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PubMed1998

Comparison of two different delay procedures in a rat skin flap model.

The overall objective of this study was to investigate how a strategic delay procedure could generate large flaps survival. On the basis of the vascular anatomy in 10 rats, a long three-territory skin flap spanning the length of the rat dorsum was designed. This flap was distally based on the deep circumflex iliac artery. The adjacent territories consisted of a large perforator of the posterior intercostal artery and the lateral thoracic artery in sequence. Two different vascular delay procedures were used and compared in nine animals. One dorsal midline incision was used to perform the two different delay procedures. The limited delay technique was performed by ligating a large cutaneous perforator of the posterior intercostal artery on one side of the rat. The extensive delay procedure was completed by ligating the cutaneous perforators of the posterior intercostal artery and the lateral thoracic artery on the other side of the rat. After a delay period of 10 days, the paired flaps were elevated, respectively, and sutured back in place. Seven days later, the area of viable skin flap was measured by the paper template technique. The animals were then killed, and the dorsal skin arteriograms were obtained by injecting a lead oxide mixture. Vascular changes of the paired flaps were assessed. In the extensive delay group, 100-percent survival was seen in four animals and distal partial necrosis was observed in five animals. The average survival area in the extensive delay group was 85.5 +/- 14.2 percent (mean +/- SD), whereas the flaps in limited delay group showed 100-percent survival in all animals (p < 0.05). In flaps that survived completely, the choke vessels among three vascular territories anastomosed throughout the flap. In the partially necrotic flaps, some choke and true anastomoses existed between the deep circumflex iliac and the posterior intercostal artery territories and the flap necrosis occurred in the third territory. This study suggests that the limited delay technique (ligation of one artery in the territory adjacent to the base of the flap) was the more effective delay procedure in the rat dorsal skin flap model.

Animals↗

PubMed1999

Host-induced, stage-specific virulence gene activation in Candida albicans during infection.

An understanding of the complex interactions between pathogenic microbes and their host must include the identification of gene expression patterns during infection. To detect the activation of virulence genes in the opportunistic fungal pathogen Candida albicans in vivo by host signals, we devised a reporter system that is based on FLP-mediated genetic recombination. The FLP gene, encoding the site-specific recombinase FLP, was genetically modified for expression in C. albicans and fused to the promoter of the SAP2 gene that codes for one of the secreted aspartic proteinases, which are putative virulence factors of C. albicans. The SAP2P-FLP fusion was integrated into one of the SAP2 alleles in a strain that contained a deletable marker that conferred resistance to mycophenolic acid and was flanked by direct repeats of the FLP recognition target (FRT). Using this reporter system, a transient gene induction could be monitored at the level of single cells by the mycophenolic acid-sensitive phenotype of the colonies generated from such cells after FLP-mediated marker excision. In two mouse models of disseminated candidiasis, SAP2 expression was not observed in the initial phase of infection, but the SAP2 gene was strongly induced after dissemination into deep organs. In contrast, in a mouse model of oesophageal candidiasis in which dissemination into internal organs did not occur, no SAP2 expression was detected at any time. Our results support a role of the SAP2 gene in the late stages of an infection, after fungal spread into deep tissue. This new in vivo expression technology (IVET) for a human fungal pathogen allows the detection of virulence gene induction at different stages of an infection, and therefore provides clues about the role of these genes in the disease process.

Animals↗

PubMed1998

Morphometry of human neck muscles.

STUDY DESIGN: Cadaveric dissections were used to study muscle morphometry. OBJECTIVE: To describe systematically the musculotendinous lengths, fascicle lengths, pennation angles, and physiologic cross-sectional areas of neck and shoulder muscles implicated in head movement. SUMMARY OF BACKGROUND DATA: In previous studies of neck-muscle anatomy, researchers described only a subset of muscle features, often using crude or indirect methods. None used microdissected muscles to correct measured parameters for the presence of multiple fiber compartments, internal aponeuroses, or variations in fiber or sarcomere length required for qualitative models of force-generating capabilities. METHODS: Muscle mass, pennation angle, fascicle length, and sarcomere length were measured in 14 neck muscles from 10 human cadavers. Architecturally complex muscles with multiple attachments were divided into subvolumes, and each subvolume was examined from both the superficial and deep surfaces, Internal aponeuroses were microdissected within muscles to characterize architectural specializations. Physiologic cross-sectional areas were calculated from the morphometric data. RESULTS: The neck musculature was architecturally complex. Many muscles crossed two or more joints and had multiple attachments to different bones. In some, the presence of tendons and aponeuroses was associated with specializations in fascicle organization. Considerable interindividual variation was found in the number and location of tendinous insertions of the scalenes and longissimus capitis muscles. In addition, rhomboideus showed significant variations in its size and shape. The cross-sectional areas of neck muscles from large and small subjects did not scale proportionately with body height and weight, nor did individual muscles with widely varying cross-sectional areas (0.3-15.3cm2) scale from on subject to another. CONCLUSIONS: The accuracy of morphometry can be improved by incorporating measurements made by microdissecting neck muscles. The presence of aponeurotic attachments can greatly shorten fascicle length; failure to identify such attachments can lead to underestimates of cross-sectional areas. Accuracy of a generalized model of the neck is also improved by normalizing sarcomere lengths in all muscles.

Aged↗

PubMed2001

[Anatomic principles of urinary incontinence].

The morphological fundamentals of urinary continence are still subject to controversy. This was the reason for a renewed examination of the sphincter musculature of the lower urinary tract. This study included 50 male and 15 female autopsy specimens. The organs of the lower urinary tract including the neighboring organs had been removed in their entirety and histologically reprocessed en bloc as a complete series of sections. We were able to demonstrate that the internal sphincter or m. sphincter vesicae is represented as a circular, distinct structure which elliptically embraces the internal urethral orifice. Lamellas of the detrusor are not involved in the formation of the internal sphincter. In females and males, the external sphincter consists of a striated and a smooth muscular part (m. sphincter urethrae transversostriatus et glaber). In transverse sections, the muscle has a horseshoe shape. It is completely separated by connective tissue from the musculature of the pelvic floor. A deep transverse perineal muscle does not exist. The histological findings were used for the construction of a digital three-dimensional model of the anatomy of the lower urinary tract. Computer animations of the model with integrated original histologies were generated and stored as a computer video on a CD-ROM attached to this journal.

Computer Simulation↗

PubMed1995

Susceptibility of different cell layers of the anterior and posterior part of the piriform cortex to electrical stimulation and kindling: comparison with the basolateral amygdala and "area tempestas".

Several lines of evidence suggest that the piriform cortex functions as a generator in the development and propagation of forebrain (limbic type) seizures, particularly in the kindling model of epilepsy. It is, however, not clear where, within the rather large piriform cortex region, the generator resides, and how much tissue is involved. Highly sensitive loci to chemical or electrical stimulation have been described both in the deep anterior and posterior parts of the piriform cortex. Furthermore, data from piriform cortex slice preparations indicated that epileptiform potentials originate in deep structures, particularly the endopiriform nucleus that underlies the piriform cortex. In the present study, in rats, we implanted stimulation and recording electrodes in various rostrocaudal locations of the piriform cortex and endopiriform nucleus, including the "area tempestas", i.e. a structure in the anterior part of the piriform cortex previously proposed to be critically involved in the generation of convulsive seizures of limbic origin. Within the piriform cortex, electrodes were aimed at different cellular layers of this structure. For comparison, additional animals received electrodes in different parts of the basolateral amygdala. A total of 19 different locations was obtained in this way. The susceptibility of these locations to electrical stimulation was characterized by determining the threshold for induction of afterdischarges. The afterdischarge threshold was lowest in layer III of the posterior piriform cortex and some locations in the endopiriform nucleus, whereas amygdala and "area tempestas" displayed higher values. In several animals, particularly those with electrodes in layer III of the posterior piriform cortex, spontaneous spiking was seen in prestimulation recordings, whereas this was never observed in recordings from the amygdala. Subsequent kindling by repeated stimulation of the various locations demonstrated marked differences in afterdischarge threshold reduction and kindling rate. The most marked decreases in afterdischarge threshold were seen in locations within layer III of the piriform cortex, whereas several other locations, including the "area tempestas", exhibited only moderate decreases or no decrease at all. In contrast to previous observations with only few locations in the piriform cortex region, the posterior piriform cortex was not in general slower to kindle than the anterior piriform cortex, although some locations in the posterior piriform cortex exhibited significantly lower kindling rates than the amygdala. The highest kindling rate was seen in the dorsal endopiriform nucleus.(ABSTRACT TRUNCATED AT 400 WORDS)

Amygdala↗

PubMed2001

Prediction of electroencephalographic spectra from neurophysiology.

A recent neurophysical model of propagation of electrical waves in the cortex is extended to include a physiologically motivated subcortical feedback loop via the thalamus. The electroencephalographic spectrum when the system is driven by white noise is then calculated analytically in terms of physiological parameters, including the effects of filtering of signals by the cerebrospinal fluid, skull, and scalp. The spectral power at low frequencies is found to vary as f(-1) when awake and f(-3) when asleep, with a breakpoint to a steeper power-law tail at frequencies above about 20 Hz in both cases; the f(-1) range concurs with recent magnetoencephalographic observations of such a regime. Parameter sensitivities are explored, enabling a model with fewer free parameters to be proposed, and showing that spectra predicted for physiologically reasonable parameter values strongly resemble those observed in the laboratory. Alpha and beta peaks seen near 10 Hz and twice that frequency, respectively, in the relaxed wakeful state are generated via subcortical feedback in this model, thereby leading to predictions of their frequencies in terms of physiological parameters, and of correlations in their occurrence. Subcortical feedback is also predicted to be responsible for production of anticorrelated peaks in deep sleep states that correspond to the occurrence of theta rhythm at around half the alpha frequency and sleep spindles at 3/2 times the alpha frequency. An additional positively correlated waking peak near three times the alpha frequency is also predicted and tentatively observed, as are two new types of sleep spindle near 5/2 and 7/2 times the alpha frequency, and anticorrelated with alpha. These results provide a theoretical basis for the conventional division of EEG spectra into frequency bands, but imply that the exact bounds of these bands depend on the individual. Three types of potential instability are found: one at zero frequency, another in the theta band at around half the alpha frequency, and a third at the alpha frequency itself.

Adult↗

PubMed1997

Increased excitability and inward rectification in layer V cortical pyramidal neurons in the epileptic mutant mouse Stargazer.

The excitability of layer V cortical pyramidal neurons was studied in vitro in the single-locus mutant mouse stargazer (stg), a genetic model of spike wave epilepsy. Field recordings in neocortical slices from mutant mice bathed in artificial cerebrospinal fluid revealed spontaneous synchronous network discharges that were never present in wild-type slices. Intracellular and whole cell recordings from stg/stg neurons in deep layers showed spontaneous giant depolarizing excitatory post-synaptic potentials generating bursts of action potentials, and a 78% reduction in the afterburst hyperpolarization. Whole cell recordings revealed gene-linked differences in active membrane properties in two types of regular spiking neurons. Single action potential rise and decay times were reduced, and the rheobase current was decreased by 68% in mutant cells. Plots of spike frequency-current relationships revealed that the gain of this relation was augmented by 29% in the mutant. Comparisons of visually identified pyramidal neurons firing properties in both genotypes revealed no difference in single action potential afterhyperpolarization. Voltage-clamp recordings showed an approximately threefold amplitude increase in a cesium-sensitive inward rectifier. No cell density or soma size differences were observed in the layer V pyramidal neuron population between the two genotypes. These results demonstrate an autonomous increase in cortical network excitability in a genetic epilepsy model. This defect could lower the threshold for aberrant thalamocortical spike wave oscillations in vivo, and may contribute to the mechanism of one form of inherited absence epilepsy.

Action Potentials↗

PubMed2023

Active learning of enhancer and silencer regulatory grammar in photoreceptors.

Cis-regulatory elements (CREs) direct gene expression in health and disease, and models that can accurately predict their activities from DNA sequences are crucial for biomedicine. Deep learning represents one emerging strategy to model the regulatory grammar that relates CRE sequence to function. However, these models require training data on a scale that exceeds the number of CREs in the genome. We address this problem using active machine learning to iteratively train models on multiple rounds of synthetic DNA sequences assayed in live mammalian retinas. During each round of training the model actively selects sequence perturbations to assay, thereby efficiently generating informative training data. We iteratively trained a model that predicts the activities of sequences containing binding motifs for the photoreceptor transcription factor Cone-rod homeobox (CRX) using an order of magnitude less training data than current approaches. The model's internal confidence estimates of its predictions are reliable guides for designing sequences with high activity. The model correctly identified critical sequence differences between active and inactive sequences with nearly identical transcription factor binding sites, and revealed order and spacing preferences for combinations of motifs. Our results establish active learning as an effective method to train accurate deep learning models of cis-regulatory function after exhausting naturally occurring training examples in the genome.

Journal Article↗

PubMed2001

Organic carbon composition of marine sediments: effect of oxygen exposure on oil generation potential.

Anaerobic sedimentary conditions have traditionally been linked to the generation of the source rocks for petroleum formation. However, the influence of sedimentary redox conditions on the composition of freshly deposited organic matter (OM) is not clear. We assessed the effect of in situ exposure time to oxic conditions on the composition of OM accumulating in different coastal and deep-sea sediments using solid-state 13C nuclear magnetic resonance (NMR). 13C NMR spectra were resolved into mixtures of model components to distinguish between alkyl carbon present in protein and nonprotein structures. There is an inverse relation between the length of exposure to oxic conditions and the relative abundance of nonprotein alkyl (alkylNP) carbon, whose concentration is two orders of magnitude higher in coastal sediments with short exposure times than in deep-sea sediments with long exposure times. All alkylNP-rich samples contain a physically separate polymethylene component similar in composition to algaenans and kerogens in type I oil shales. The duration of exposure to oxic conditions appears to directly influence the quality and oil generation potential of OM in marine shales.

Journal Article↗

PubMed2021

Deep generative neural network for accurate drug response imputation.

Drug response differs substantially in cancer patients due to inter- and intra-tumor heterogeneity. Particularly, transcriptome context, especially tumor microenvironment, has been shown playing a significant role in shaping the actual treatment outcome. In this study, we develop a deep variational autoencoder (VAE) model to compress thousands of genes into latent vectors in a low-dimensional space. We then demonstrate that these encoded vectors could accurately impute drug response, outperform standard signature-gene based approaches, and appropriately control the overfitting problem. We apply rigorous quality assessment and validation, including assessing the impact of cell line lineage, cross-validation, cross-panel evaluation, and application in independent clinical data sets, to warrant the accuracy of the imputed drug response in both cell lines and cancer samples. Specifically, the expression-regulated component (EReX) of the observed drug response achieves high correlation across panels. Using the well-trained models, we impute drug response of The Cancer Genome Atlas data and investigate the features and signatures associated with the imputed drug response, including cell line origins, somatic mutations and tumor mutation burdens, tumor microenvironment, and confounding factors. In summary, our deep learning method and the results are useful for the study of signatures and markers of drug response.

Antineoplastic Agents↗

PubMed2001

Classical and quantum periodically driven scattering in one dimension.

Irregular scattering at harmonically driven one-dimensional potential wells is studied both on the classical and the quantum level. We show that an ac-driven single square well, and a smooth well with oscillating bottom, are sufficient to generate chaotic scattering. For a square well with oscillating bottom, we introduce the concept of pseudointegrable scattering. The quantum dynamics of these models is treated using Floquet scattering theory, which is exact for arbitrary amplitude and frequency of the driving. In the deep quantum regime, scattering is dominated by multiphoton exchanges with the driving field, leading to complex resonance structures in transmission and reflection. For strong and fast driving, the ac-driven square well develops an effective double-well potential that introduces coherent tunneling in the scattering. We identify signatures of classical chaotic scattering in a phase-space representation of the quantum dynamics.

Journal Article↗

PubMed2025

Smarter stomata: emergent technologies unlocking yield potential in a changing climate.

Stomata, the gatekeepers of leaf gas exchange, regulate carbon dioxide uptake and water loss, functions increasingly critical as crops face more frequent, intense heat and drought. Under dry conditions, stomatal conductance (g s) typically decreases, limiting carbon assimilation and yield. Heat stress, in contrast, elicits variable g S responses: sometimes increasing to facilitate transpirational cooling, while at other times decreasing, especially when combined with drought. Heat and drought also induce complex, context-dependent shifts in stomatal anatomy. Smaller, denser stomata improve drought resilience in some cases, while reduced density confers greater tolerance in others. The optimal stomatal ideotype remains unknown, and different or even opposing traits may confer resilience dependent on the environmental scenario. Substantial genotypic variation in g s and stomatal anatomy, high heritability and co-localized quantitative trait loci for stomatal traits and yield highlight their untapped potential as breeding targets for climate-resilient crops. However, stomatal traits remain largely absent from breeding pipelines due to challenges of phenotyping at scale. This is changing rapidly. Advances in deep learning, porometry, digital microscopy, and remote sensing now enable high-throughput measurement of stomatal physiology and anatomy. Next-generation breeding technologies including clustered regularly interspaced short palindromic repeats (CRISPR), multi-omics approaches, and artificial intelligence-driven ideotype selection models could revolutionize breeding, allowing precise engineering of stomatal traits for resilience to environmental stress. The time has come to move beyond characterizing stomatal traits and start actively incorporating them into breeding strategies. By leveraging these technologies, stomatal traits can become high value targets, unlocking their potential to enhance crop performance in a hotter, drier future.

abiotic stress↗

PubMed1997

Cycle anatomy and variability in the storm-dominated type cincinnatian (Upper Ordovician): coming to grips with cycle delineation and genesis.

Although parasequence and sequence are scale-independent terms, they are frequently applied only to specific scales of cycles. For example, meter-scale cycles are commonly assumed to be parasequences or PACs. In the Upper Ordovician Kope and Fairview Formations of northern Kentucky, we examined a succession of 50 meter-scale cycles that have been variously interpreted as deepening-upward, shallowing-upward, or showing no relationship with water depth. Our analysis shows that these cycles, characterized by shifts in storm-bed proximality, are highly variable in their thickness and internal construction. Most cycles are best considered high-frequency sequences, because deepening-upward intervals are common, and many cycles contain evidence of abrupt basinward shifts in facies as expected at sequence boundaries. A minority fit the parasequence model of shallowing-upward cycles bounded by flooding surfaces. Larger, 20 m scale cycles are defined by systematic thickening and thinning trends of meter-scale cycles. However, meter-scale cycles do not display any systematic trends in cycle anatomy as a function of position within the 20 m cycles or position within the Kope and Fairview Formations. The high cycle variability and the lack of systematic stratigraphic organization with respect to longer-term cyclicity reflect either the irregularity of relative sea-level changes, the poor recording of sea-level changes in this deep-water setting, or the generation of these cycles by climate-induced cyclicity in storm intensity. These three mechanisms would generate similar patterns at the outcrop scale, so it is not possible at the present to distinguish between them.

Factor Analysis, Statistical↗

PubMed2002

A hole in the skull distorts substantially the distribution of extracranial electrical fields in an in vitro model.

The purpose of this study was to quantify the distortion of electrical fields by skull foramina using an in vitro model. Extracranial voltage generated by current dipoles located inside a human calva immersed in saline were measured when a 4-mm hole was open and when it was blocked with paraffin wax. Dipoles were located either along the internal surface of the bone (superficial dipoles) or at increasing distances from the bone (deep dipoles). With the hole open, extracranial signals had a substantially greater amplitude than with the hole blocked. The locations of the largest voltage values recorded outside the skull depended on the distance of the recording electrode from the hole rather than on the location of the internal dipole. For superficial dipoles, voltage values with the hole open were as much as 116 times greater than when the hole was blocked. Furthermore, when the hole was open, the largest extracranial signals were seen at the hole even when the dipole was 5 to 6 cm away from the hole. The effects of skull holes were less prominent for deep dipoles than for superficial dipoles. Skull discontinuities can be major determinants for the distribution of extracranial EEG signals. These results have implications for EEG interpretation and for source localization.

Electric Conductivity↗

PubMed1997

In vitro formation of mineralized cartilagenous tissue by articular chondrocytes.

Study of the deep articular cartilage and adjacent calcified cartilage has been limited by the lack of an in vitro culture system which mimics this region of the cartilage. In this paper we describe a method to generate mineralized cartilagenous tissue in culture using chondrocytes obtained from the deep zone of bovine articular cartilage. The cells were plated on Millipore CMR filters. The chondrocytes in culture accumulated extracellular matrix and formed cartilagenous tissue which calcified when beta-glycerophosphate was added to the culture medium. The cartilagenous tissue generated in vitro contains both type II and type X collagens, large sulfated proteoglycans, and alkaline phosphatase activity. Ultrastructurally, matrix vesicles were seen in the extracellular matrix. Selected area electron diffraction confirmed that the calcification was composed of hydroxyapatite crystals. The chondrocytes, as characterized thus far, appear to maintain their phenotype under these culture conditions which suggests that these cultures could be used as a model to examine the metabolism of cells from the deep zone of cartilage and mineralization of cartilagenous tissue in culture.

Alkaline Phosphatase↗

PubMed1985

Influence of hypothermia and circulatory arrest on cerebral temperature distributions.

A finite element model of the bioheat transfer equation has been developed to simulate the temperature distribution in the head of a subhuman primate. Simulations were made of the induction of deep hypothermia and of subsequent hypothermic circulatory arrest (HCA). Simulations of the circulatory arrest phase were performed with different values of surface heat transfer coefficient and tissue metabolic heat generation. Numerical results were compared with experimental data for the same procedure. The simulations indicate the brain cools rapidly to a near isothermal condition in response to an infusion of cold arterial blood. However, extracerebral structures cool much more slowly. The bulk of heat gain by the brain during HCA is due to heat transfer from these warmer extra-cerebral tissues. These results suggest extended cooling by cardiopulmonary bypass (CPB) combined with surface cooling pads should reduce or even prevent the rise of brain temperatures during HCA.

Animals↗

PubMed1985

Variability of heating patterns in animals by magnetic induction hyperthermia.

In a test of electromagnetic induction hyperthermia to deep viscera of a live dog model, we found that heating was not uniform to any depth, but was quite variable. In general, there was a thermal gradient between peripheral and central portions of the transposed spleen of about 1 degree C. Though heat generation within the abdomen was not uniform, its temperature pattern in the alive animal resulted in significant heating of that part of the organ that had been surgically placed at the center of the animal. This heating could not be explained by perfusion with regionally heated core blood. Our results indicate that extensive investigations in living systems and complex dynamic phantoms will be necessary before individual patient response can be predicted.

Abdomen↗

PubMed2001

Multiphoton microscopy in biological research.

From its conception a decade ago, multiphoton microscopy has evolved from a photonic novelty to an indispensable tool for gleaning information from subcellular events within organized tissue environments. Its relatively deep optical penetration has recently been exploited for subcellularly resolved investigations of disease models in living transgenic mice. Its enhanced spectral accessibility enables aberration-free imaging of fluorescent molecules absorbing in deep-UV energy regimes with simultaneous imaging of species having extremely diverse emission spectra. Although excited fluorescence is the primary signal for multiphoton microscopy, harmonic generation by multiphoton scattering processes are also valuable for imaging species with large anharmonic modes, such as collagen structures and membrane potential sensing dyes.

Biological Science Disciplines↗