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At least 19 recordsLinked to original sources
PubMed2000

Inverse design and CFD investigation of blood pump impeller.

In this paper, a three-dimensional inverse design method using mean swirl specification is applied to the design of centrifugal blood pump impeller blades. CFD investigation of the passage flows is carried out to analyze the flow field and pressure generated across the blade. The results show that the possibility of blood cells' damage may not be increased when the pressure developed is increased. This technique can provide designers valuable insight on the development of efficient blood pump with reduced risk of blood traumatization.

Computer Simulation↗
PubMed2006

Inverse design for full control of spontaneous emission using light emitting scattering optical elements.

Full control of spontaneous emission is essential in various fields of optics. This work presents an inverse designed light-emitting scattering optical element that includes full control of spontaneously emitted photons (i.e., enhancement at a central frequency and suppression at neighboring frequencies) and directionality of the output beam. This is achieved by embedding a one-dimensional optical active element inside a cluster of square shaped gallium arsenide dielectric rods whose positions are optimized by a genetic algorithm. Large spontaneous emission enhancement of > 70 is predicted at the transition wavelength if high-quality sources are employed. Moreover, neighboring wavelengths are simultaneously suppressed over 10 times. Finally, the radiated beam is highly collimated to only 6 degrees and contains 30 times the energy emitted by the source placed in free space.

Journal Article↗
PubMed2002

An inverse design of an open, head/neck RF coil for MRI.

Radio-frequency (RF) coils are a necessary component of magnetic resonance imaging (MRI) systems. When used in transmit operation, they act to generate a homogeneous RF magnetic field within a volume of interest and when in receive operation, they act to receive the nuclear magnetic resonance signal from the RF-excited specimen. This paper outlines a procedure for the design of open RF coils using the time-harmonic inverse method. This method entails the calculation of an ideal current density on a multipaned planar surface that would generate a specified magnetic field within the volume of interest. Because of the averaging effect of the regularization technique in the matrix solution, the specified magnetic field is shaped within an iterative procedure until the generated magnetic field matches the desired magnetic field. The stream-function technique is used to ascertain conductor positions and a method of moments package is then used to finalize the design. An open head/neck coil was designed to operate in a clinical 2T MRI system and the presented results prove the efficacy of this design methodology.

Algorithms↗
PubMed2006

Modeling and inverse controller design for an unmanned aerial vehicle based on the self-organizing map.

The next generation of aircraft will have dynamics that vary considerably over the operating regime. A single controller will have difficulty to meet the design specifications. In this paper, a self-organizing map (SOM)-based local linear modeling scheme of an unmanned aerial vehicle (UAV) is developed to design a set of inverse controllers. The SOM selects the operating regime depending only on the embedded output space information and avoids normalization of the input data. Each local linear model is associated with a linear controller, which is easy to design. Switching of the controllers is done synchronously with the active local linear model that tracks the different operating conditions. The proposed multiple modeling and control strategy has been successfully tested in a simulator that models the LoFLYTE UAV.

Aircraft↗
PubMed2006

Adaptation of multiple logistic regression to a multiple inverse sampling design: application to the Isfahan healthy heart program.

In observational and experimental studies in the health sciences involving human populations, it is sometimes considered desirable to recruit subjects according to designs that specify a predetermined number of subjects in each of several mutually exclusive classes (generally but not necessarily demographic in nature). This type of adaptive sampling design, now generally referred to as multiple inverse sampling (MIS), has received recent attention, and estimation methods are now available for several sequential MIS sampling designs. In this class of designs, subjects are sampled randomly and sequentially, usually one at a time, until all classes have the pre-specified number of subjects. In this paper, we extend MIS for finite population sampling to estimation of the parameters in multiple logistic regression under MIS. Using estimated logistic regression parameters and cost components obtained from the Isfahan Healthy Heart Program (IHHP), we report findings from a simulation experiment in which it appears that, at fixed cost, MIS at the last stage of sampling compares favourably to simple random sampling. The IHHP is a large community intervention study for prevention of cardiovascular disease being conducted in Isfahan, Iran and two other cities in Iran. The IHHP identified subjects through a multistage sample survey in which MIS was used at the final stage of sampling. MIS is one of several methods of adaptive sampling that are generating considerable interest and show promise of being useful in a wide variety of applications.

Age Factors↗
PubMed2001

Virtual darwinian drug design: QSAR inverse problem, virtual combinatorial chemistry, and computational screening.

The generation of diversity and its further selection by an external system is a common mechanism for the evolution of the living species and for the current drug design methods. This assumption allows us to label the methods based on generation and selection of molecular diversity as "Darwinian" ones, and to distinguish them from the structure-based, structure-modulation approaches. An example of a Darwinian method is the inverse QSAR. It consists of the computational generation of candidate chemical structures and their selection according to a previously established QSAR model. New trends in the field of combinatorial chemical syntheses comprise the concepts of virtual combinatorial synthesis and virtual or computational screening. Virtual combinatorial synthesis, closely related to inverse QSAR, can be defined as the computational simulation of the generation of new chemical structures by using a combinatorial strategy to generate a virtual library. Virtual screening is the selection of chemical structures having potential desirable properties from a database or virtual library in order to be synthesized and assayed. This review is mainly focused on graph theoretical drug design approaches, but a survey with key references is provided that covers other simulation methods.

Biological Evolution↗
PubMed2026

Predicting food taste with bound-driven optimization.

The prediction of sensory attributes from ingredient-level formulations is an emerging challenge at the intersection of food science and artificial intelligence. We address the fundamental question of whether the taste of a food can be predicted from its ingredients by treating recipes as composite materials. We apply Hashin-Shtrikman (HS) and Reuss-Voigt (RV) bounds, techniques originally developed for elastic moduli, as a null-hypothesis additive baseline for five taste dimensions (sweetness, sourness, bitterness, umami, saltiness) on a curated dataset of 70 recipes decomposed into 115 distinct ingredients scored against a library of 209 ingredient-level taste references with trained-panel ground truth. This baseline systematically under-predicts perceived taste: 77% of actual taste values exceeded the HS upper bound, with the exceedance rate ranging from 26% (bitterness) to 97% (saltiness). We traced this gap to specific processing chemistry (Maillard reactions, caramelization, evaporative concentration, protein hydrolysis, and nucleotide synergy) and introduced a hybrid model that augments the HS baseline with eight chemistry-proxy features encoding these mechanisms. Our results show that our interpretable hybrid model eliminates the systematic bias and reduces mean absolute error by 27%-62% for sweetness, sourness, umami, and saltiness while using only 10 interpretable features, achieving performance comparable to a black-box Lasso regression on 115 per-ingredient features. We further demonstrate constrained inverse design via Differential Evolution, recovering ingredient formulations that match target taste profiles subject to compositional bounds. Our work demonstrates how key chemical processes during food preparation can inform and augment physics-based and machine learning models, providing a quantitative fingerprint of processing chemistry's contribution to taste perception and paving the way for model-driven food formulation with targeted sensory characteristics.

Composite material bounds↗
PubMed2006

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

Computational Biology↗
PubMed2006

Sperm chromosome analysis in two cases of paracentric inversion.

OBJECTIVE: To examine sperm meiotic segregation in men with paracentric inversions. DESIGN: Cases reports, literature review. SETTING: Departments of reproductive biology, cytogenetics, gynaecology, and obstetrics. PATIENT(S): Two patients referred for infertility, heterozygous for a paracentric inversion. INTERVENTION(S): Fluorescence in situ hybridization (FISH) with specific probes and X/Y/18 centromeric probes on 1,000 spermatozoa for the 2 patients and 10 controls. MAIN OUTCOME MEASURE(S): Sperm aneuploidy frequency. RESULT(S): The FISH analysis using the specific probes for the paracentric inversion indicated low disequilibrium (0.4% and 0.5%). The FISH analysis using X/Y/18 centromeric probes indicated aneuploidy frequencies (0.3% and 1.1%), identical to those of control patients with the same sperm parameters. CONCLUSION(S): Paracentric inversion seems to be associated with a very low risk of aneuploidy. A larger study is necessary to explore all chromosome inversions.

Adult↗
PubMed2006

Computational design of proteins stereochemically optimized in size, stability, and folding speed.

Artificial proteins potentially barrier-free in the folding kinetics are approached computationally under the guidance of protein-folding theories. The smallest and fastest folding globular protein triple-helix-bundle (THB) is so modified as to minimize or eliminate its presumed barriers in folding speed. As the barriers may reside in the ordering of either secondary or tertiary structure, the elements of both secondary and tertiary structure in the protein are targeted for prenucleation with suitable stereochemically constrained amino acid residues. The required elements of topology and sequence for the THB are optimized independently; first the topology is optimized with simulated annealing in polypeptides of highly simplified alphabet; next, the sequence in side chains is optimized using the standard inverse design methods. The resultant three best-adapted THBs, variable in topology and distinctive in sequences, are assessed by comparing them with a few benchmark proteins. The results of mainly molecular dynamics (MD) comparisons, undertaken in explicit water at different temperatures, show that the designed sequences are favorably placed against the chosen benchmarks as THB proteins potentially thermostable in the native folds. Folding simulation experiments with MD establish that the designed sequences are rapid in the folding of individual helices, but not in the evolution of tertiary structure; energetic cum topological frustrations remain but could be the artifacts of the starting conformations that were chosen in the THBs in the folding simulations. Overall, a practical high-throughput approach for de novo protein design has been developed that may have fruitful application for any type of tertiary structure.

Amino Acid Sequence↗
PubMed1996

Inversion monophyly in African anopheline malaria vectors.

The African Anopheles gambiae complex of six sibling species has many polymorphic and fixed paracentric inversions detectable in polytene chromosomes. These have been used to infer phylogenetic relationships as classically done with Drosophila. Two species, A. gambiae and A. merus, were thought to be sister taxa based on a shared X inversion designated Xag. Recent DNA data have conflicted with this phylogenetic inference as they have supported a sister taxa relationship of A. gambiae and A. arabiensis. A possible explanation is that the Xag is not monophyletic. Here we present data from a gene (soluble guanylate cyclase) within the Xag that strongly supports the monophyly of the Xag. We conjecture that introgression may be occurring between the widely sympatric species A. gambiae and A. arabiensis and that the previous DNA phylogenies have been detecting the introgression. Evidently, introgression is not uniform across the genome, and species-specific regions, like the X-chromosome inversions, do not introgress probably due to selective elimination in hybrids and backcrosses.

Animals↗
PubMed1995

Ankle inversion injury and hypermobility: effect on hip and ankle muscle electromyography onset latency.

OBJECTIVE: Changes in reflexes associated with chronically sprained ankles were examined by measuring the reflex response latency of hip and ankle muscles during instantaneous ankle/foot inversion. DESIGN: Randomized trials. SETTING: All studies were performed in the Research Department laboratories at a major rehabilitation center in a large metropolitan area. PATIENTS AND OTHER PARTICIPANTS: Twenty subjects were assigned to 2 groups (normal and hypermobile) based on goniometry testing. Subjects were recruited from hospital and University staff and had a mean age of 31 +/- 5 years. OUTCOME MEASURES: Subjects stood on a platform constructed such that either foot/ankle could be instantaneously inverted. Latency was measured by EMG surface electrodes placed over the right and left gluteus medius and peroneal muscles. Two-factor analysis of variance was calculated to determine significant muscle onset latency differences (p < .01) between groups. RESULTS: Significant EMG latency differences were found in comparing right gluteus medius of the hypermobile group (127.35 +/- 6.02msec) with the normal group (150.49 +/- 6.49msec) during right ankle perturbation, and the left gluteus medius of the hypermobile group (120.71 +/- 6.16msec) with the normal group (136.24 +/- 5.88msec) during left ankle perturbation. CONCLUSIONS: These data suggest that there is decreased latency of hip muscle activation after ankle inversion in the hypermobile population. In treating ankle instability, clinicians must decide to address the altered hip muscle recruitment pattern or accept this recruitment pattern as an injury-adaptive strategy and thus accept unknown long-term consequences of premature muscle activation (ie, possible articular predisposition to degenerative changes, altered joint reaction forces, and muscle imbalances).

Adult↗
PubMed1991

Intracellular H+ buffering power and its dependency on intracellular pH.

Intracellular hydrogen ion (H+) buffering power, conventionally defined as the amount of acid or base that would have to be introduced into the cell cytosol to decrease or increase ipH by one pH unit, is generally said to increase as intracellular pH (ipH) decreases. This implies that the cell has a lesser capability to resist acute acid or base perturbations at its steady state ipH than at any lower ipH. We re-examined this notion, reasoning that the logarithmic nature of the pH unit could limit the validity of the conventional expression of buffering power in imparting physiologic insight into the mechanisms of cellular H+ homeostasis. The mathematical derivation of the formula, delta i[NH4+]/delta ipH, conventionally used to estimate buffering power using the NH4Cl technique, revealed that this parameter is, by design, inversely proportional to the exponential of ipH. This a priori dependence on pH dictates an increase in buffering power with decreasing ipH, and thereby interferes with the assessment of the physiologic capability of the intracellular milieu to buffer protons at different ipH levels. To circumvent this problem, buffering power was defined as the amount of hydrogen ions that would have to be added to or removed from the cell to effect a change in the concentration of H+ in the cell cytosol of 1 mM (a term heretofore referred to as the cell H+ buffering coefficient). The mathematical derivation of the formula used to calculate the cell H+ buffering coefficient, delta i[NH4+]/delta[H+]i, does not suffer from an a priori dependence on ipH.(ABSTRACT TRUNCATED AT 250 WORDS)

Acid-Base Equilibrium↗
PubMedDate not supplied

Design and implementation of magnetization transfer pulse sequences for clinical use.

The transfer of magnetization between a free and a bound pool of spins is described in terms of the respective longitudinal relaxation times and the life times of spins in each pool. The effect of an off resonance radiofrequency (RF) pulse in producing saturation in the bound pool and a consequent decrease in both the available longitudinal magnetization and the T1 of spins in the free pool is described. The effects of increasing duration of the saturating RF pulse on image pixel signal intensity were used to determine values for the decrease in both T1 and the available magnetization in gray and white matter of the brain as well as in muscle, fat, and CSF. At 0.15 T the available magnetization of muscle was reduced by approximately 60% and its T1 was decreased from 350 to 150 ms. The available magnetization of white and gray matter was reduced by 40% and their values of T1 were reduced by 80-110 ms. The reduction in available magnetization was used to increase contrast on proton density weighted or T2-weighted SE pulse sequences. These changes were also used to design inversion recovery (IR) pulse sequences with particular contrast properties. A short inversion time (TI) magnetization transfer (MT) IR (MT-STIR) pulse sequence was used to reduce the signal from normal muscle to zero to produce an angiographic effect in the leg. Increased tissue contrast was observed with a T2-weighted (MT-SE) sequence in a patient with bilateral cerebral infarction and with an MT-IR pulse sequence in a patient who had an intracranial hematoma. Three patients with cerebral tumors showed high lesion contrast with MT-STIR sequences. Components within two tumors were changed to different degrees by MT and in one case change in the brain attributable to recent radiotherapy treatment was only identified with an MT-STIR sequence. Magnetization transfer can be used to manipulate both the available longitudinal magnetization and the T1 of normal and abnormal tissues. The changes in tissue contrast produced by this can be very substantial and are likely to be of importance in clinical imaging.

Adult↗
PubMed2006

Differential toolbox to shape dispersion behavior in photonic crystal fibers.

We present an analytical procedure to compute the first derivatives of the propagation constants with respect to several structural parameters in photonic crystal fibers (PCFs). From them we can easily evaluate the same derivatives of other directly related magnitudes. The above derivatives provide the trend of the magnitude at issue, which allows us to take advantage of a gradient-based algorithm to shape the properties of the guiding structure. In this way we implement an optimization process to carry out real inverse design in PCFs. We focus our attention on designing PCFs with a specific chromatic dispersion behavior. Likewise, the same approach makes it possible to analyze their fabrication tolerances.

Journal Article↗
PubMed2026

Geometric mechanogenomics: engineering boundary conditions for deterministic cell fate control.

In tissue development and regeneration, cellular behavior has traditionally been interpreted through biochemical signaling frameworks. However, cells exist within physically defined environments, where geometric boundary conditions - including confinement, curvature, anisotropy, and multicellular architecture - define the mechanical state space in which mechanical forces are generated, transmitted, and interpreted. Here, we introduce geometric mechanogenomics, a conceptual framework that positions geometry as an upstream spatial regulator linking tissue-scale boundary conditions to nuclear mechanics, chromatin organization, and genome regulation. We propose a boundary-to-nucleus axis through which geometric information is decoded by adhesion-mediated mechanotransduction, cytoskeletal force transmission, and nuclear mechanoregulation to regulate chromatin accessibility, epigenetic remodeling, and transcriptional programs. Rather than introducing new mechanotransduction pathways, this framework emphasizes that geometry spatially organizes conserved mechanotransductive machinery to generate context-dependent mechanogenomic outcomes. We further discuss how engineered geometries reduce morphogenetic stochasticity, coordinate multicellular organization, and establish mechanical memory that influences long-term cell fate. Finally, we highlight current challenges in establishing predictive geometry-to-genome relationships and discuss emerging opportunities enabled by spatial omics, artificial intelligence-assisted inverse design, and dynamic biomaterials for programmable mechanobiology, regenerative medicine, developmental biology, and disease modeling.

genome organization↗