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At least 19 recordsLinked to original sources

Bio-heat transfer model of deep brain stimulation-induced temperature changes.

There is a growing interest in the use of chronic deep brain stimulation (DBS) for the treatment of medically refractory movement disorders and other neurological and psychiatric conditions. Fundamental questions remain about the physiologic effects of DBS. Previous basic research studies have focused on the direct polarization of neuronal membranes by electrical stimulation. The goal of this paper is to provide information on the thermal effects of DBS using finite element models to investigate the magnitude and spatial distribution of DBS-induced temperature changes. The parameters investigated include stimulation waveform, lead selection, brain tissue electrical and thermal conductivities, blood perfusion, metabolic heat generation during the stimulation and lead thermal conductivity/heat dissipation through the electrode. Our results show that clinical DBS protocols will increase the temperature of surrounding tissue by up to 0.8 degrees C depending on stimulation/tissue parameters.

Algorithms↗

Integration of single cell multiomics data by deep transfer hypergraph neural network.

Multi-omics characterization of individual cells offers remarkable potential for analyzing the dynamics and relationships of gene regulatory states across millions of cells. How to integrate multimodal data is an open problem, existing integration methods struggle with accuracy and modality-specific biological variation retention. In this paper, we present scHyper (scalable, interpretable machine learning for single cell integration), a low-code and data-efficient deep transfer model designed for integrating paired and unpaired single-cell multimodal data. We benchmark scHyper against datasets from different multimodal data. ScHyper learns a low-dimensional representation and aligns the covariance matrices of the measured modalities, achieving high accuracy even with large scale atlas-level datasets with low memory and computational time across different cell lines, shedding light on regulatory relationships between different types of omics. Altogether, we show that scHyper is a versatile and robust tool for cell-type label transfer and integration from multimodal single-cell datasets.

Single-Cell Analysis↗

Segmental cable modelling of electrotonic transfer properties of deep superior colliculus neurons in the cat.

A segmental cable model of tecto-reticulo-spinal neurons of cat superior colliculus was constructed, based on detailed anatomical measurements from three neurons. The calculated membrane resistance for which the model best fitted the measured input resistance was 2,300-3,000 omega cm2. Electrotonic length of dendrites fell under 0.59-1.20 and 0.52-1.05 length constants, while the mean electrotonic length for the three cells averaged 0.91, 0.79, 0.81 and 0.80, 0.70, 0.71 (for sealed-end and open-end cable termination, respectively). Dendrite-to-soma conductance ratios averaged 16.0, 10.7, 7.5 and 21.3, 14.1, 11.4 for the two different end conditions, respectively. Synaptic efficacy was estimated by the transfer of steady-state voltage or current reaching the soma from distal dendritic locations. While voltage transfer was less than 1%, almost 60% of injected current (or charge) reached the soma. Analysis of voltage transients recorded experimentally in TRSNs demonstrated considerable difference between parameters derived from either equivalent-cylinder model or segmental cable model. The obvious deviations of TRSNs both in anatomical and electrotonic respect from the assumptions of the equivalent-cylinder model indicate that the detailed cable model will give a more appropriate description of these neurons. The significance of the estimated electrotonic parameters for the particular burst generation mechanism of TRSNs is discussed.

Animals↗

Hepatocyte proteome destabilization and novel targets for PFASs unveiled through combined thermal proteome profiling and deep transfer learning.

Identifying protein targets for per- and polyfluoroalkyl substances (PFASs) is essential to understand their toxicity and health risks. However, knowledge about their interacting proteins is limited since reliable identification methods are lacking. We developed an integrated approach combining thermal proteome profiling (TPP) and deep transfer learning (DTL) modeling to efficiently identify cellular targets of PFAS. TPP measured PFAS binding proteins and the affinities by nanospray liquid chromatography tandem mass spectrometry, while DTL models were constructed to predict PFAS-protein affinities using neural network algorithms. TPP results revealed that PFASs uniquely destabilized the proteome of HepG2 cells, unlike the stabilizing effects by other xenobiotics. Key protein targets for three representative PFASs (PFOA, GenX and Novec 649) were identified, which exhibited weak binding affinities (median EC50 ≈ 30 μM). The number of protein targets increased with molecular weights among the three PFASs. The DTL model achieved a higher Pearson correlation coefficient of 0.89, and reduced mean squared errors by 54 % over previous models for drug-protein interactions. Notably, TPP and DTL jointly pinpointed ribosomal proteins as novel targets of GenX, potentially linking it to cell apoptosis through disrupted protein synthesis. Biolayer interferometry validated GenX binding to RPL4 protein, driven by electrostatic interactions and halogen bonds. This integrated approach effectively uncovers novel PFASs targets, advancing insights into their adverse health effects.

Humans↗

Experimental and clinical use of pH monitoring of free tissue transfers.

No current method of flap monitoring is ideal for use in all types of free tissue transfers. No method provides objective, easily communicated data that is identical in all types of transfers. In particular, reliable monitoring of buried transfers has proved difficult with available methods. The rat anterior thigh flap based on the external iliac vascular pedicle was introduced by us as a model of deep free tissue transfer. Four sets of 10 flaps were raised in the following groups: Group A (control), Group B (arterial occlusion), Group C (venous occlusion), and Group D (arterial and venous occlusion). Postoperative muscle flap pH was measured with a micro-pH electrode (1.2 mm) and correlated with arterial blood gas. Results showed excellent correlation of flap and serum pH over time (mean flap pH, 7.28; mean serum pH, 7.30). Arterial occlusion produced a rapid drop in flap pH of 0.66 pH units at 1 hour. Venous occlusion pH drop was 0.27 pH units at 1 hour, 0.53 pH units at 3 hours. Arterial and venous occlusion produced a pH drop of 0.55 pH units at 1 hour. The most rapid rate of pH drop occurred immediately after vessel occlusion. We have used continuous pH monitoring in 21 free tissue transfers for up to 84 hours after surgery. PH values remained constant in each transfer (range, 7.20-7.50; grand mean, 7.35). There was one flap failure among the monitored group of flaps, which was predicted by pH drop before loss of Doppler pulse.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

Optimization of temperature distributions for regional hyperthermia based on a nonlinear heat transfer model.

We describe an optimization process specially designed for regional hyperthermia of deep seated tumors in order to achieve desired steady-state temperature distributions. A nonlinear three-dimensional heat-transfer model based on temperature-dependent blood perfusion is applied to predict the temperature. Optimal heating is obtained by minimizing an integral object function which measures the distance between desired and model predicted temperatures. Sequential minima are calculated from successively improved constant-rate perfusion models employing a damped Newton method in an inner iteration. Numerical results for a Sigma 60 applicator are presented.

Humans↗

Enhanced production of neutron-rich rare isotopes in peripheral collisions at Fermi energies.

A large enhancement in the production of neutron-rich projectile residues is observed in the reactions of a 25 MeV/nucleon 86Kr beam with the neutron-rich 124Sn and 64Ni targets relative to the predictions of the EPAX parametrization of high-energy fragmentation, as well as relative to the reaction with the less neutron-rich 112Sn target. A hybrid model based on a deep-inelastic transfer (DIT) code followed by a statistical deexcitation code accounts for part of the observed large cross sections. The DIT simulation indicates that the production of neutron-rich nuclides in these reactions is associated with peripheral nucleon exchange in which the neutron skins of the neutron-rich 124Sn and 64Ni target nuclei may play an important role. From a practical viewpoint, such reactions offer a novel synthetic avenue to access extremely neutron-rich rare isotopes towards the neutron-drip line.

Journal Article↗

The effect of export to the deep sea on the long-range transport potential of persistent organic pollutants.

BACKGROUND: Export to the deep sea has been found to be a relevant pathway for highly hydrophobic chemicals. The objective of this study is to investigate the influence of this process on the potential for long-range transport (LRT) of such chemicals. METHODS: The spatial range as a measure of potential for LRT is calculated for seven PCB congeners with the multimedia fate and transport model ChemRange. Spatial ranges for cases with and without deep sea export are compared. RESULTS AND DISCUSSION: Export to the deep sea leads to increased transfer from the air to the surface ocean and, thereby, to lower spatial ranges for PCB congeners whose net deposition rate constant is similar to or greater than the atmospheric degradation rate constant. This is fulfilled for the PCB congeners 101, 153, 180, and 194. The spatial ranges of the congeners 8, 28, and 52, in contrast, are not affected by deep sea export. With export to the deep sea included in the model, the spatial ranges of the heavier congener are similar to those of the lighter ones, while the intermediate congeners 101 and 153 have the highest potential for long-range transport. CONCLUSIONS: Transfer to the deep ocean affects the mass balance and the potential for LRT of highly hydrophobic chemicals and should be included in multimedia fate models containing a compartment for ocean water.

Air Movements↗

Crystal structure of a complex between lumiflavin and 2,6-diamino-9-ethylpurine: a flavin adenine dinucleotide model exhibiting charge-transfer interactions.

The x-ray structure of the deep red crystalline complex lumiflavin-2,6-diamino-9-ethylpurine has been determined. The flavin and adenine derivatives form hydrogen-bonded base pairs of the Watson-Crick type. The molecules in the crystal also associate via extensively overlapped flavin/adenine and flavin/flavin stacking interactions in which there are several contacts that are closer than van der Waals distances. This, together with the red color of the crystals, is indicative of the formation of a charge-transfer complex.

Adenine↗

EvoSNR-Prom: Predicting promoters at single-nucleotide resolution with label-aware transfer learning of the pretrained EVO model.

The precise identification of promoters is crucial for understanding gene regulation. Deep learning methods have achieved considerable success in promoter prediction, yet most operate at the sequence level with coarse-grained labels. This means they label an entire DNA segment as either a "promoter" or "non-promoter," which results in a lack of the nucleotide-level resolution in prediction. In this study, we propose EvoSNR-Prom, a model designed for promoter prediction at single-nucleotide resolution. EvoSNR-Prom is built on the Evo foundation model and formulates promoter identification as a token-level sequence labeling problem, analogous to named entity recognition in natural language processing. To address the limited contextual information available in single-nucleotide tokenization, we introduce a lexicon-enhanced embedding strategy that incorporates biologically meaningful DNA lexicons, enriching contextual representations and improving the model's ability to capture complex sequence motifs. Furthermore, to enhance predictive performance on small size datasets, we integrate a label-aware transfer learning framework to leverage knowledge from well-annotated source species to a target organism. The results across various prokaryotic datasets show that EvoSNR-Prom achieves excellent performance. This work provides a valuable computational framework for the high-precision analysis of gene regulatory elements, contributing to the advancement of promoter prediction at single-nucleotide resolution.

Promoter Regions, Genetic↗

Crystallization of yeast iso-2-cytochrome c using a novel hair seeding technique.

A hair seeding technique has been developed to obtain diffraction quality crystals of yeast (Saccharomyces cerevisiae) iso-2-cytochrome c, a model for studies of protein folding and biological electron transfer reactions. Deep red crystals of this protein were obtained from 88 to 92% saturated solutions of ammonium sulfate containing 20 mg protein/ml, 0.1 M-sodium phoshate, 0.3 M-sodium chloride, 0.04 M-dithiothreitol and adjusted to phosphate, 0.3 M-sodium chloride, 0.04 M-dithiothreitol and adjusted to pH 6.0. Rapid crystal growth was observed, but only along the path of the seeding hair stroke. The space group is P4(3)2(1)2 (or P4(1)2(1)2) with a = b = 36.4 A, c = 137.8 A (1 A = 0.1 nm) and Z = 8. Crystals are stable in the X-ray beam for more than 10 days and diffract to at least 2.5 A resolution. The same hair seeding methodology has proven useful in obtaining crystals of specifically designed mutant iso-2 proteins and in other protein systems where consistent crystal growth had previously proven difficult to attain.

Crystallization↗

Pleural-based mesothelioma in immune competent rats: a model to study adenoviral gene transfer.

BACKGROUND: Despite multimodality approaches, pleural-based malignant mesothelioma remains a disease with a very poor prognosis. Novel therapeutic strategies such as gene therapy clearly are needed to improve the survival of patients with this neoplasm. To aid in the evaluation of new treatment strategies, animal models that closely mimic human disease are required. This article describes the establishment of a pleural-based model of malignant mesothelioma in immune-competent Fischer rats. METHODS: Via a modified left anterior lateral thorocotomy, a syngeneic malignant mesothelioma cell line, called II-45, was placed into the pleural cavity of Fischer rats. RESULTS: Placement of II-45 cells into the pleural cavity of Fischer rats results in a model of pleural mesothelioma that closely resembles the disease seen in patients and is highly reproducible, with animals dying within 1 month. We also demonstrate the feasibility of adenoviral-mediated gene transfer to normal mesothelial cells lining the pleural cavity, as well as to malignant cells deep within the substance of pleural-based malignant mesothelioma. CONCLUSIONS: The model described here offers the opportunity to study a variety of new treatment modalities, especially somatic gene transfer, against pleural-based malignant mesothelioma in an immune competent setting.

Adenoviridae↗

Subthalamic GAD gene transfer in Parkinson disease patients who are candidates for deep brain stimulation.

This gene transfer experiment is the first Parkinson's Disease (PD) protocol to be submitted to the Recombinant DNA Advisory Committee. The principal investigators have uniquely focused their careers on both pre-clinical work on gene transfer in the brain and clinical expertise in management and surgical treatment of patients with PD. They have extensively used rodent models of PD for proof-of-principle experiments on the utility of different vector systems. PD is an excellent target for gene therapy, because it is a complex acquired disease of unknown etiology (apart from some rare familial cases) yet it is characterized by a specific neuroanatomical pathology, the degeneration of dopamine neurons of the substantia nigra (SN) with loss of dopamine input to the striatum. This pathology results in focal changes in the function of several deep brain nuclei, which have been well-characterized in humans and animal models and which account for many of the motor symptoms of PD. Our original approaches, largely to validate in vivo gene transfer in the brain, were designed to facilitate dopamine transmission in the striatum using an AAV vector expressing dopamine-synthetic enzymes. Although these confirmed the safety and potential efficacy of AAV, complex patient responses to dopamine augmenting medication as well as poor results and complications of human transplant studies suggested that this would be a difficult and potentially dangerous clinical strategy using current approaches. Subsequently, we and others investigated the use of growth factors, including GDNF. These showed some encouraging effects on dopamine neuron survival and regeneration in both rodent and primate models; however, uncertain consequences of long-term growth factor expression and question regarding timing of therapy in the disease course must be resolved before any clinical study can be contemplated. We now propose to infuse into the subthalamic nucleus (STN) recombinant AAV vectors expressing the two isoforms of the enzyme glutamic acid decarboxylase (GAD-65 and GAD-67), which synthesizes the major inhibitory neurotransmitter in the brain, GABA. The STN is a very small nucleus (140 cubic mm or 0.02% of the total brain volume, consisting of approximately 300,000 neurons) which is disinhibited in PD, leading to pathological excitation of its targets, the internal segment of the globus pallidus (GPi) and substantia nigra pars reticulata (SNpr). Increased GPi/SNpr outflow is believed responsible for many of the cardinal symptoms of PD, i.e., tremor, rigidity, bradykinesia, and gait disturbance. A large amount of data based on lesioning, electrical stimulation, and local drug infusion studies with GABA-agonists in human PD patients have reinforced this circuit model of PD and the central role of the STN. Moreover, the closest conventional surgical intervention to our proposal, deep brain stimulation (DBS) of the STN, has shown remarkable efficacy in even late stage PD, unlike the early failures associated with recombinant GDNF infusion or cell transplantation approaches in PD. We believe that our gene transfer strategy will not only palliate symptoms by inhibiting STN activity, as with DBS, but we also have evidence that the vector converts excitatory STN projections to inhibitory projections. This additional dampening of outflow GPi/SNpr outflow may provide an additional advantage over DBS. Moreover, of perhaps the greatest interest, our preclinical data suggests that this strategy may also be neuroprotective, so this therapy may slow the degeneration of dopaminergic neurons. We will use both GAD isoforms since both are typically expressed in inhibitory neurons in the brain, and our data suggest that the combination of both isoforms is likely to be most beneficial. Our preclinical data includes three model systems: (1) old, chronically lesioned parkinsonian rats in which intraSTN GAD gene transfer results not only in improvement in both drug-induced asymmetrical behavior (apomorphine symmetrical rotations), but also in spontaneous behaviors. In our second model, GAD gene transfer precedes the generation of a dopamine lesion. Here GAD gene transfer showed remarkable neuroprotection. Finally, we carried out a study where GAD-65 and GAD-67 were used separately in monkeys that were resistant to MPTP lesioning and hence showed minimal symptomatology. Nevertheless GAD gene transfer showed no adverse effects and small improvements in both Parkinson rating scales and activity measures were obtained. In the proposed clinical trial, all patients will have met criteria for and will have given consent for STN DBS elective surgery. Twenty patients will all receive DBS electrodes, but in addition they will be randomized into two groups, to receive either a solution containing rAAV-GAD, or a solution which consists just of the vector vehicle, physiological saline. Patients, care providers, and physicians will be blind as to which solution any one patient receives. All patients, regardless of group, will agree to not have the DBS activated until the completion and unblinding of the study. Patients will be assessed with a core clinical assessment program modeled on the CAPSIT, and in addition will also undergo a preop and several postop PET scans. At the conclusion of the study, if any patient with sufficient symptomatic improvement will be offered DBS removal if they so desire. Any patients with no benefit will simply have their stimulators activated, which would normally be appropriate therapy for them and which requires no additional operations. If any unforeseen symptoms occur from STN production of GABA, this might be controlled by blocking STN GABA release with DBS, or STN lesioning could be performed using the DBS electrode. Again, this treatment would not subject the patient to additional invasive brain surgery. The trial described here reflects an evolution in our thinking about the best strategy to make a positive impact in Parkinson Disease by minimizing risk and maximizing potential benefit. To our knowledge, this proposal represents the first truly blinded, completely controlled gene or cell therapy study in the brain, which still provides the patient with the same surgical procedure which they would normally receive and should not subject the patient to additional surgical procedures regardless of the success or failure of the study. This study first and foremost aims to maximally serve the safety interests of the individual patient while simultaneously serving the public interest in rigorously determining in a scientific fashion if gene therapy can be effective to any degree in treating Parkinson's disease.

Cell Nucleus↗

Measuring force transfers in the deep flexors of the musician's hand: theoretical analysis, clinical examples.

In the present paper the anatomical and functional interdependencies which regularly exist between the deep flexor tendons of the different fingers are modelled. The model results are validated by measurements on real hands. The results show that intertendinous force transfers may be caused by (i) coactivation of muscle fibres inserting in different tendons, and (ii) passive connections between tendons or muscle bellies. The coactivation is validated by the measuring results of a hand in which all intertendinous connections were surgically removed. The present models and measurements are currently used for diagnosis of hand problems in musicians at our hand clinic.

Fingers↗

Predicting diffused-bubble oxygen transfer rate using the discrete-bubble model.

A discrete-bubble model that predicts the rate of oxygen transfer in diffused-bubble systems is evaluated. Key inputs are the applied gas flow rate and the initial bubble size distribution. The model accounts for changes in the volume of individual bubbles due to transfer of oxygen and nitrogen (and hence changing partial pressure), variation in hydrostatic pressure, and changes in temperature. The bubble-rise velocity and mass-transfer coefficient, both known functions of the bubble diameter, are continually adjusted. The model is applied to predict the results of diffused-bubble oxygen transfer tests conducted in a 14-m deep tank at three air flow rates. All of the test data are predicted to within 15%. The range of bubble diameters (0.2-2 mm) spans the region of greatest variation in rise velocity and mass-transfer coefficient. For simplicity, the Sauter-mean diameter is used rather than the full bubble size distribution without loss of accuracy. The model should prove useful in the design and optimization of hypolimnetic oxygenation systems, as well as other diffused-bubble applications.

Air Movements↗

The relative importance of the deep and superficial vascular systems for delay of the transverse rectus abdominis musculocutaneous flap as demonstrated in a rat model.

The use of some form of delay maneuver for "high-risk" patients before transfer of the superior pedicled lower transverse rectus abdominis musculocutaneous (TRAM) flap for breast reconstruction has augmented the rate of success in both the experimental and clinical arenas. A common method of vascular delay has been the bilateral division of both the superficial inferior epigastric and deep inferior epigastric vessels. Whether all of these must be divided to adequately effect the delay is unknown. For that matter, the relative importance of the superficial versus the deep vascular systems is unclear. To investigate this uncertainty, a delay was attempted in 61 Sprague-Dawley rats by division of either the superficial inferior epigastric or deep cranial epigastric vessels (the latter is the homologue to the human deep inferior epigastric) in unilateral or bilateral fashion. Division of the contralateral superficial inferior epigastric vessel resulted in significantly greater TRAM flap survival than either ipsilateral or bilateral superficial inferior epigastric vessel division (p = 0.0034 or p = 0.0093, respectively). Division of the ipsilateral or bilateral deep cranial epigastric vessel resulted in significantly greater flap survival than just contralateral deep cranial epigastric vessel division (p = 0.0034 or p = 0.006, respectively). No significant difference was observed between the group having contralateral superficial inferior epigastric or groups with ipsilateral deep cranial epigastric division, implying that either alone would be efficacious to achieve the desired delay effect. This would allow the other vascular system to be retained intact for later potential salvage maneuvers as needed.

Animals↗

A preclinical model of minimal residual cancer in the muscle highlights challenges associated with adenovirus-mediated p53 gene transfer.

PURPOSE: Clinical studies have revealed that tumors may recur at the operative site if radioresistant p53 mutation-positive residual disease remains in the body after treatment. Destruction of these remaining malignant cells, which can be present in both mucosal and deep muscle margins, may be achieved using p53-mediated gene transfer techniques. Most preclinical studies designed to assess the feasibility of harnessing this approach have used s.c. tumor models in nude mice, but it is anticipated that transduction of tumor cells in the muscle in immune-competent hosts may be more difficult. EXPERIMENTAL DESIGN: To address this point a new rodent model of residual cancer was established implanting PDVC57B tumor cells to create multiple tumor tracts in the muscle of syngeneic immune-competent C57Bl/6 mice. s.c. tumors and a s.c. model of residual disease were used as comparators. RESULTS: In the s.c. model of residual disease a single administration of 5 x 10(10) viral particles of Ad5CMV-p53 suppressed the growth of encapsulated tumor at the treatment site in six of six animals, but two of these animals had viable nests of tumor outside of the encapsulated zone. However, Ad5CMV-p53 had no apparent effect on tumor cell progression in the model of residual cancer in the muscle. Creating the muscle model of residual cancer with a lower number of cells in the initial inoculum showed that immune-mediated effects, as well as those attributable to the transgene, are important in preventing tumor outgrowth. The frequency of transduction of tumor cells in the muscle, as determined after administration of Ad-beta-galactosidase, was typically <3% and markedly different from the 20% transduction observed for the s.c. tumor model. CONCLUSIONS: These studies highlight the need to devise strategies to improve delivery of adenovirus-mediated gene transfer to nests of tumor in muscle before this modality is used to treat residual cancer at this site. These may involve approaches such as intravascular delivery, strategies to improve vector diffusion, or combination with chemotherapy or radiotherapy to enhance gene delivery at these less accessible sites of disease.

Adenoviridae↗

Electronic properties of sulfhydryl- and imidazole-containing peptide-cobalt(II) complexes: their relationship to cobalt(II)-substituted "blue" copper proteins.

The electronic properties of 2:1 sulfhydryl- and imidazole-containing peptide-Co(II) complexes have been investigated and compared with those of Co(II)-substituted "blue" copper proteins. The Co(II) complexes of N-mercaptoacetyl-L-histidine and 3-mercaptopropionyl-L-histidine gave the ligand field parameters of deltat = 4110 and B = 756 cm(-1), and of deltat = 4120 and B = 724 cm(-1), respectively. These values correspond well to those (deltat = 4900 and B = 730 cm(-1)) of Co(II)-substituted "blue" copper proteins. The energy differences between S leads to M(II) charge transfer bands of Co(II)-Cu(II) couples were about 14,000 cm(-1) in both the proteins and the model complexes. The spectral results suggest that "blue" copper site has a pseudotetrahedral geometry and a deep absorption near 600 nm atributes to S leads to Cu(II) charge transfer.

Cobalt↗