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Biomedical subjects

Jie Yang

Publications and source records attributed to Jie Yang.

At least 109 records · Page 6Linked to original sources

Design of recombinant stem cell factor-macrophage colony stimulating factor fusion proteins and their biological activity in vitro.

Stem cell factor (SCF) and macrophage colony stimulating factor (M-CSF) can act in synergistic way to promote the growth of mononuclear phagocytes. SCF-M-CSF fusion proteins were designed on the computer using the Homology and Biopolymer modules of the software packages InsightII. Several existing crystal structures were used as templates to generate models of the complexes of receptor with fusion protein. The structure rationality of the fusion protein incorporated a series of flexible linker peptide was analyzed on InsightII system. Then, a suitable peptide GGGGSGGGGSGG was chosen for the fusion protein. Two recombinant SCF-M-CSF fusion proteins were generated by construction of a plasmid in which the coding regions of human SCF (1-165aa) and M-CSF (1-149aa) cDNA were connected by this linker peptide coding sequence followed by subsequent expression in insect cell. The results of Western blot and activity analysis showed that these two recombinant fusion proteins existed as a dimer with a molecular weight of approximately 84 KD under non-reducing conditions and a monomer of approximately 42 KD at reducing condition. The results of cell proliferation assays showed that each fusion protein induced a dose-dependent proliferative response. At equimolar concentration, SCF/M-CSF was about 20 times more potent than the standard monomeric SCF in stimulating TF-1 cell line growth, while M-CSF/SCF was 10 times of monomeric SCF. No activity difference of M-CSF/SCF or SCF/M-CSF to M-CSF (at same molar) was found in stimulating the HL-60 cell linear growth. The synergistic effect of SCF and M-CSF moieties in the fusion proteins was demonstrated by the result of clonogenic assay performed with human bone mononuclear, in which both SCF/M-CSF and M-CSF/SCF induced much higher number of CFU-M than equimolar amount of SCF or M-CSF or that of two cytokines mixture.

Animals↗

Using fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types.

Membrane proteins are generally classified into the following five types: (1) type I membrane protein, (2) type II membrane protein, (3) multipass transmembrane proteins, (4) lipid chain-anchored membrane proteins, and (5) GPI-anchored membrane proteins. Given the sequence of an uncharacterized membrane protein, how can we identify which one of the above five types it belongs to? This is important because the biological function of a membrane protein is closely correlated with its type. Particularly, with the explosion of protein sequences entering into databanks, it is in high demand to develop an automated method to address this problem. To realize this, the key is to catch the statistical characteristics for each of the five types. However, it is not easy because they are buried in a pile of long and complicated sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. (2001). PROTEINS: Structure, Function, and Genetics 43: 246-255), the technique of Fourier spectrum analysis is introduced. By doing so, the sample of a protein is represented by a set of discrete components that can incorporate a considerable amount of the sequence order effects as well as its amino acid composition information. On the basis of such a statistical frame, the support vector machine (SVM) is introduced to perform predictions. High success rates were yielded by the self-consistency test, jackknife test, and independent dataset test, suggesting that the current approach holds a promising potential to become a high throughput tool for membrane protein type prediction as well as other related areas.

Amino Acids↗

Utility of radiology, laser fluorescence, and transillumination.

This article provides readers with an overview of the latest developments in caries detection using radiology, laser fluorescence, and transillumination. Different imaging techniques, methods to assess diagnostic accuracy, and factors affecting the diagnostic accuracy of imaging in film and digital receptors are discussed. In addition, the DIAGNOdent and DIFOTI devices are introduced as possible supplemental techniques for detecting incipient and hidden carious lesions.

Dental Caries↗

Structure-based engineering of E. coli galactokinase as a first step toward in vivo glycorandomization.

In vitro glycorandomization is a rapid chemoenzymatic strategy to diversify complex natural product scaffolds. The glycorandomization sugar activation pathway is dependent upon the efficient construction of diverse sugar-1-phosphate libraries. In the context of the previously evolved GalK Y371H "gatekeeper" mutation, the active site M173L mutation described herein presents a kinase with remarkably broadened substrate range to include 28 diverse natural and unnatural sugars. Among these new substrates, 6-azido-6-deoxy-galactose and 6-azido-6-deoxy-glucose present unique chemical probes to assess the utility of an E. coli Y371H/M173L-GalK-overproducing strain to generate unnatural sugar-1-phosphates in vivo. Remarkably, the in vivo conversion of both unnatural sugars rival that demonstrated in vitro. This notable in vivo success stands as the first step toward constructing short sugar-activation pathways in vivo and, ultimately, in vivo natural-product glycorandomization.

Binding Sites↗

IL-17R activation of human airway smooth muscle cells induces CXCL-8 production via a transcriptional-dependent mechanism.

Airway neutrophilia has been recognized as a predominant feature of acute lung disorders. While it has been shown that IL-17 induces expression of the CXC chemokines in the airways leading to neutrophil recruitment, the IL-17R expression in human ASM cells and the molecular mechanism by which IL-17 mediates neutrophilic chemo-attractant CXCL-8 (IL-8) production have not been determined. Our study showed that ASM cells express steady state IL-17R protein, mRNA and surface-bound receptor. Interestingly, airway sections from COPD patients revealed IL-17R-positive immunostaining within ASM bundles. IL-17 was capable of stimulating CXCL-8 protein release from ASM cells which was significantly decreased by neutralizing anti-IL-17 mAb. Furthermore, IL-17 induction of CXCL-8 mRNA and protein release from ASM cells was abrogated by transcriptional inhibitor actinomycin D. CXCL-8 promoter reporter analysis using wild type and site specific mutant constructs demonstrated a key role for AP1 and NF-kappaB binding sites in IL-17-induced CXCL-8 expression. These data demonstrate that IL-17 mediates CXCL-8 expression in ASM cells via a transcriptional mechanism depending on NF-kappaB and AP-1 pathways. Together, our findings suggest that ASM cells play an important role in airway neutrophilia.

Humans↗

Semi-automated brain tumor and edema segmentation using MRI.

PURPOSE: Manual segmentation of brain tumors from magnetic resonance images is a challenging and time-consuming task. A semi-automated method has been developed for brain tumor and edema segmentation that will provide objective, reproducible segmentations that are close to the manual results. Additionally, the method segments non-enhancing brain tumor and edema from healthy tissues in magnetic resonance images. METHODS AND MATERIALS: In this study, a semi-automated method was developed for brain tumor and edema segmentation and volume measurement using magnetic resonance imaging (MRI). Some novel algorithms for tumor segmentation from MRI were integrated in this medical diagnosis system. We exploit a hybrid level set (HLS) segmentation method driven by region and boundary information simultaneously, region information serves as a propagation force which is robust and boundary information serves as a stopping functional which is accurate. Ten different patients with brain tumors of different size, shape and location were selected, a total of 246 axial tumor-containing slices obtained from 10 patients were used to evaluate the effectiveness of segmentation methods. RESULTS: This method was applied to 10 non-enhancing brain tumors and satisfactory results were achieved. Two quantitative measures for tumor segmentation quality estimation, namely, correspondence ratio (CR) and percent matching (PM), were performed. For the segmentation of brain tumor, the volume total PM varies from 79.12 to 93.25% with the mean of 85.67+/-4.38% while the volume total CR varies from 0.74 to 0.91 with the mean of 0.84+/-0.07. For the segmentation of edema, the volume total PM varies from 72.86 to 87.29% with the mean of 79.54+/-4.18% while the volume total CR varies from 0.69 to 0.85 with the mean of 0.79+/-0.08. The HLS segmentation method perform better than the classical level sets (LS) segmentation method in PM and CR. CONCLUSIONS: The results of this research may have potential applications, both as a staging procedure and a method of evaluating tumor response during treatment, this method can be used as a clinical image analysis tool for doctors or radiologists.

Algorithms↗

Differential expression of survivin-2B and survivin-DeltaEx3 is inversely associated with disease relapse and patient survival in non-small-cell lung cancer (NSCLC).

Although it was observed that inhibition of the antiapoptotic protein survivin expression in lung cancer cells induces apoptosis, the expression and role of survivin variants (survivin-2B and survivin-DeltaEx3) in lung cancer have not yet been characterized. We analyzed 24 non-small-cell lung cancer (NSCLC) samples by semi-quantitative RT-PCR. Surprisingly, our results revealed that high-level expression of survivin-2B is significantly associated with the patient category of "no relapse and alive" (p-value<0.0001). In contrast, high-level expression of survivin-DeltaEx3 is highly associated with the patient category of "relapse and dead" (p-value<0.0001). Consistent with this observation, exogenous expression of survivin-2B in A549 lung cancer cells inhibited cell growth, disrupted the mitochondria potential, and induced apoptotic cell death, while expression of survivin-DeltaEx3 protected the mitochondria potential and facilitated cell survival. These findings provide evidence that survivin-2B and survivin-DeltaEx3 play opposite roles in disease relapse and NSCLC cell survival, which is likely through the differential modulation of mitochondrial potential. Thus, controlling the differential expression of survivin-2B and survivin-DeltaEx3 may represent novel approaches for cancer therapeutics in NSCLC.

Apoptosis↗

Dosimetric advantage and clinical implication of a micro-multileaf collimator in the treatment of prostate with intensity-modulated radiotherapy.

This paper investigates the dosimetric benefits of a micro-multileaf (4-mm leaf width) collimator (mMLC) for intensity-modulated radiation therapy (IMRT) treatment planning of the prostate cancer and its potential application for dose escalation and hypofractionation. We compared treatment plans for IMRT delivery using 2 different multileaf collimator (MLC) leaf widths (4 vs. 10 mm) for 10 patients with prostate cancer. Treatment planning was performed on the XknifeRT2 treatment planning system. All beams and optimization parameters were identical for the mMLC and MLC plans. All of the plans were normalized to ensure that 95% of the planning target volume (PTV) received 100% of the prescribed dose (74 Gy). The differences in dose distribution between the 2 groups of plans using the mMLC and the MLC were assessed by dose-volume histogram (DVH) analysis of the target and critical organs. Significant reductions in the volume of rectum receiving medium to higher doses were achieved using the mMLC. The average decrease in the volume of the rectum receiving 40, 50, and 60 Gy using the mMLC plans was 40.2%, 33.4%, and 17.7%, respectively, with p-values less than 0.0001 for V40 and V50 and 0.012 for V60. The mean dose reductions for D17 and D35 for the rectum were 20.0% (p < 0.0001) and 18.3% (p < 0.0002), respectively, when compared to those with the MLC plans. There were consistent reductions in all dose indices studied for the bladder. The target dose inhomogeneity was improved in the mMLC plans by an average of 32%. In the high-dose range, there was no significant difference in the dose deposited in the "hottest" 1 cc of the rectum between the 2 MLC plans for all cases (p > 0.78). Because of the reduction of rectal volume receiving medium to higher doses, dose to the prostate target can be escalated by about 20 Gy to over 74 Gy, while keeping the rectal dose (either denoted by D17 or D35) the same as those with the use of the MLC. The maximum achievable dose, derived when the rectum is allowed to reach the tolerance level, was found to be in the range of 113-172 Gy (using the tolerance value of D17). We conclude that the use of the mMLC for IMRT of the prostate may facilitate dose hypofractionation due to its dosimetric advantage in significantly improving the DVH parameters of the prostate and critical organs. When used for conventional fractionation scheme, mMLC for IMRT of the prostate may reduce the toxicity to the critical organs.

Equipment Design↗

Radiomorphometric indices and their relation to gender, age, and dental status.

OBJECTIVES: To evaluate the antegonial index (AI) and the mental index (MI) in edentulous and dentate patients, in different age groups and between genders. STUDY DESIGN: We evaluated 312 panoramic radiographs and grouped them into 4 10-year age groups. Gender, dentition status and age were recorded. The measurements were performed by 2 researchers independently. RESULTS: The AI and MI were significantly smaller in older females, whereas they were greater for older males (P < 0.01). Edentulous individuals had a lower AI than dentate and partially dentate individuals (P < 0.01). CONCLUSIONS: There is a continuous remodelling in the mandibular cortex with age and this is influenced by dental status and gender. The difficulty of measuring the AI in a reproducible manner, its interaction with dental status and low correlation with MI in younger patients should discourage its use in detecting patients at risk of osteoporosis.

Adult↗

Gene expression alteration during redox-dependent enhancement of arsenic cytotoxicity by emodin in HeLa cells.

Emodin (1,3,8-trihydroxy-6-methylanthraquinone) could enhance the sensitivity of tumor cells to arsenic trioxide (As2O3)-induced apoptosis via generation of ROS, but the molecular mechanism has not been elucidated. Here, we carried out cDNA microarray-based global transcription profiling of HeLa cells in response to As2O3/emodin cotreatment, comparing with As2O3-only treatment. The results showed that the expression of a number of genes was substantially altered at two time points. These genes are involved in different aspects of cell function. In addition to redox regulation and apoptosis, ROS affect genes encoding proteins associated with cell signaling, organelle functions, cell cycle, cytoskeleton, etc. These data suggest that based on the cytotoxicity of As2O3, emodin mobilize every genomic resource through which the As2O3-induced apoptosis is facilitated.

Apoptosis↗

NestinnegCD24low/- population from fetal Nestin-EGFP transgenic mice enriches the pancreatic endocrine progenitor cells.

OBJECTIVES: To identify whether Nestin-positve cells or Nestin-negative cells in pancreas enrich potential pancreatic stem/progenitor cells. METHODS: We generated transgenic mice carrying enhanced green fluorescent protein (EGFP) under the control of the nestin second-intronic enhancer and subsequently divided their embryonic pancreatic cells into different subpopulations according to the expression of EGFP and CD24 and characterized these subpopulations by in vitro culture. RESULTS: The EGFP expression correlated well with that of endogenous Nestin. Only the NestinCD24 subpopulation was able to proliferate and generate immature islet-like cell clusters in long-term culture. Immature islet-like cell clusters could be induced to differentiate into insulin-, glucagon-, and somatostatin-positive cells. CONCLUSIONS: Pancreatic endocrine stem/progenitor cells are enriched in the NestinCD24 population of embryonic pancreas.

Animals↗

Crystal structure of the E230Q mutant of cAMP-dependent protein kinase reveals an unexpected apoenzyme conformation and an extended N-terminal A helix.

Glu230, one of the acidic residues that cluster around the active site of the catalytic subunit of cAMP-dependent protein kinase, plays an important role in substrate recognition. Specifically, its side chain forms a direct salt-bridge interaction with the substrate's P-2 Arg. Previous studies showed that mutation of Glu230 to Gln (E230Q) caused significant decreases not only in substrate binding but also in the rate of phosphoryl transfer. To better understand the importance of Glu230 for structure and function, we solved the crystal structure of the E230Q mutant at 2.8 A resolution. Surprisingly, the mutant preferred an open conformation with no bound ligands observed, even though the crystals were grown in the presence of MgATP and the inhibitor peptide, IP20. This is in contrast to the wild-type protein that, under the same conditions, prefers the closed conformation of a ternary complex. The structure highlights the importance of the electrostatic surface not only for substrate binding and catalysis, but also for the mechanism for closing the active site cleft. This surface mutation clearly disrupts the recognition and binding of substrate peptide so that the enzyme prefers an open conformation that cannot trap ATP. This is consistent with the reinforcing concepts of conformational dynamics and the synergistic binding of ATP and substrate peptide. Another unusual feature of the structure is the observation of the entire N terminus (Gly1-Thr32) assumes an extended alpha-helix conformation. Finally, based on temperature factors, this mutant structure is more stable than the wild-type C-subunit in the apo state.

Adenosine Triphosphate↗

Intranasal inoculation of Chlamydia trachomatis mouse pneumonitis agent induces significant neutrophil infiltration which is not efficient in controlling the infection in mice.

Previous studies have shown that chlamydial infection is accompanied by significant infiltration of neutrophils at the site of infection. However, the role of neutrophils in host defence against chlamydial infection is not clearly understood. Using genetically different inbred mouse strains and CXCR-2 gene knockout (KO) mice, we examined the mechanism for neutrophil recruitment and the role of neutrophils during chlamydial lung infection. Our data showed that C3H mice exhibited significantly higher and more persistent neutrophil infiltration in the lung than did C57BL/6 mice following Chlamydia trachomatis mouse pneumonitis infection. The massive neutrophil infiltration in C3H mice was paralleled by high-level expression of CXCR-2 and its ligands, CXC chemokines (macrophage inflammatory protein 2, cytokine-induced neutrophil attractant (KC) and lipopolysaccharide-induced CXC chemokine), and proinflammatory cytokines (tumour necrosis factor-alpha, interleukin-1 and interleukin-6) in the lung. Although much greater infiltration of neutrophils was observed in C3H mice than in C57BL/6 mice, the former mice had more severe disease and higher in vivo chlamydial growth than the latter. Moreover, CXCR-2 KO mice, which revealed a dramatic reduction in neutrophil activity, showed comparable chlamydial infection to wild-type mice. These results suggest that neutrophils are not efficient for controlling chlamydial lung infection.

Administration, Intranasal↗

Resistance to chlamydial lung infection is dependent on major histocompatibility complex as well as non-major histocompatibility complex determinants.

Our previous work has shown that C3H/HeN and C57BL/6 mice have differential susceptibility to Chlamydia trachomatis mouse pneumonitis (C. muridarum) lung infection. C3H/HeN (H-2(k)) mice were found to be highly susceptible to C. muridarum infection with higher mortality and more severe morbidity compared to C57BL/6 (H-2(b)) mice. To examine the role of major histocompatibility complex (MHC) genes on host resistance to chlamydial lung infection, we compared MHC congenic mice, B6.H2k [C57BL/6 background, C3H MHC (H-2(k))] and C3H.H2b [C3H/HeN background, C57BL/6 MHC (H-2(b))] and their corresponding wild type C57BL/6 mice and C3H/HeN mice, respectively, in susceptibility to C. muridarum infection. We found that B6.H2k, C3H.H2b and C3H/HeN mice are more susceptible to chlamydial lung infection compared to the wild type C57BL/6 mice by showing more serious body weight loss, higher in vivo chlamydial growth and more severe pathologic changes. Congenic B6.H2k mice showed significantly lower levels of IL-12 and IFN-gamma production compared to C57BL/6 as well as C3H/HeN and C3H.H2b mice. One the other hand, although congenic C3H.H2b mice displayed similar cytokine response to C57BL/6 mice, they were highly susceptible to C. muridarum infection. Overall, the results suggest that protection against chlamydial lung infection is both MHC and non-MHC gene dependent, and that the interaction between MHC and non-MHC elements may contribute to host resistance to chlamydial infection.

Animals↗

Predictive model of blood-brain barrier penetration of organic compounds.

AIM: To build up a theoretical model of organic compounds for the prediction of the activity of small molecules through the blood-brain barrier (BBB) in drug design. METHODS: A training set of 37 structurally diverse compounds was used to construct quantitative structure-activity relationship (QSAR) models. Intermolecular and intramolecular solute descriptors were calculated using molecular mechanics, molecular dynamics simulations, quantum chemistry and so on. The QSAR models were optimized using multidimensional linear regression fitting and stepwise method. A test set of 8 compounds was evaluated using the models as part of a validation process. RESULTS: Significant QSAR models (R=0.955, s=0.232) of the BBB penetration of organic compounds were constructed. BBB penetration was found to depend upon the polar surface area, the octanol/water partition coefficient, Balaban Index, the strength of a small molecule to combine with the membrane-water complex, and the changeability of the structure of a solute-membrane-water complex. CONCLUSION: The QSAR models indicate that the distribution of organic molecules through BBB is not only influenced by organic solutes themselves, but also relates to the properties of the solute-membrane-water complex, that is, interactions of the molecule with the phospholipid-rich regions of cellular membranes.

Blood-Brain Barrier↗

Predicting MDCK cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis.

AIM: To use membrane-interaction quantitative structure-activity relationship analysis (MI-QSAR) to develop predictive models of partitioning of organic compounds in gastrointestinal cells. METHODS: A training set of 22 structurally diverse compounds, whose apparent permeability across cellular membranes of Madin-Darby canine kidney (MDCK) cells were measured, were used to construct MI-QSAR models. Molecular dynamic simulations were used to determine the explicit interaction of each test compound (solute) with a dimyristoyl-phosphatidyl-choline monolayer membrane model. An additional set of intramolecular solute descriptors were computed and considered in the trial pool of descriptors for building MI-QSAR models. The QSAR models were optimized using multidimensional linear regression fitting and the stepwise method. A test set of 8 compounds were evaluated using the MI-QSAR models as part of a validation process. RESULTS: MI-QSAR models of the gastrointestinal absorption process were constructed. The descriptors found in the best MI-QSAR models are as follows: 1) ClogP (the logarithm of the 1-octanol/water partition coefficient); 2) E(HOMO) (the highest occupied molecular orbital energy); 3) E(s) (stretch energy); 4) PM(Y) (the principal moment of inertia Y, the inertia along the y axis in the rectangular coordinates; 5) C(t) (total connectivity); and 6) E(nb) (the energy of interactions between all of the non-bonded atoms). The most important descriptor in the models is ClogP. CONCLUSION: Permeability is not only determined by the properties of drug molecules, but is also very much influenced by the molecule-membrane interaction process.

Animals↗

A new method of incorporating systematic uncertainties in intensity-modulated radiotherapy optimization.

Uncertainties in tumor position during intensity-modulated radiotherapy (IMRT) plan optimization are usually accounted for by adding margins to a clinical target volume (CTV), or additionally, to organs at risk (OAR). The former approach usually favors target coverage over OAR protection, whereas the latter does not account for correlation in target and OAR movement. We investigate a new approach to incorporate systematic errors in tumor and organ position. The method models a distribution of systematic errors due to setup error and organ motion with displaced replicas of volumes of interest, each representing the patient geometry for a possible systematic error, and maximizes a score function that counts the number of replicas meeting dose or biological constraints for both CTV and OAR. Dose constraints are implemented by logistic functions of Niemierko's generalized model of equivalent uniform dose (EUD). The method is applied to prostate and nasopharynx IMRT plans, in which CTV and OAR each consists of five replicas, one representing no error (the position in the planning CT) and the other four discrete systematic setup displacements in one dimension with equal probability. The resulting IMRT plans are compared with those from two other EUD-based optimizations: a standard planning target volume (PTV) approach consisting of a single replica of each OAR in the planned position and a single PTV encompassing all CTV replicas, and a PTV-PRV approach consisting of a single PTV and a single planning risk volume (PRV) for each OAR encompassing all replicas. When systematic error is present, multiple-replica optimization provides better critical organ protection while maintaining similar target coverage compared with the PTV approach, and provides better CTV-to-OAR therapeutic ratio compared with the PTV-PRV instances where there is substantial PTV-PRV overlap. The method can be used for other systematic errors due to organ motion and deformation.

Body Burden↗

Analysis of rat calvaria defects implanted with a platelet-rich plasma preparation: radiographic observations.

BACKGROUND: Platelet-rich plasma (PRP) harbors growth factors identified in bone. It has been suggested that these factors enhance osteogenesis. The objective of this study was to conduct a radiographic evaluation on local bone formation following surgical implantation of a PRP preparation using a critical-size rat calvaria defect model. METHODS: Thirty 22-week-old male Sprague-Dawley rats were used. The PRP preparation was obtained from 10 ml of whole blood drawn from one age-matched donor rat. The preparation was processed by gradient density centrifugation and stored at -80 degrees C until use. Using aseptic techniques, the PRP preparation soak-loaded onto an absorbable collagen sponge (ACS) carrier or ACS alone was surgically implanted into contralateral critical-size 6 mm rat calvaria osteotomies in 18 animals. Twelve animals received ACS alone versus sham surgery in contralateral defects. Animals were sacrificed at 4 and 8 weeks when biopsies were collected and radiographs were obtained using a standardized protocol. Three masked examiners independently evaluated the radiographic images of the defect sites. Examiner reproducibility was examined by repeat evaluation of all defect sites (r=0.6; P <0.0001). RESULTS: The animals were maintained without adverse events. Defect sites in two animals receiving ACS versus sham surgery (4-week healing interval) were not evaluated due to specimen damage. Seventy-five percent of the sites (PRP/ACS or ACS) exhibited partial closure at 4 weeks; one site (ACS) exhibited full closure without significant differences between protocols (P=0.1797). Fifty percent of the sites receiving PRP/ACS exhibited full closure and 20% partial closure at 8 weeks versus 20% and 80%, respectively, for the ACS control (P=0.7532). There were no noteworthy differences between sites receiving ACS versus sham surgery at 4 or 8 weeks. CONCLUSION: The results suggest that the PRP preparation does not have a significant effect on osteogenesis.

Animals↗