180 research outputs found
The properties of attractors of canalyzing random Boolean networks
We study critical random Boolean networks with two inputs per node that
contain only canalyzing functions. We present a phenomenological theory that
explains how a frozen core of nodes that are frozen on all attractors arises.
This theory leads to an intuitive understanding of the system's dynamics as it
demonstrates the analogy between standard random Boolean networks and networks
with canalyzing functions only. It reproduces correctly the scaling of the
number of nonfrozen nodes with system size. We then investigate numerically
attractor lengths and numbers, and explain the findings in terms of the
properties of relevant components. In particular we show that canalyzing
networks can contain very long attractors, albeit they occur less often than in
standard networks.Comment: 9 pages, 8 figure
The computational complexity of Kauffman nets and the P versus NP problem
Complexity theory as practiced by physicists and computational complexity
theory as practiced by computer scientists both characterize how difficult it
is to solve complex problems. Here it is shown that the parameters of a
specific model can be adjusted so that the problem of finding its global energy
minimum is extremely sensitive to small changes in the problem statement. This
result has implications not only for studies of the physics of random systems
but may also lead to new strategies for resolving the well-known P versus NP
question in computational complexity theory.Comment: 4 pages, no figure
Fabrication of gelatin methacrylate (GelMA) scaffolds with nano- and micro-topographical and morphological features
The design of biomimetic biomaterials for cell culture has become a great tool to study and understand cell behavior, tissue degradation, and lesion. Topographical and morphological features play an important role in modulating cell behavior. In this study, a dual methodology was evaluated to generate novel gelatin methacrylate (GelMA)-based scaffolds with nano and micro topographical and morphological features. First, electrospinning parameters and crosslinking processes were optimized to obtain electrospun nanofibrous scaffolds. GelMA mats were characterized by SEM, FTIR, DSC, TGA, contact angle, and water uptake. Various nanofibrous GelMA mats with defect-free fibers and stability in aqueous media were obtained. Then, micropatterned molds produced by photolithography were used as collectors in the electrospinning process. Thus, biocompatible GelMA nanofibrous scaffolds with micro-patterns that mimic extracellular matrix were obtained successfully by combining two micro/nanofabrication techniques, electrospinning, and micromolding. Taking into account the cell viability results, the methodology used in this study could be considered a valuable tool to develop patterned GelMA based nanofibrous scaffolds for cell culture and tissue engineering.Fil: Aldana, Ana Agustina. Consejo Nacional de Investigaciones CientĂficas y TĂŠcnicas. Centro CientĂfico TecnolĂłgico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y TecnologĂa de Materiales. Universidad Nacional de Mar del Plata. Facultad de IngenierĂa. Instituto de Investigaciones en Ciencia y TecnologĂa de Materiales; ArgentinaFil: Malatto, Laura. Instituto Nacional de TecnologĂa Industrial; ArgentinaFil: Rehman, M. A. U.. Universitat Erlangen-Nuremberg; AlemaniaFil: Boccaccini, A. R.. Universitat Erlangen-Nuremberg; AlemaniaFil: Abraham, Gustavo Abel. Consejo Nacional de Investigaciones CientĂficas y TĂŠcnicas. Centro CientĂfico TecnolĂłgico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y TecnologĂa de Materiales. Universidad Nacional de Mar del Plata. Facultad de IngenierĂa. Instituto de Investigaciones en Ciencia y TecnologĂa de Materiales; Argentin
Prediction of lethal and synthetically lethal knock-outs in regulatory networks
The complex interactions involved in regulation of a cell's function are
captured by its interaction graph. More often than not, detailed knowledge
about enhancing or suppressive regulatory influences and cooperative effects is
lacking and merely the presence or absence of directed interactions is known.
Here we investigate to which extent such reduced information allows to forecast
the effect of a knock-out or a combination of knock-outs. Specifically we ask
in how far the lethality of eliminating nodes may be predicted by their network
centrality, such as degree and betweenness, without knowing the function of the
system. The function is taken as the ability to reproduce a fixed point under a
discrete Boolean dynamics. We investigate two types of stochastically generated
networks: fully random networks and structures grown with a mechanism of node
duplication and subsequent divergence of interactions. On all networks we find
that the out-degree is a good predictor of the lethality of a single node
knock-out. For knock-outs of node pairs, the fraction of successors shared
between the two knocked-out nodes (out-overlap) is a good predictor of
synthetic lethality. Out-degree and out-overlap are locally defined and
computationally simple centrality measures that provide a predictive power
close to the optimal predictor.Comment: published version, 10 pages, 6 figures, 2 tables; supplement at
http://www.bioinf.uni-leipzig.de/publications/supplements/11-01
Spin and magnetization effects in plasmas
We give a short review of a number of different models for treating
magnetization effects in plasmas. In particular, the transition between kinetic
models and fluid models is discussed. We also give examples of applications of
such theories. Some future aspects are discussed.Comment: 18 pages, 1 figure. To appear in Plasma Physics and Controlled
Fusion, Special Issue for the 37th ICPP, Santiago, Chil
Breakdown of stabilization of atoms interacting with intense, high-frequency laser pulses
Published versio
Degeneracy: a link between evolvability, robustness and complexity in biological systems
A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology.
This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability
What constitutes responsiveness of physicians: A qualitative study in rural Bangladesh
Responsiveness entails the social actions by health providers to meet the legitimate expectations
of patients. It plays a critical role in ensuring continuity and effectiveness of care
within people centered health systems. Given the lack of contextualized research on
responsiveness, we qualitatively explored the perceptions of outpatient users and providers
regarding what constitute responsiveness in rural Bangladesh. An exploratory study was
undertaken in Chuadanga, a southwestern Bangladeshi District, involving in-depth interviews
of physicians (n = 17) and users (n = 7), focus group discussions with users (n = 4),
and observations of patient provider interactions (three weeks). Analysis was guided by a
conceptual framework of responsiveness, which includes friendliness, respecting, informing
and guiding, gaining trust and optimizing benefits. In terms of friendliness, patients expected
physicians to greet them before starting consultations; even though physicians considered
this unusual. Patients also expected physicians to hold social talks during consultations,
which was uncommon. With regards to respect patients expected physicians to refrain from
disrespecting them in various ways; but also by showing respect explicitly. Patients also had
expectations related to informing and guiding: they desired explanation on at least the diagnosis,
seriousness of illness, treatment and preventive steps. In gaining trust, patients
expected that physicians would refrain from illegal or unethical activities related to patients,
e.g., demanding money against free services, bringing patients in own private clinics by brokers
(dalals), colluding with diagnostic centers, accepting gifts from pharmaceutical representatives.
In terms of optimizing benefits: patients expected that physicians should be
financially sensitive and consider individual need of patients. There were multiple dimensions
of responsiveness- for some, stakeholders had a consensus; context was an important
factor to understand them. This being an exploratory study, further research is
recommended to validate the nuances of the findings. It can be a guideline for responsiveness
practices, and a tipping point for future research
Strong vacuum squeezing from bichromatically driven Kerrlike cavities: from optomechanics to superconducting circuits
Squeezed light, displaying less fluctuation than vacuum in some observable, is key in the flourishing field of quantum technologies. Optical or microwave cavities containing a Kerr nonlinearity are known to potentially yield large levels of squeezing, which have been recently observed in optomechanics and nonlinear superconducting circuit platforms. Such Kerr-cavity squeezing however suffers from two fundamental drawbacks. First, optimal squeezing requires working close to turning points of a bistable cycle, which are highly unstable against noise thus rendering optimal squeezing inaccessible. Second, the light field has a macroscopic coherent component corresponding to the pump, making it less versatile than the so-called squeezed vacuum, characterised by a null mean field. Here we prove analytically and numerically that the bichromatic pumping of optomechanical and superconducting circuit cavities removes both limitations. This finding should boost the development of a new generation of robust vacuum squeezers in the microwave and optical domains with current technology
Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator
A recently published transcriptional oscillator associated with the yeast cell cycle provides clues and raises questions about the mechanisms underlying autonomous cyclic processes in cells. Unlike other biological and synthetic oscillatory networks in the literature, this one does not seem to rely on a constitutive signal or positive auto-regulation, but rather to operate through stable transmission of a pulse on a slow positive feedback loop that determines its period. We construct a continuous-time Boolean model of this network, which permits the modeling of noise through small fluctuations in the timing of events, and show that it can sustain stable oscillations. Analysis of simpler network models shows how a few building blocks can be arranged to provide stability against fluctuations. Our findings suggest that the transcriptional oscillator in yeast belongs to a new class of biological oscillators
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