chain of type IV collagen) and for antibodies to proteinase 3 and myeloperoxidase--the two types of ANCA of diagnostic value. RESULTS Of 88 patients with evidence of lung hemorrhage and nephritis, 48 had ANCAs, six had anti-GBM antibodies, and seven had both. In 48 patients with ANCAs, the pathologic findings that accounted for the pulmonary renal syndrome were pauci-immune necrotizing and crescentic glomerulonephritis and pulmonary capillaritis. Only eight had convincing evidence (during life) of Wegener's granulomatosis and only one other had documented arteritis. In 27 patients without ANCAs or anti-GBM antibodies, a variety of unrelated renal and pulmonary diseases were found. CONCLUSIONS The largest group of patients who present with the syndrome of lung hemorrhage and nephritis have ANCAs and not anti-GMB antibodies. Appropriate tests for antibodies to proteinase 3, antibodies to myeloperoxidase, and anti-GBM antibodies provide reliable guides for making a diagnosis in patients with this pulmonary renal syndrome.
Diversity of thermophilic bacteria in milk assessed by culturing , PCR-DGGE , and 1 pyrosequencing 2 3

Diversity of thermophilic bacteria in milk assessed by culturing, PCR-DGGE, and 1 pyrosequencing 2 3 Elena Fernández 1 , Caio T. C. C. Rachid 2 , Tomasz Rychlik 1 , Ángel Alegría 1 , Raquel S. 4 Peixoto 2 , Susana Delgado 1 , and Baltasar Mayo 1 * 5 6 Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de 7 Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain 1 , and 8 Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal 9 do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, 10 Rio de Janeiro, RJ, Brazil 2 11 12
Diffusion-weighted MR imaging of cholesteatoma in pediatric and adult patients who have undergone middle ear surgery.

OBJECTIVE The aim of this prospective study was to determine the role of diffusion-weighted MR imaging combined with conventional MR imaging for the detection of residual or recurrent cholesteatoma in patients who have undergone middle ear surgery. SUBJECTS AND METHODS Twenty-two patients who had undergone resection of cholesteatoma were referred for MR imaging. MR imaging (1.5 T) was performed using a diffusion-weighted single-shot spin-echo echoplanar sequence, a proton density and T2-weighted double-echo turbo spin-echo sequence, and T1-weighted spin-echo sequences before and after IV injection of gadopentetate dimeglumine (0.1 mmol/kg of body weight). An experienced reviewer evaluated the diffusion-weighted MR images for the presence of a high-signal-intensity cholesteatoma. Imaging findings were correlated with findings from surgery in 17 patients and with findings from clinical follow-up examination in five patients. RESULTS Diffusion-weighted MR imaging combined with conventional MR imaging depicted 10 of 13 cholesteatomas (sensitivity, 77%). The three lesions that were missed were smaller than 5 mm. All the MR images of patients without cholesteatoma were correctly interpreted as showing negative findings for cholesteatoma (specificity, 100%). The positive predictive value and negative predictive value were 100% and 75%, respectively. CONCLUSION Diffusion-weighted MR imaging combined with conventional MR imaging can confirm residual or recurrent cholesteatoma in patients who have undergone middle ear surgery by showing a high-signal-intensity lesion. Because tumors smaller than 5 mm may be missed, a diffusion-weighted MR imaging study with negative findings does not exclude small residual or recurrent cholesteatoma.
Stereoacuity versus fixation disparity as indicators for vergence accuracy under prismatic stress

Background: Fixation disparity has been widely used as an indicator for vergence accuracy under prismatic stress. However, the targets used for measuring fixation disparity contain artificial features in that the fusional contours are thinned out. We considered that stereoacuity might be a preferable indicator of vergence accuracy, as stereo targets represent natural viewing conditions.
Do Clinical Parameters Predict First Planned Extubation Outcome in the Pediatric Intensive Care Unit?

Context: There is absence of evidence-based guidelines to determine extubation readiness in the pediatric intensive care unit (PICU). Objective: Evaluate our practice of determining extubation readiness based on physician judgment of preextubation ventilator settings, blood gas analysis, and other factors potentially affecting extubation outcome. Design: Prospective cohort study from August 2010 to April 2012. Setting: Academic, multidisciplinary PICU. Patients: A total of 319 PICU patients undergoing first planned extubation attempt. Interventions: None. Measurements: Determine the extubation success rate and evaluate factors potentially affecting extubation outcome. The PICU length of stay (LOS) and cost were also recorded. Subgroup analysis was performed based on days of mechanical ventilation (MV). Results: A total of 319 consecutive patients underwent first planned extubation attempt with a 91% success rate. Factors associated with extubation failure were the length of MV (P < .0001, odds ratio [OR] 2.20); age (P = .02, OR 0.54); preextubation steroids (P = .04, OR 2.40); and postextubation stridor (P < .01, OR 3.40). Ventilator settings and blood gas results had no association with extubation outcome with 1 exception, ventilator rates ≤ 8 were associated with extubation failure in patients with ≤1 day of MV. Extubation failure was associated with prolonged PICU LOS and excess cost, with failures staying 14 days longer (P < .0001) and costing 3.2 time more (P < .0001) than successes. Conclusions: Physician judgment to determine extubation readiness led to a first planned extubation success rate of 91%. Age and the length of MV were primary risk factors for failed extubation. In patients with ≤1 day of MV, our findings suggest that confidence in extubation readiness following weaning to low ventilator rates may not be justified. Furthermore, reliance on preextubation ventilator settings and blood gas results to determine extubation readiness may lead to unnecessary prolongation of MV, thereby increasing the PICU LOS and excess cost. These findings are hypothesis generating and require further study for confirmation.
The validity of visual observation to assess posture in a laboratory-simulated, manual material handling task.

A wide range of methods to evaluate posture in work situations relies on simple, unaided visual observation. In the present study the validity of visual observation to assess posture in a dynamic job was evaluated. Postural aspects were observed and recorded during a manual materials handling job simulated in a laboratory. The results from these observations, concerning gross body posture, torso flexion, arms and legs position, and load to be handled, were compared to the results obtained by direct opto-electronic recording. The agreement on a sample-to-sample basis (expressed by Cohen's kappa) was poor for the variables torso flexion (mean value for kappa = 0.38), position of arms (kappa = 0.43) and legs (kappa = 0.46) and load to be handled (kappa = 0.50) and acceptable only for the gross body posture (kappa = 0.79). Moreover, for each variable except gross body posture, the crude distributions of all observations and recordings across categories (irrespective of time) were significantly different. The results demonstrate that the observations are not valid. It is concluded that dynamic work situations require less simple, more time consuming methods (e.g., analyzing film or video records of the job) than a posture registration method based on direct visual observation.
The use of fluorescein diacetate and phenosafranine for determining viability of cultured plant cells.

Various stains were tested with suspension cell cultures of Nicotiana tabacum (tobacco), Oryza sativa (rice), Glycine max (soybean), Daucus carota (carrot) and Lycopersicon esculentum (tomato). A drop of the culture medium containing each dye was mixed with a drop of cells on a microscope slide and viewed after 5 min. The most suitable dyes tested were fluorescein diacetate for viable cells and phenosafranine for dead cells. These dyes stained specifically whether the cells were from cultures of different ages, of different species or if the cells had been treated in various, often toxic, ways. The viability of the cells was confirmed by observing cyclosis and plasmolysis, and whether the cells could grow further when cultured.