Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiation of human immunodeficiency virus type 1 (HIV-1) infections with HIV-2-cross-reacting antibody from mixed infections with HIV-1 and HIV-2 by serological absorption test

The interpretation of dual seroreactivity with human immunodeficiency virus type 1 (HIV-1) and HIV-2 in blood samples is a serious problem facing AIDS researchers worldwide. Some samples of sera from HIV-1-infected patients showed a serological cross-reaction with HIV-2, causing confusion regarding the serodiagnosis. Therefore, we tried to differentiate these serum samples from those containing real mixed infections with both types of virus. Sera from patients with HIV-1 infections with HIV-2 cross-reacting antibody in Japan were distinguished from sera from patients with mixed infections with HIV-1 and HIV-2 in West Africa by our serological cross-absorption test, which proved to be highly specific and useful for serodiagnosis.
Comparing Like with Like: The Power of Knowing Where You Are

Magnetic resonance imaging can now provide human brain images of structure, function, and connectivity with isotropic voxels smaller than one millimeter, and thus much smaller than the cortical thickness. This resolution, achievable in a scan time of less than 1 h, enables visualization of myeloarchitectural layer structure, intracortical variations in functional activity--recorded in changes in blood oxygenation level dependent signal or cerebral blood volume CBV--and intracortical axonal orientational structure via diffusion-weighted magnetic resonance imaging. While recent improvements in radiofrequency receiver coils now enable excellent image data to be obtained at 3T, scanning at the ultra-high field of 7 T offers further gains in signal-to-noise ratio and speed of image acquisition, with a structural image resolution of about 300 μm. These improvements throw into sharp question the strategies that have become conventional for the analysis of functional imaging data, especially the practice of spatial smoothing of raw functional data before further analysis. Creation of a native cortical map for each human subject that provides a reliable individual parcellation into cortical areas related to Brodmann Areas enables a strikingly different approach to functional image analysis. This proposed approach involves surface registration of the cortices of groups of subjects using maps of the longitudinal relaxation time T1 as an index of myelination, and methods for inferring statistical significance that do not entail spatial smoothing. The outcome should be a far more precise comparison of like-with-like cortical areas across subjects, with the potential to greatly increase experimental power, to discriminate activity in neighboring cortical areas, and to enable correlation of function and connectivity with specific cytoarchitecture. Such analyses should enable a far more convincing modeling of brain mechanisms than current graph-based methods that require gross over-simplification of brain activity patterns in order to be computationally tractable.
Subsemigroups of Cancellative Amenable Semigroups

We generalize a theorem of Frey by giving sufficient conditions for a subsemigroup T of a cancellative left amenable semigroup S to be left amenable. In particular, we show that if S is left amenable and T does not contain a free subsemigroup on two generators, then T is left amenable as well.
Intraseasonal Variability of the Saharan Heat Low and Its Link with Midlatitudes

Abstract The Saharan heat low (SHL) is thought to be a key feature of the West African monsoon, and its variations during the summer season have not yet been systematically assessed. To characterize the intraseasonal variations of the SHL, real and complex empirical orthogonal function analyses were applied to the 850-hPa potential temperature field over northern Africa and the Mediterranean, using NCEP–Department of Energy (DOE) Atmospheric Model Intercomparison Project (AMIP-II) reanalysis results. A robust quasi-propagative mode was highlighted over North Africa and the Mediterranean. This mode consists of two phases. The west phase corresponds to a maximum temperature over the coast of Morocco–Mauritania, propagating southwestward, and a minimum between Libya and Sicily, propagating southeastward. The east phase corresponds to the opposite temperature structure, which propagates as in the west phase. A lag-composite analysis revealed that this SHL mode was preceded by large-scale, midlatitude, intrase.
Hypothesis Testing for Complex Agents

As agents approach animal-like complexity, evaluating them becomes as difficult as evaluating animals. This paper describes the application of techniques for characterizing animal behavior to the evaluation of complex agents. We describe the conditions that lead to the behavioral variability that requires experimental methods. We then review the state of the art in psychological experimental design and analysis, and show its application to complex agents. We also discuss a specific methodological concern of agent research: how the robots versus simulations debate interacts with statistical evaluation. Finally, we make a specific proposal for facilitating the use of scientific method. We propose the creation of a web site that functions as a repository for platforms suitable for statistical testing, for results determined on those platforms, and for the agents that have generated those results.
Variability of Visual Responses of Superior Colliculus Neurons Depends on Stimulus Velocity

Visually responding neurons in the superficial, retinorecipient layers of the cat superior colliculus receive input from two primarily parallel information processing channels, Y and W, which is reflected in their velocity response profiles. We quantified the time-dependent variability of responses of these neurons to stimuli moving with different velocities by Fano factor (FF) calculated in discrete time windows. The FF for cells responding to low-velocity stimuli, thus receiving W inputs, increased with the increase in the firing rate. In contrast, the dynamics of activity of the cells responding to fast moving stimuli, processed by Y pathway, correlated negatively with FF whether the response was excitatory or suppressive. These observations were tested against several types of surrogate data. Whereas Poisson description failed to reproduce the variability of all collicular responses, the inclusion of secondary structure to the generating point process recovered most of the observed features of responses to fast moving stimuli. Neither model could reproduce the variability of low-velocity responses, which suggests that, in this case, more complex time dependencies need to be taken into account. Our results indicate that Y and W channels may differ in reliability of responses to visual stimulation. Apart from previously reported morphological and physiological differences of the cells belonging to Y and W channels, this is a new feature distinguishing these two pathways.
Limited potential of school textbooks to prevent tobacco use among students grade 1–9 across multiple developing countries: a content analysis study

Objective To evaluate the content of school textbooks as a tool to prevent tobacco use in developing countries. Design Content analysis was used to evaluate if the textbooks incorporated the following five core components recommended by the WHO: (1) consequences of tobacco use; (2) social norms; (3) reasons to use tobacco; (4) social influences and (5) resistance and life skills. Setting Nine developing countries: Bangladesh, Cambodia, Laos, Nepal, Sri Lanka, Benin, Ghana, Niger and Zambia. Textbooks analysed Of 474 textbooks for primary and junior secondary schools in nine developing countries, 41 were selected which contained descriptions about tobacco use prevention. Results Of the 41 textbooks, the consequences of tobacco use component was covered in 30 textbooks (73.2%) and the social norms component was covered in 19 (46.3%). The other three components were described in less than 20% of the textbooks. Conclusions A rather limited number of school textbooks in developing countries contained descriptions of prevention of tobacco use, but they did not fully cover the core components for tobacco use prevention. The chance of tobacco prevention education should be seized by improving the content of school textbooks.
Acute right ventricular dilatation in response to ischemia significantly impairs left ventricular systolic performance.

BACKGROUND Right ventricular (RV) dilatation that occurs as a consequence of RV infarction is thought to produce hemodynamic instability by reducing left ventricular (LV) preload and compliance. We hypothesized that these geometric changes may also adversely affect LV systolic performance. METHODS AND RESULTS Twelve 40-kg pigs were studied. Integrated conductance catheters and micromanometers were placed in both the LV and RV to allow simultaneous recordings of pressure and volume and derivation of indices of contractile function. RV ischemia was induced by balloon occlusion of the proximal right coronary artery (RCA) under 3 conditions: 1) with the pericardium intact, 2) with the pericardium intact and inotropic support, and 3) with the pericardium wide open. With an intact pericardium, RCA occlusion produced a decrease in LV end-diastolic volume associated with a marked decline in the contractile function. With the pericardium open, the same ischemic insult resulted in both LV and RV dilatation, which produced a significantly smaller negative effect on cardiac output (P=0.03), LV systolic pressure (P=0.02), LV preload-recruitable stroke work (P<0. 01), and LV end-systolic pressure-volume relations (P<0.01). Similarly, administration of dobutamine during RCA occlusion decreased the ventricular volume changes and produced a relative improvement in LV contractile performance. CONCLUSIONS The hemodynamic compromise seen in association with acute RV dilatation within an intact pericardium is partly attributable to impaired LV systolic performance and cannot be wholly ascribed to changes in LV preload or compliance.
Upconversion Nanoparticle-Based Förster Resonance Energy Transfer for Detecting DNA Methylation

Aberrant methylation of a crucial CpG island is the main mechanism for the inactivation of CDKN2A in the early stages of carcinogenesis. Therefore, the detection of DNA methylation with high sensitivity and specificity is important, and various detection methods have been developed. Recently, upconversion nanoparticles (UCNPs) have been found to display a high signal-to-noise ratio and no photobleaching, making them useful for diagnostic applications. In this pilot study, we applied UCNPs to the detection of CDKN2A methylation and evaluated the feasibility of this system for use in molecular diagnostics. DNA PCR was performed using biotinylated primers, and the PCR amplicon was then intercalated with SYTOX Orange dye, followed by incubation with streptavidin-conjugated UCNPs. Fluorescence detection of the Förster resonance energy transfer (FRET) of the UCNPs (MS-UC-FRET) was then performed, and the results were compared to those from real-time PCR (RQ-PCR) and pyrosequencing. Detection by MS-UC-FRET was more sensitive than that by either RQ-PCR or pyrosequencing. Our results confirmed the success of our MS-UC-FRET system for detecting DNA methylation and demonstrated the potential application of this system in molecular diagnostics.
Stochastic Variational Inference for the HDP-HMM

We derive a variational inference algorithm for the HDP-HMM based on the two-level stick breaking construction. This construction has previously been applied to the hierarchical Dirichlet processes (HDP) for mixed membership models, allowing for efficient handling of the coupled weight parameters. However, the same algorithm is not directly applicable to HDP-based infinite hidden Markov models (HDP-HMM) because of extra sequential dependencies in the Markov chain. In this paper we provide a solution to this problem by deriving a variational inference algorithm for the HDP-HMM, as well as its stochastic extension, for which all parameter updates are in closed form. We apply our algorithm to sequential text analysis and audio signal analysis, comparing our results with the beamsampled iHMM, the parametric HMM, and other variational inference approximations.
Comparison of NEXRAD and Rain Gauge Precipitation Measurements in South Florida

The South Florida Water Management District (SFWMD) relies on a network of nearly 300 rain gauges in order to provide rainfall data for use in operations, modeling, water supply planning, and environmental projects. However, the prevalence of convective and tropical disturbances in South Florida during the wet season presents a challenge in that the current rain gauge network may not fully capture rain events that demonstrate high spatial variability. Next Generation Radar (NEXRAD) technology offers the advantage of providing a spatial account of rainfall, although the quality of radar-rainfall measurements remains largely unknown. The comparison of rainfall estimates from a gauge-adjusted, NEXRAD-based product developed by the OneRain Company with precipitation measurements from SFWMD rain gauges was performed for the Upper and Lower Kissimmee River Basins over a four-year period from 2002 to 2005. Overall, NEXRAD was found to underestimate rainfall with respect to the rain gauges for the study period, d.
Synaptic vesicle proteins and early endosomes in cultured hippocampal neurons: differential effects of Brefeldin A in axon and dendrites

The pathways of synaptic vesicle (SV) biogenesis and recycling are still poorly understood. We have studied the effects of Brefeldin A (BFA) on the distribution of several SV membrane proteins (synaptophysin, synaptotagmin, synaptobrevin, p29, SV2 and rab3A) and on endosomal markers to investigate the relationship between SVs and the membranes with which they interact in cultured hippocampal neurons developing in isolation. In these neurons, SV proteins are detected as punctate immunoreactivity that is concentrated in axons but is also present in perikarya and dendrites. In the same neurons, the transferrin receptor, a well established marker of early endosomes, is selectively concentrated in perikarya and dendrites. In the perikaryal- dendritic region, BFA induced a dramatic tubulation of transferrin receptors as well as a cotubulation of the bulk of synaptophysin. Synaptotagmin, synaptobrevin, p29 and SV2 immunoreactivities retained a primarily punctate distribution. No tubulation of rab3A was observed. In axons, BFA did not produce any obvious alteration of the distribution of SV proteins, nor of peroxidase- or Lucifer yellow- labeled early endosomes. The selective effect of BFA on dendritic membranes suggests the existence of functional differences between the endocytic systems in dendrites and axons. Cotubulation of transferrin receptors and synaptophysin in the perikaryal-dendritic region is consistent with a functional interconnection between the traffic of SV proteins and early endosomes. The heterogeneous effects of BFA on SV proteins in this cell region indicates that SV proteins are differentially sorted upon exit from the TGN and are coassembled into SVs at the cell periphery.
Probing the time-variation of the fine-structure constant: Results based on Si IV doublets from a UVES sample

We report a new constraint on the variation of the fine-structure constant based on the analysis of 15 Si IV doublets selected from a ESO-UVES sample. We find Δ α/α = (+0.15 ± 0.43) × 10 -5 over a redshift range of 1.59 ≤ z ≤ 2.92 which is consistent with no variation in α. This result represents a factor of three improvement on the constraint on Δα/α based on Si IV doublets compared to the published results in the literature. The alkali doublet method used here avoids the implicit assumptions used in the many-multiplet method that chemical and ionization inhomogeneities are negligible and isotopic abundances are close to the terrestrial value.
Oestrogen‐dependent tracing in the rat CNS after pseudorabies virus infection

This study examines the hypothesis that neuronal infectivity and the spreading of the pseudorabies virus (PRV) through the synapses in the central nervous system (CNS) are influenced by the oestrogen levels. The arcuate nucleus (ARC) and the subfornical organ (SFO) were chosen as models for analysis; the neurons in both structures possess oestrogen receptors and are mutually connected. A genetically engineered pseudorabies virus (Ba‐DupLac) was used as a transneuronal tract tracer. This virus is taken up preferably by axon terminals, and transported very specifically through the synapses in a retrograde manner. Ba‐DupLac was injected into the ARC of rats, followed by monitoring of the PRV‐immunoreactivity (PRV‐IR) in the SFO 72 h following inoculation. We found no PRV immunolabelling in the SFO of ovariectomized (OVX) rats, or in those OVX animals that received oestrogen shortly (4 h) before PRV infection (OVX + E 4 h). In contrast, in those OVX animals that received oestrogen 12 h before PRV infection (OVX + E 12 h), and also in intact control animals, PRV‐IR was demonstrated in the SFO in all cases. Surprisingly, a reverse labelling was observed in the OVX rats; PRV‐IR appeared in the pyriform cortex, whereas PRV‐IR could not be detected in the control and OVX + E 12 h animals. As far as we are aware, this is the first study to demonstrate that transneuronal PRV labelling depends on the effects of oestrogen on certain CNS structures and connections.
Late Cenozoic right‐lateral strike‐slip faulting in southern Tibet

Field observations collected during the Sino-French Himalaya-Tibet cooperation project (1980–1982) show that right-lateral faulting between southern and northern Tibet, roughly along the “chord” joining the eastern and western syntaxes of the Himalayan arc, is a major component of the active tectonics north of the Himalayas. Just north of the well developed rifts of southern Tibet, we studied three right-lateral, 100–200 km long, strike-slip faults forming an en echelon array along that chord. Evidence for earthquake surface breaks was found on each of these faults. For the M = 8, Beng Co (or Damxung) strike-slip earthquake of November 18, 1951, rupture parameters could be constrained to be ū = 8 ± 2 m and L = 90 km. Offset glacial and postglacial morphological markers (105 years and 104 years B.P.) imply displacement rates of the order of 1–2 cm/yr on the three faults. The en echelon fault zone appears to extend westward ≈2000 km across the plateau to the Karakorum fault and is thus referred to as the Karakorum-Jiali fault zone (KJFZ). Fast rates of slip on it and on faults along the northern rim of Tibet appear to contrast with the slower rates of deformations in the interior of the plateau. Our estimates of slip rates on the strike-slip and normal faults of southeastern Tibet suggest that eastward extrusion of North Tibet between the right-lateral KJFZ and the left-lateral Altyn Tagh and Kun Lun faults absorbs at least 30% of the present convergence between India and Asia. We propose an instantaneous velocity model of the active tectonics of Asia compatible with such faulting rates and geometries. Evidence for Tertiary right-lateral strike-slip movements in southern Tibet and around the eastern syntaxis of the Himalayas is also found in the structural record. Offsets of various large-scale geological features imply that these movements have been large.
Crowding Out Informal Care? Evidence from a Field Experiment in Germany

This paper evaluates the effects of a professionally assisted consumer-directed program (Personal Budgets) compared to the standard home care programs of the German long-term care insurance. The evaluation makes use of a long-run social experiment at seven different sites with a random assignment into a treatment group receiving personal budgets and a control group in standard home care programs, i.e. an in-kind benefit (agency care) and cash payments. Compared to agency care personal budgets yield better care outcomes with regard to the overall support of formal and informal caregivers. In contrast, personal budgets do not improve care outcomes compared to the much less generous cash payments due to a strong crowding out of informal by formal care.
N-boson time-dependent problem: A reformulation with stochastic wave functions

act numerical calculation of the properties of the gas is available, using the quantum Monte Carlo techniques, based on Feynman path integral formulation of quantum mechanics @11,12#. The aim of this paper is to present an alternative exact and numerically tractable solution to the problem of the interacting Bose gas, a method not restricted to the case of thermal equilibrium but which allows for the study of the dynamics of the gas. The method is based on a stochastic evolution of Hartree states, in which all atoms have the same wave function, these Hartree states being either Fock states ~fixed number of atoms! or coherent states. As a particular case of this solution with coherent states, we recover the stochastic scheme corresponding to the evolution of the density operator of the system in the positive P representation @13‐15#. This scheme, which has been applied already to study the dynamics of Bose-Einstein condensates in @16,17#, is known to lead to strong unstability problems, which fortunately do not show up for other implementations of the present method. The outline of the paper is the following: In Sec. II, we present the stochastic formulation of the evolution of these Hartree states which, after average over the stochastic component, leads to the exact evolution. Section III is devoted to the presentation of two particular schemes implementing this stochastic formulation. We first present a ‘‘simple’’ scheme, which minimizes the statistical spread of the calculated N-atom density matrix. We also investigate a more elaborate scheme in which the trace of the calculated density matrix remains strictly constant in the evolution. With this constraint, we recover for coherent states the known stochastic simulation associated with the positive P representation @16#. Finally we investigate in Secs. IV and V two examples, a two-mode model system and a one-dimensional Bose gas, respectively. These examples illustrate the accuracy and the limitations of the method. Generally speaking we find that the ‘‘simple’’ scheme simulations are only limited by the computation power: the number of realizations needed for a good statistical accuracy increases exponentially with time for the simulation with Fock states. On the contrary the simulations with constant trace are subject to divergences of
Brain Morphology in Children with Epilepsy and ADHD

Background Attention deficit hyperactivity disorder (ADHD) is a common comorbidity of childhood epilepsy, but the neuroanatomical correlates of ADHD in epilepsy have yet to be comprehensively characterized. Methods Children with new and recent-onset epilepsy with (n = 18) and without (n = 36) ADHD, and healthy controls (n = 46) underwent high resolution MRI. Measures of cortical morphology (thickness, area, volume, curvature) and subcortical and cerebellar volumes were compared between the groups using the program FreeSurfer 5.1. Results Compared to the control group, children with epilepsy and ADHD exhibited diffuse bilateral thinning in the frontal, parietal and temporal lobes, with volume reductions in the brainstem and subcortical structures (bilateral caudate, left thalamus, right hippocampus). There were very few group differences across measures of cortical volume, area or curvature. Conclusions Children with epilepsy and comorbid ADHD exhibited a pattern of bilateral and widespread decreased cortical thickness as well as decreased volume of subcortical structures and brainstem. These anatomic abnormalities were evident early in the course of epilepsy suggesting the presence of antecedent neurodevelopmental changes, the course of which remains to be determined.