1,415 research outputs found
A computational framework to emulate the human perspective in flow cytometric data analysis
Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation.
<p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods.
<p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics
Opuntia in México: Identifying Priority Areas for Conserving Biodiversity in a Multi-Use Landscape
BACKGROUND: México is one of the world's centers of species diversity (richness) for Opuntia cacti. Yet, in spite of their economic and ecological importance, Opuntia species remain poorly studied and protected in México. Many of the species are sparsely but widely distributed across the landscape and are subject to a variety of human uses, so devising implementable conservation plans for them presents formidable difficulties. Multi-criteria analysis can be used to design a spatially coherent conservation area network while permitting sustainable human usage. METHODS AND FINDINGS: Species distribution models were created for 60 Opuntia species using MaxEnt. Targets of representation within conservation area networks were assigned at 100% for the geographically rarest species and 10% for the most common ones. Three different conservation plans were developed to represent the species within these networks using total area, shape, and connectivity as relevant criteria. Multi-criteria analysis and a metaheuristic adaptive tabu search algorithm were used to search for optimal solutions. The plans were built on the existing protected areas of México and prioritized additional areas for management for the persistence of Opuntia species. All plans required around one-third of México's total area to be prioritized for attention for Opuntia conservation, underscoring the implausibility of Opuntia conservation through traditional land reservation. Tabu search turned out to be both computationally tractable and easily implementable for search problems of this kind. CONCLUSIONS: Opuntia conservation in México require the management of large areas of land for multiple uses. The multi-criteria analyses identified priority areas and organized them in large contiguous blocks that can be effectively managed. A high level of connectivity was established among the prioritized areas resulting in the enhancement of possible modes of plant dispersal as well as only a small number of blocks that would be recommended for conservation management
Genetic Improvement of Rice for Multiple Stress Tolerance in Unfavorable Rainfed Ecology
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A Self-Consistent Model for Positronium Formation from Helium Atoms
The differential and total cross sections for electron capture by positrons
from helium atoms are calculated using a first-order distorted wave theory
satisfying the Coulomb boundary conditions. In this formalism a parametric
potential is used to describe the electron screening in a consistent and
realistic manner. The present procedure is self consistent because (i) it
satisfies the correct boundary conditions and post-prior symmetry, and (ii) the
potential and the electron binding energies appearing in the transition
amplitude are consistent with the wave functions describing the collision
system. The results are compared with the other theories and with the available
experimental measurements. At the considered range of collision energies, the
results agree reasonably well with recent experiments and theories.
[Note: This paper will be published on volume 42 of the Brazilian Journal of
Physics
Acquired constriction ring syndrome as a cause of inconsolable cry in a child: a case report
Acute constriction ring syndrome (ACRS) is a rare clinical condition characterized by formation of a circumferential constriction ring around an appendage or genitalia. Cases are mostly reported in infants and young children. Early recognition and a definitive treatment are of paramount importance in order to avoid irreversible ischemia and possible auto-amputation. We describe a case of a 14-month-old child presented to casualty with a history of refusal to feed and inconsolable cry. Parents noticed a recent swelling of left third toe. On careful examination the child was found to have an acquired constriction ring secondary to a tightly wrapped hair around left third toe. An urgent surgical decompression was done by the orthopaedic team with complete resolution of symptoms. We summarized the pathophysiology of ACRS underlining the need of awareness in treating physicians. The possible medico legal implications should be kept in mind bearing a suggested link with non-accidental injury
State-space Manifold and Rotating Black Holes
We study a class of fluctuating higher dimensional black hole configurations
obtained in string theory/ -theory compactifications. We explore the
intrinsic Riemannian geometric nature of Gaussian fluctuations arising from the
Hessian of the coarse graining entropy, defined over an ensemble of brane
microstates. It has been shown that the state-space geometry spanned by the set
of invariant parameters is non-degenerate, regular and has a negative scalar
curvature for the rotating Myers-Perry black holes, Kaluza-Klein black holes,
supersymmetric black holes, - configurations and the
associated BMPV black holes. Interestingly, these solutions demonstrate that
the principal components of the state-space metric tensor admit a positive
definite form, while the off diagonal components do not. Furthermore, the ratio
of diagonal components weakens relatively faster than the off diagonal
components, and thus they swiftly come into an equilibrium statistical
configuration. Novel aspects of the scaling property suggest that the
brane-brane statistical pair correlation functions divulge an asymmetric
nature, in comparison with the others. This approach indicates that all above
configurations are effectively attractive and stable, on an arbitrary
hyper-surface of the state-space manifolds. It is nevertheless noticed that
there exists an intriguing relationship between non-ideal inter-brane
statistical interactions and phase transitions. The ramifications thus
described are consistent with the existing picture of the microscopic CFTs. We
conclude with an extended discussion of the implications of this work for the
physics of black holes in string theory.Comment: 44 pages, Keywords: Rotating Black Holes; State-space Geometry;
Statistical Configurations, String Theory, M-Theory. PACS numbers: 04.70.-s
Physics of black holes; 04.70.Bw Classical black holes; 04.70.Dy Quantum
aspects of black holes, evaporation, thermodynamics; 04.50.Gh
Higher-dimensional black holes, black strings, and related objects. Edited
the bibliograph
Novel Cell- and Tissue-Based Assays for Detecting Misfolded and Aggregated Protein Accumulation Within Aggresomes and Inclusion Bodies
Aggresomes and related inclusion bodies appear to serve as storage depots for misfolded and aggregated proteins within cells, which can potentially be degraded by the autophagy pathway. A homogenous fluorescence-based assay was devised to detect aggregated proteins inside aggresomes and inclusion bodies within an authentic cellular context. The assay employs a novel red fluorescent molecular rotor dye, which is essentially nonfluorescent until it binds to structural features associated with the aggregated protein cargo. Aggresomes and related structures were generated within cultured cells using various potent, cell permeable, proteasome inhibitors: MG-132, lactacystin, epoxomicin and bortezomib, and then selectively detected with the fluorescent probe. Employing the probe in combination with various fluorescein-labeled primary antibodies facilitated co-localization of key components of the autophagy system (ubiquitin, p62, and LC3) with aggregated protein cargo by fluorescence microscopy. Furthermore, cytoplasmic aggregates were highlighted in SK-N-SH human neuroblastoma cells incubated with exogenously supplied amyloid beta peptide 1–42. SMER28, a small molecule modulator of autophagy acting via an mTOR-independent mechanism, prevented the accumulation of amyloid beta peptide within these cells. The described assay allows assessment of the effects of protein aggregation directly in cells, without resorting to the use of non-physiological protein mutations or genetically engineered cell lines. With minor modification, the assay was also adapted to the analysis of frozen or formalin-fixed, paraffin-embedded tissue sections, with demonstration of co-localization of aggregated cargo with β-amyloid and tau proteins in brain tissue sections from Alzheimer’s disease patients
Spectrum of clinical disease in a series of 135 hospitalised HIV-infected patients from north India
BACKGROUND: Literature on the spectrum of opportunistic disease in human immunodeficiency virus (HIV)-infected patients from developing countries is sparse. The objective of this study was to document the spectrum and determine the frequency of various opportunistic infections (OIs) and non-infectious opportunistic diseases, in hospitalised HIV-infected patients from north India. METHODS: One hundred and thirty five consecutive, HIV-infected patients (age 34 ± 10 years, females 17%) admitted to a tertiary care hospital in north India, for the evaluation and management of an OI or HIV-related disorder between January 2000 and July 2003, were studied. RESULTS: Fever (71%) and weight loss (65%) were the commonest presenting symptoms. Heterosexual transmission was the commonest mode of HIV-acquisition. Tuberculosis (TB) was the commonest OI (71%) followed by candidiasis (39.3%), Pneumocystis jiroveci pneumonia (PCP) (7.4%), cryptococcal meningitis and cerebral toxoplasmosis (3.7% each). Most of the cases of TB were disseminated (64%). Apart from other well-recognised OIs, two patients had visceral leishmaniasis. Two cases of HIV-associated lymphoma were encountered. CD4+ cell counts were done in 109 patients. Majority of the patients (82.6%) had CD4+ counts <200 cells/μL. Fifty patients (46%) had CD4+ counts <50 cells/μL. Only 50 patients (37%) received antiretroviral therapy. Twenty one patients (16%) died during hospital stay. All but one deaths were due to TB (16 patients; 76%) and PCP (4 patients; 19%). CONCLUSIONS: A wide spectrum of disease, including both OIs and non-infectious opportunistic diseases, is seen in hospitalised HIV-infected patients from north India. Tuberculosis remains the most common OI and is the commonest cause of death in these patients
Search for Charged Higgs Bosons in e+e- Collisions at \sqrt{s} = 189 GeV
A search for pair-produced charged Higgs bosons is performed with the L3
detector at LEP using data collected at a centre-of-mass energy of 188.6 GeV,
corresponding to an integrated luminosity of 176.4 pb^-1. Higgs decays into a
charm and a strange quark or into a tau lepton and its associated neutrino are
considered. The observed events are consistent with the expectations from
Standard Model background processes. A lower limit of 65.5 GeV on the charged
Higgs mass is derived at 95 % confidence level, independent of the decay
branching ratio Br(H^{+/-} -> tau nu)
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