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OmicsTweezer: A distribution-independent cell deconvolution model for multi-omics Data.

Cell deconvolution estimates cell type proportions from bulk omics data, enabling insights into tissue microenvironments and disease. However, practical applications are often hindered by batch effects between bulk data and referenced single-cell data, a challenge that is frequently overlooked. To address this discrepancy, we developed OmicsTweezer, a distribution-independent cell deconvolution model. By integrating optimal transport with deep learning, OmicsTweezer aligns simulated and real data in a shared latent space, effectively mitigating data shifts and inter-omics distribution differences. OmicsTweezer is versatile, capable of deconvolving bulk RNA-seq, bulk proteomics, and spatial transcriptomics. Extensive evaluations on simulated and real-world datasets demonstrate its robustness and accuracy. Furthermore, applications in prostate and colon cancer showcase OmicsTweezer's ability to identify biologically meaningful cell types. As a unified deconvolution framework for multi-omics data, OmicsTweezer offers an efficient and powerful tool for studying disease microenvironments.

Humans↗

View dependence in scene recognition after active learning.

Human spatial encoding of three-dimensional navigable space was studied, using a virtual environment simulation. This allowed subjects to become familiar with a realistic scene by making simulated rotational and translational movements during training. Subsequent tests determined whether subjects could generalize their recognition ability by identifying novel-perspective views and topographic floor plans of the scene. Results from picture recognition tests showed that familiar direction views were most easily recognized, although significant generalization to novel views was observed. Topographic floor plans were also easily identified. In further experiments, novel-view performance diminished when active training was replaced by passive viewing of static images of the scene. However, the ability to make self-initiated movements, as opposed to watching dynamic movie sequences, had no effect on performance. These results suggest that representation of navigable space is view dependent and highlight the importance of spatial-temporal continuity during learning.

Adult↗

A k-space method for large-scale models of wave propagation in tissue.

Large-scale simulation of ultrasonic pulse propagation in inhomogeneous tissue is important for the study of ultrasound-tissue interaction as well as for development of new imaging methods. Typical scales of interest span hundreds of wavelengths; most current two-dimensional methods, such as finite-difference and finite-element methods, are unable to compute propagation on this scale with the efficiency needed for imaging studies. Furthermore, for most available methods of simulating ultrasonic propagation, large-scale, three-dimensional computations of ultrasonic scattering are infeasible. Some of these difficulties have been overcome by previous pseudospectral and k-space methods, which allow substantial portions of the necessary computations to be executed using fast Fourier transforms. This paper presents a simplified derivation of the k-space method for a medium of variable sound speed and density; the derivation clearly shows the relationship of this k-space method to both past k-space methods and pseudospectral methods. In the present method, the spatial differential equations are solved by a simple Fourier transform method, and temporal iteration is performed using a k-t space propagator. The temporal iteration procedure is shown to be exact for homogeneous media, unconditionally stable for "slow" (c(x) < or = c0) media, and highly accurate for general weakly scattering media. The applicability of the k-space method to large-scale soft tissue modeling is shown by simulating two-dimensional propagation of an incident plane wave through several tissue-mimicking cylinders as well as a model chest wall cross section. A three-dimensional implementation of the k-space method is also employed for the example problem of propagation through a tissue-mimicking sphere. Numerical results indicate that the k-space method is accurate for large-scale soft tissue computations with much greater efficiency than that of an analogous leapfrog pseudospectral method or a 2-4 finite difference time-domain method. However, numerical results also indicate that the k-space method is less accurate than the finite-difference method for a high contrast scatterer with bone-like properties, although qualitative results can still be obtained by the k-space method with high efficiency. Possible extensions to the method, including representation of absorption effects, absorbing boundary conditions, elastic-wave propagation, and acoustic nonlinearity, are discussed.

Adipose Tissue↗

Assessing uncertainty in microsimulation modelling with application to cancer screening interventions.

Microsimulation is fast becoming the approach of choice for modelling and analysing complex processes in the absence of mathematical tractability. While this approach has been developed and promoted in engineering contexts for some time, it has more recently found a place in the mainstream of the study of chronic disease interventions such as cancer screening. The construction of a simulation model requires the specification of a model structure and sets of parameter values, both of which may have a considerable amount of uncertainty associated with them. This uncertainty is rarely quantified when reporting micro-simulation results. We suggest a Bayesian approach and assume a parametric probability distribution to mathematically express the uncertainty related to model parameters. First, we design a simulation experiment to achieve good coverage of the parameter space. Second, we model a response surface for the outcome of interest as a function of the model parameters using the simulation results. Third, we summarize the variability in the outcome of interest, including variation due to parameter uncertainty, using the response surface in combination with parameter probability distributions. We illustrate the proposed method with an application of a microsimulator designed to investigate the effect of prostate specific antigen (PSA) screening on prostate cancer mortality rates.

Adult↗

Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.

NMR structure determination of nucleic acids presents an intrinsically difficult problem since the density of short interproton distance contacts is relatively low and limited to adjacent base pairs. Although residual dipolar couplings provide orientational information that is clearly helpful, they do not provide translational information of either a short-range (with the exception of proton-proton dipolar couplings) or long-range nature. As a consequence, the description of the nonbonded contacts has a major impact on the structures of nucleic acids generated from NMR data. In this paper, we describe the derivation of a potential of mean force derived from all high-resolution (2 A or better) DNA crystal structures available in the Nucleic Acid Database (NDB) as of May 2000 that provides a statistical description, in simple geometric terms, of the relative positions of pairs of neighboring bases (both intra- and interstrand) in Cartesian space. The purpose of this pseudopotential, which we term a DELPHIC base-base positioning potential, is to bias sampling during simulated annealing refinement to physically reasonable regions of conformational space within the range of possibilities that are consistent with the experimental NMR restraints. We illustrate the application of the DELPHIC base-base positioning potential to the structure refinement of a DNA dodecamer, d(CGCGAATTCGCG)(2), for which NOE and dipolar coupling data have been measured in solution and for which crystal structures have been determined. We demonstrate by cross-validation against independent NMR observables (that is, both residual dipolar couplings and NOE-derived intereproton distance restraints) that the DELPHIC base-base positioning potential results in a significant increase in accuracy and obviates artifactual distortions in the structures arising from the limitations of conventional descriptions of the nonbonded contacts in terms of either Lennard-Jones van der Waals and electrostatic potentials or a simple van der Waals repulsion potential. We also demonstrate, using experimental NMR data for a complex of the male sex determining factor SRY with a duplex DNA 14mer, which includes a region of highly unusual and distorted DNA, that the DELPHIC base-base positioning potential does not in any way hinder unusual interactions and conformations from being satisfactorily sampled and reproduced. We expect that the methodology described in this paper for DNA can be equally applied to RNA, as well as side chain-side chain interactions in proteins and protein-protein complexes, and side chain-nucleic acid interactions in protein-nucleic acid complexes. Further, this approach should be useful not only for NMR structure determination but also for refinement of low-resolution (3-3.5 A) X-ray data.

DNA↗

Cerebral lateralization for motor tasks in simulated microgravity a transcranial Doppler technique for astronauts.

In Space, central cognitive operations are unaffected but humans are slower in perceptual-motor performance. Transcranial Doppler ultrasonography was used to monitor blood flow velocity in both middle cerebral arteries during unilateral and bilateral fingers' movements before, during and after -6 degrees 24 hours of head-down tilt (HDT) in 14 (8 males and 6 females) subjects. Physiologic hemisphere dominance was assessed by breath-holding test. There was a significant main effect of motor task, F(4, 328) = 16.05, p<0.00000001, MSe = 48.2. There was a gender vs head-position interaction F(3,246) = 4.90 p<0.002) MSe = 120. At pre-HDT females were right lateralized and males were left lateralized. A left shift in lateralization pattern was seen during 24hrs-HDT for both genders. There was a significant main effect of breath-holding test and a breath-holding test vs head position vs motor task interaction. HDT alters cerebral lateralization for motor control and this may be responsible for slowing in perceptual-motor performance in Space. TCD monitoring may be required for motor performance tasks in Space.

Journal Article↗

Psychological evaluation and support during EXEMSI. Experimental Campaign for the European Manned Space Infrastructure.

The aim of this study was to investigate changes in the psychological state of the crew members and the needs for psychological support during prolonged isolation. For the purpose methods employed that have been widely used in psychological evaluation during Soviet spaceflights. Communication between Commander and Crew Interface Coordinator (CIC) was analyzed. Crew disposition was observed and analyzed for information about the process of group formation and the role of each crew member in this process. Operation of the CIC's was investigated for evidence of a psychological support function. During isolation certain adaptive changes in communication took place: (1) use of unplanned contacts and intensive contacts with a preferred ground crew member, (2) resistance to penetration in the life of the crew (increase of aggressive statements and self-justifications, reduction of report length and claims), and (3) closing communication to "outsiders" by using a special code and decreasing discussion of problems. A process of group formation was noted in the course of isolation, but the final structure of the group was not stable. The relations of subjects B, D and G were crucial in the creation of an effective crew. The woman in the crew was never involved in conflicts and acted as a peacemaker. The crew regarded the communication channel between Commander and CIC as belonging to the entire crew for expressing feelings about crew relations, administration and services, and the CIC can provide needed psychological support, confirming earlier experience from Soviet simulated and actual spaceflights.

Astronauts↗

Modelling passive cardiac conductivity during ischaemia.

The results of a geometric model of cardiac tissue, used to compute the bidomain conductivity tensors during three phases of ischaemia, are described. Ischaemic conditions were simulated by model parameters being changed to match the morphological and electrical changes of three phases of ischaemia reported in literature. The simulated changes included collapse of the interstitial space, cell swelling and the closure of gap junctions. The model contained 64 myocytes described by 2 million tetrahedral elements, to which an external electric field was applied, and then the finite element method was used to compute the associated current density. In the first case, a reduction in the amount of interstitial space led to a reduction in extracellular longitudinal conductivity by about 20%, which is in the range of reported literature values. Moderate cell swelling in the order of 10-20% did not affect extracellular conductivity considerably. To match the reported drop in total tissue conductance reported in experimental studies during the third phase of ischaemia, a ten fold increase in the gap junction resistance was simulated. This ten-fold increase correlates well with the reported changes in gap junction densities in the literature.

Electric Conductivity↗

The transmembrane oligomers of coronavirus protein E.

We have tested the hypothesis that severe acute respiratory syndrome (SARS) coronavirus protein E (SCoVE) and its homologs in other coronaviruses associate through their putative transmembrane domain to form homooligomeric alpha-helical bundles in vivo. For this purpose, we have analyzed the results of molecular dynamics simulations where all possible conformational and aggregational space was systematically explored. Two main assumptions were considered; the first is that protein E contains one transmembrane alpha-helical domain, with its N- and C-termini located in opposite faces of the lipid bilayer. The second is that protein E forms the same type of transmembrane oligomer and with identical backbone structure in different coronaviruses. The models arising from the molecular dynamics simulations were tested for evolutionary conservation using 13 coronavirus protein E homologous sequences. It is extremely unlikely that if any of our assumptions were not correct we would find a persistent structure for all the sequences tested. We show that a low energy dimeric, trimeric and two pentameric models appear to be conserved through evolution, and are therefore likely to be present in vivo. In support of this, we have observed only dimeric, trimeric, and pentameric aggregates for the synthetic transmembrane domain of SARS protein E in SDS. The models obtained point to residues essential for protein E oligomerization in the life cycle of the SARS virus, specifically N15. In addition, these results strongly support a general model where transmembrane domains transiently adopt many aggregation states necessary for function.

Binding Sites↗

Range image segmentation by an effective jump-diffusion method.

This paper presents an effective jump-diffusion method for segmenting a range image and its associated reflectance image in the Bayesian framework. The algorithm works on complex real-world scenes (indoor and outdoor), which consist of an unknown number of objects (or surfaces) of various sizes and types, such as planes, conics, smooth surfaces, and cluttered objects (like trees and bushes). Formulated in the Bayesian framework, the posterior probability is distributed over a solution space with a countable number of subspaces of varying dimensions. The algorithm simulates Markov chains with both reversible jumps and stochastic diffusions to traverse the solution space. The reversible jumps realize the moves between subspaces of different dimensions, such as switching surface models and changing the number of objects. The stochastic Langevin equation realizes diffusions within each subspace. To achieve effective computation, the algorithm precomputes some importance proposal probabilities over multiple scales through Hough transforms, edge detection, and data clustering. The latter are used by the Markov chains for fast mixing. The algorithm is tested on 100 1D simulated data sets for performance analysis on both accuracy and speed. Then, the algorithm is applied to three data sets of range images under the same parameter setting. The results are satisfactory in comparison with manual segmentations.

Algorithms↗

Particle in cell simulation of laser-accelerated proton beams for radiation therapy.

In this article we present the results of particle in cell (PIC) simulations of laser plasma interaction for proton acceleration for radiation therapy treatments. We show that under optimal interaction conditions protons can be accelerated up to relativistic energies of 300 MeV by a petawatt laser field. The proton acceleration is due to the dragging Coulomb force arising from charge separation induced by the ponderomotive pressure (light pressure) of high-intensity laser. The proton energy and phase space distribution functions obtained from the PIC simulations are used in the calculations of dose distributions using the GEANT Monte Carlo simulation code. Because of the broad energy and angular spectra of the protons, a compact particle selection and beam collimation system will be needed to generate small beams of polyenergetic protons for intensity modulated proton therapy.

Computer Simulation↗

Measurement of hydraulic characteristics of porous media used to grow plants in microgravity.

Understanding the effect of gravity on hydraulic properties of plant growth medium is essential for growing plants in space. The suitability of existing models to simulate hydraulic properties of porous medium is uncertain due to limited understanding of fundamental mechanisms controlling water and air transport in microgravity. The objective of this research was to characterize saturated and unsaturated hydraulic conductivity (K) of two particle-size distributions of baked ceramic aggregate using direct measurement techniques compatible with microgravity. Steady state (Method A) and instantaneous profile measurement (Method B) methods for K were used in a single experimental unit with horizontal flow through thin sections of porous medium providing an earth-based analog to microgravity. Comparison between methods was conducted using a crossover experimental design compatible with limited resources of space flight. Satiated (natural saturation) K ranged from 0.09 to 0.12 cm s-1 and 0.5 to >1 cm s-1 for 0.25- to 1- and 1- to 2-mm media, respectively. The K at the interaggregate/intraaggregate transition was approximately 10(-4) cm s-1 for both particle-size distributions. Significant differences in log(10)K due to method and porous medium were less than one order of magnitude and were attributed to variability in air entrapment. The van Genuchten/Mualem parametric models provided an adequate prediction of K of the interaggregate pore space, using residual water content for that pore space. The instantaneous profile method covers the range of water contents relevant to plant growth using fewer resources than Method A, all advantages for space flight where mass, volume, and astronaut time are limited.

Aluminum Silicates↗

Management of missing maxillary lateral incisors.

BACKGROUND: Missing maxillary lateral incisors create an esthetic problem with specific orthodontic and prosthetic considerations. The purpose of this article is to describe treatment protocols and problems encountered in the management of this disorder. CASE DESCRIPTION: The two common treatment options are orthodontic space opening for future restorations or orthodontic space closure using canines to replace the missing maxillary lateral incisors. The required amount of space opening and the various prosthetic options are discussed. The methods for reshaping canines in orthodontic space closure and building them up to simulate lateral incisors also are described. The indications, advantages and disadvantages of both treatment modalities are outlined to help clinicians make decisions in borderline situations. CLINICAL IMPLICATIONS: Teamwork between the orthodontist, general practitioner and restorative dentist is important when analyzing factors related to individual patients and establishing overall treatment plans. This also will allow treatment modalities and the various options for replacing missing maxillary lateral incisors in space opening to be discussed between team members and the patient.

Anodontia↗

Effects of microgravity on osteoblast growth.

Studies from space flights over the past two decades have demonstrated that basic physiological changes occur in humans during space flight. These changes include cephalic fluid shifts, loss of fluid and electrolytes, loss of muscle mass, space motion sickness, anemia, reduced immune response, and loss of calcium and mineralized bone. The cause of most of these manifestations is not known and until recently, the general approach was to investigate general systemic changes, not basic cellular responses to microgravity. Recently analyzed data from the 1973-1974 Skylabs disclose that there is a rise in the systemic hormone, cortisol, which may play a role in bone loss in flight. In two flights where bone growth was measured (Skylabs 3 and 4), the crew members had a significant loss of calcium accompanied by a rise in 24 hour urinary cortisol during the entire flight period. In ground-based work on osteoblasts, we have demonstrated that equivalent amounts of glucocorticoids can inhibit osteoblast cell growth. In addition, this laboratory has recently studied gene growth and activation of mouse osteoblasts (MC3T3-E1) during spaceflight. Osteoblast cells were grown on glass coverslips, loaded in the Biorack plunger boxes 18 hours before launch and activated 19 hours after launch in the Biorack incubator under microgravity conditions. The osteoblasts were launched in a serum deprived state, activated and collected in microgravity. Samples were collected at 29 hours after sera activation (0-g, n=4; 1-g, n=4). The osteoblasts were examined for changes in gene expression and cell morphology. Approximately one day after growth activation, remarkable differences were observed in gene expression in 0-g and 1-g flight samples. The 0-g activated cells had increased c-fos mRNA when compared to flight 1-g controls. The message of immediate early growth gene, cox-2 was decreased in the microgravity activated cells when compared to ground or 1-g flight controls. Cox-1 was not detected in any of the samples. There were no significant differences in the expression of actin mRNA between the 0-g and 1-g samples. These data indicate that quiescent osteoblasts are slower to enter the cell cycle in microgravity, suggesting that the force of gravity itself may be a significant factor in bone loss in spaceflight. Preliminary data from our STS 76 flight experiment support our hypothesis that a basic biological response occurs at the tissue, cellular, and molecular level in 0-g. Here we examine ground-based and space flown data on osteoblast growth in ground-based experiments mimicking space flight conditions and in microgravity to simulate lack of gravity stress to help us understand the mechanism of bone loss by experiments.

Animals↗

Preparation and results of a 24-hour orbital flight.

The space age presents man with unprecedented opportunities for discovery and for cooperative endeavors to benefit all mankind. My flight of August 6-7, 1961 was conducted for the purpose of determining whether man can stay and work effectively and whether all systems of the spaceship can operate successfully during a period of 24 hours in space. The flight of Vostok II represents an experimental step in a logical sequence which included the first earth orbiting flight of USSR citizen Yuri A. Gagarin. Preparation for the flight included the study of theoretical and applied subjects, testing in various kinds of apparatus which provide acceleration, heat and isolation experience, brief airborne weightless flights and parachute landings, in addition to extensive training in a real spacecraft having simulators for normal and emergency contingencies of space flight. The actual flight was therefore carried out with a sense of confidence and familiarity and with continuous close radio contact with ground centers from whom my fellow cosmonauts served as spokesmen. Sequential boosters totaling 600 000 kg thrust placed the 4731 kg spaceship into a perfect orbit varying in altitude from 178-246 km in a plane 64 degrees 58' inclined to the equator. The spaceship made 17 orbits around the earth landing 25 hours, 18 minutes after take-off. The cabin had full atmospheric pressure and a comfortable habitability which could be extended for 10 days. I was able to maneuver the spaceship and perform many other control functions, make observations and take pictures of the earth and its cloud cover, eat meals and sleep all with good efficiency. I experienced mild symptoms suggestive of seasickness which were aggravated by head turning, ameliorated by sleep and entirely relieved by resumption of g-loading during descent. Altogether analyses of the physical and structural performance of the spaceship and the continuously monitored physiological responses of the pilot indicate that all systems operated with high reliability and according to our scientific expectations.

Aerospace Medicine↗

Point mutations as an optimal search process in biological evolution.

Point mutations are pictured as jumps in a phase space representing the sequences of amino acids or nucleotides as discrete points. It is shown that this space can be given a natural metric by quantifying common physical and chemical properties of amino acid constituents in terms of a natural measure. Evolution through point mutations is simulated by the search for points in the phase space representing amino acid sequences of high survival fitness. Due to the local compactness of the distribution of these functionally allowed points in phase space any successful search procedure has characteristics qualitatively different from those in the case of a random distribution. This is demonstrated by model calculations. A specified distribution of allowed points is generated with subsequent evaluation of the success of the retrieval process as a function of the jump probabilities between lattice sites. The results of such simulations are compared with data obtained from the analysis of the DNA or mRNA sequences coding related proteins. By counting silent and expressed nucleotide replacement frequencies one can draw conclusions as to the efficacy of the natural evolutionary search processes in the phase space of amino acid sequences. There are cases, where the highest possible information gain of one bit per accepted point mutation is achieved. In general the information gain is found to be somewhat sub-maximal due to functional requirements.

Amino Acid Sequence↗

Accuracy of a robotic system for the reproduction of condylar movements: a preliminary report.

OBJECTIVE: Methods in restorative dentistry have to meet stringent accuracy requirements. The accuracy of robotic systems used for the reproduction of condylar movements has not been determined. The purpose of this study was to assess the accuracy of the robot system, ROSY, a robotlike electronic simulator (developed by the author) that reproduces condylar movements previously recorded on a patient. METHOD AND MATERIALS: The simulator consists of a custom-designed ultrasonic system that records mandibular movements in all three dimensions (vertical, horizontal, and coronal) with six degrees of freedom. The simulator automatically reproduces all movements around these axes with a robotic system with six stepper motors. The accuracy of the simulator was measured for all directions in space by registering eccentric jaw positions on both sides of 10 subjects in two ways: (1) by the ultrasound registration system; and (2) simultaneously with an interocclusal recording medium. The standard deviation and interquartile range of the differences between the measurements based on these two approaches were used to statistically describe the accuracy of ROSY. RESULTS: The accuracy of the entire system was better than 0.28 mm. CONCLUSION: The electronic simulator comes with an accuracy that may render it suitable for clinical applications.

Computer Simulation↗

European isolation and confinement study. Confinement and immune function.

During spaceflight, several unusual factors act on the physiology of the astronaut: weightlessness, radiation, confinement, isolation, living and working in a small group, workload, and anxiety. The resulting physiological changes are known to include alterations of the immune system. It is difficult to determine from observations on astronauts which space-related factor(s) are responsible for the immune changes. Studies of analogous environments on Earth have supplied only scarce information. Dedicated simulation studies provide a better tool, where some space-related stress factors (weightlessness, radiation) are absent, but others are or can be present: isolation and confinement, small group living, workload, and anxiety. A reduction in immune activity was found in bed rest studies and in long-term Soviet confinement experiments (after 90 days). In the ISEMSI confinement experiment (28 days), a tendency to immune activation (PHA-reactivity and interleukin-2 production) was observed in two out of six subjects. There is a need for further experiments, in which a large number of immunological parameters can be analyzed.

Humans↗