Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction

3DPD: A photogrammetric pipeline for a PUSH frame stereo cameras

Purpose: Arbitrary Lagrangian‐Eulerian (ALE) moving mesh is a finite‐element based technique that preserves mass and topology during deformation. We have developed a two‐dimensional (2D) image registration method using ALE moving mesh. This study is aimed to extend the method for three‐dimensional (3D) deformable image registration.Method and Materials: The image registration is contour‐based. 3D structures are reconstructed using slice images. A dynamic contour method is used to establish the correspondence of the surface points between a reference image and a target image. ALE mesh is generated in the reference image. With the correspondence of the surface points, the surface of the reference image is deformed to match the surface of the target image. The displacement of the moving surface propagates to the interior nodes throughout the domain. Displacement vectors of the volume can be obtained and the deformation of the interior can be tracked. Results: Two sets of 3D CTimages of a patient's head and neck tumor were used in the study, which were taken on different dates. The external contour (volume) of the first set of images was taken as the reference and that of the second set of images was taken as the target. By moving the surface of the reference to match the surface of the target, displacement vectors of the domain enclosed by the surface were derived from the moving mesh, which were then examined with the deformation of gross target volume (GTV). The image‐warped GTV was found similar to the GTV of the second set of images.Conclusions: It is feasible to perform 3D deformable image registration using ALE moving mesh. Further studies are needed to verify the accuracy of this method by either improving the technique for surface matching or comparing with other more established method of deformable image registration.

The threshold of cyclin E expression at G1/S boundary is a characteristic feature of cell cycle progressing. In this study, we tried to develop a quantitative approach to analyze cyclin E threshold by multiparameter flow cytometry. The expression of cyclin E in exponentially growing MOLT-4 cells was detected under different photomultiplier tube (PMT) voltages by cyclin E/DNA multiparameter flow cytometry. Additionally, cyclin E was detected in cells which were treated with caffeine and cycloheximide (CHX) under the same PMT voltage. Moreover, the expression of cyclin E in MOLT-4 cells was compared with that in JURKAT cells. Cyclin E threshold was quantified by formula B2/AxC (A, B, C indicates the minimum, threshold, and maximum of cyclin E fluorescence intensity, respectively). Results showed that in MOLT-4 cells, cyclin E threshold calculated by formula B2/AxC was invariable under different PMT settings. It was decreased in cells treated with caffeine and remained changeless in cells treated with cycloheximide. Cyclin E threshold in JURKAT cells was much lower than that in MOLT-4 cells. It was suggested that Formula B2/AxC we firstly set up could be used to analyze cyclin E expression threshold quantitatively.

In the photoelectric detection system, the photoelectric detector can convert the optical signal to be measured into a current signal, and the current amplifier transforms the current signal output by the detector into a voltage signal for amplification. In this study, the photo-multiplier tube (PMT) is selected as the photoelectric detector. Compared with other photoelectric detectors, it can obtain higher internal gain, higher sensitivity, and better response performance. The current amplifier is prepared by pre-amplifier and voltage amplifier. In order to capture photoelectric signals well, a large-format scanning system is set up to design each component module, control module, and host computer module of the system. Besides, a machine learning-based algorithm is proposed, namely semi-supervised manifold image recognition algorithm, which is used for identify photoelectric detection images. In the test process, the printed circuit board (PCB) and sapphire material are firstly used as the substrate of the current amplifier, and their influences in the circuit are compared. The peak value of the output noise of each substrate circuit is around 2.8 mV when the input of the current amplifier is short-circuited. Then, the signal gain and signal bandwidth of the photoelectric detection system remain stable when there is no optical signal input. During the process of changing the system signal gain ratio, the noise output of the system is the lowest when the voltage of PMT is 0.50 V and the current amplifier gain is set to 2.2 × 105 V/A. The proposed recognition algorithm can identify different types of targets well. After the image is projected into a two-dimensional space by the algorithm, the distance between classes increases, and the targets in the class promote aggregation, thereby enhancing the identify-ability between samples.

BackgroundParkinson’s disease is the second most common age-related neurodegenerative disease after Alzheimer’s. Pathogenic factors in Parkinson’s include inflammation and oxidative stress, which lead to dopaminergic cell apoptosis. The case–control study aims to determine the expression level of long non-coding RNAs (lncRNAs) of the apoptosis pathway in Parkinson’s patients compared to healthy individuals. In the case–control study, 50 patients with Parkinson’s disease were examined, along with 50 healthy individuals matched in age and sex. In both groups, the expression of long non-coding RNAs, including taurine upregulated 1 (TUG1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), nuclear-enriched abundant transcript 1 (NEAT1), and growth arrest-specific 5 (GAS5), was compared using real-time polymerase chain reaction (PCR).ResultsThe ratio of MALAT1, NEAT1, and TUG1 gene expression in the case group was statistically significantly higher than in healthy individuals. The ratio of GAS5 gene expression in people with Parkinson’s disease was lower, with a statistically significant difference. The ratio of HULC gene expression was higher in the case group, but it did not show a statistically significant difference with the control group.ConclusionThe involvement of long lncRNAs that increase apoptosis may play a role in the pathogenesis of the disease, which may be used for identification and therapeutic purposes.

Low osteocalcin/collagen type I bone gene expression ratio is associated with hip fragility fractures

Comparative analysis of amplified and nonamplified RNA for hybridization in cDNA microarray

The apoptosis inducing effect of Glycosmis pentaphylla (Retz.) Correa and its influence on gene expression in hepatocellular carcinoma cell line, Hep3 B

The fading of TLD-100 as a function of crystal size, radiation energy, and total dose is being studied. A light source (tritium-activated phosphor) is used as a standard in a commercial reader (Model S-2LC, Madison Research and Development Laboratories, Inc.). The response of TLD-100 is recorded and then normalized to the variations of the “standard.” The fading indicated by these normalized readings is thought to represent a truer picture of the actual fading than results obtained without normalizing to a standard. The TLD-100 was separated into three different crystal sizes, using the U. S. Standard Sieve Series—powder that remained on the #100 and on the #200, and that which passed through the #200 Tyler equivalent mesh. A 50-50 mixture of the #100 and #200 also was used. Exposures of approximately 100 R from C060 and 200 kVp x rays were used to study the effect of different energies and crystal sizes; exposures of 50 R and 500 R from C060 were employed to study the effect of different exposures. The powder dispenser as furnished by Madison Research and Development Laboratories, Inc., was utilized. The photomultiplier tube voltage was 1,777 volts for the 100 R exposures, and 1,400 volts for the 50 R and 500 R C060 exposures. The heating cycle was terminated at the end of twenty-two seconds; peak temperature of the heater pan was 345° C. Readings of the light source and for some of the powder at various times after exposure of the powder are shown in Figure 1, A. The variations in the readings of the light source can be attributed to such causes as voltage changes and fatigue and thermal effects. Normalizing the readings for the powder to the readings of the light source gives values which represent the fading of the powder (Fig. 1, B). These normalized curves have fewer fluctuations and compare favorably with the fading curves of others (1), including a return to approximately the initial value at seven weeks. It appears that fading is not a function of radiation energy, crystal size, or total dose for this batch of powder. We are currently examining several different batches of powder in the same manner.

355 Background: Management of patients with localized or locally advanced renal cell cancer (RCC) involves surgical resection. However, 20-40% of all localized kidney cancer patients experience a recurrence. Adjuvant treatment in high-risk kidney cancer has not proven to successfully improve overall survival (OS) and the only drug approved so far in this setting is vascular endothelial growth factor (VEGF) inhibitor, sunitinib. As multiple trials are evaluating drugs including immune checkpoint inhibitors in patients with high risk localized clear cell RCC, there is an urgent need to identify biomarkers to help with therapeutic decisions as well as for risk stratification. Here we present analysis pertaining to genes involved in metabolic reprogramming in kidney cancer. Methods: A deep transcriptomic analysis of patients with stage III ccRCC in the TCGA KIRC Firehose Legacy cohort was undertaken. Caucasian males with stage III ccRCC in the TCGA cohort for whom recurrence data was available with a minimum follow-up of 2 years were identified for the analysis. Expression profiles of differentially expressed genes were clustered using the Bayesian infinite mixture model and samples clustered using average linkage hierarchical clustering based on pairwise Pearson’s correlations as the measure of similarity. Enrichment analysis of up- and down-regulated genes was performed using logistic regression. R package was used to generate Kaplan-Meier curves and assess statistical significance of differences in overall and disease-free survival using log-rank test. Results: The cohort evaluated for this study included Caucasian male patients that remained disease free for at least 24 months after surgery (n = 22) and patients whose cancer recurred within 24 months (n = 20). We identified metabolic genes, encoding subunits of mitochondrial electron transport chain as well as malate aspartate shuttle (MAS), where loss of coordinated co-expression between these genes identified patients at risk of recurrence after surgery. The gene signature stratified the 42 patients into three subtypes: significantly enriched for a) recurrence (subtype 1), for b) disease free status (subtype 2) and b) intermediate (subtype 3). Work is underway to combine the use of individual gene expression and ratios of gene expression within the signature to optimize prognostic biomarkers for localized ccRCC. Conclusions: In this analysis, we have identified a novel metabolic gene signature which can help identify patients with localized ccRCC at high risk of recurrence after surgery to guide aggressive therapy. These findings require further validation in tumors collected from patients with stage III ccRCC.

Innovative airglow instrument based on constant photon count control

Thyroid hormones play a vital function in the maturation in the course of mind development. Regarding the well-known effects of choline on brain-derived neurotrophic factor (BDNF), the study examined the effects of choline on hippocampal BDNF gene expression in maternal hypothyroidism rats. To induce the hypothyroidism, 6-propyl-2-thiouracil was introduced to the ingesting water from the sixth day of gestation to twenty-first postnatal day (PND). Choline-treatment started twice a day on the first day of gestation until PND 21. On PND28, pups were sacrificed. The expression of BDNF gene was evaluated after the hippocampus was harvested. Our results demonstrated that both male and female pre-pubertal offspring rats' BDNF gene expression was decreased by developmental hypothyroidism. Choline increases the ratio of relative gene expression of BDNF in the hippocampus of males and females in the control/hypothyroidism group, especially in males. It can be concluded that maternal choline supplementation on the first day of gestation until PND 21 improves brain development and cognitive function in pre-pubertal offspring rats regarding control/hypothyroidism groups.

After screening a bacterial artificial chromosome of human genomic DNA library with human HS-40, zeta-, alpha-, and theta-globin probes, a 110-kb clone bearing the whole human alpha-globin gene cluster was obtained and rare restriction endonuclease mapping was performed. The bacterial artificial chromosome DNA was isolated, and transgenic mice were generated. Three founders were detected from 35 newborn mice. The copy numbers were 1, 2, and 2, and the expression of human alpha-globin genes in various tissues at different developmental stages in the transgenic mice was assayed. The human alpha-globin mRNA can be detected in bone marrow, kidney, liver, brain, but not in muscle, testis, or thymus. The human zeta-globin genes were switched off, and the alpha-globin genes were switched at day 11.5 in mouse embryo, indicating that developmental stage-specific expression of the alpha-like globin genes was properly regulated. The human alpha-globin mRNA ranged between 17-68% of the endogenous mouse alpha-globin, suggesting that the expression of human alpha-globin genes is integration site-dependent in transgenic mice. The ratio of human alpha(2)- and alpha(1)-globin gene expression in adult transgenic mouse is about 2.5:1 similar to the expression in human.

3 We have initiated studies to test the hypothesis that altered intra-renal NFκB regulation and increased expression of NFκB-regulated proteins such as IL-8 and angiotensinogen are involved in the pathogenesis of post-transplant recurrent FSGS. IκBα binds to NFκB, preventing this nuclear factor from upregulating the expression of proinflammatory proteins. Steroids enhance IκBα gene expression. Altered NFκB regulation could result in increased expression of NFκB-regulated factors, allowing pathological processes to be resistant to steroid therapy. We used reverse transcription-assisted competitive PCR to quantify the magnitude of intragraft gene expression of NFκB (p65), IκBα, angiotensinogen, and IL-8 in 65 pediatric renal allograft biopsies including 20 with FSGS and 45 without FSGS. Results are expressed as mean ± s.e. for the quantitative ratio of target gene expression corrected for expression of GAPDH. Our results show elevated intragraft expression of NFκB/IκBα ratio, IL-8, and angiotensinogen in FSGS vs. NON-FSGS, although only angiotensinogen reached statistical significance: TableIn order to perform combined gene analysis, samples were deemed positive for a target gene if the amount of target gene expression was above the 95% upper confidence limit of gene expression for NON-FSGS. Samples positive for 2 or more target genes were separated from samples positive for one or no genes. Of all the FSGS samples, 55% of samples were observed in the group with ≥ 2 genes positive while only 17.8% of NON-FSGS samples were observed in this group (χ2 = 9.274, p<0.005). These preliminary results demonstrate altered expression of NFκB and NFκB-regulated proteins in post-transplant recurrent FSGS. It is likely that altered NFκB regulation accounts for the variable clinical picture of recurrent FSGS post-transplantation. Angiotensin II, the final end-product of angiotensinogen may mediate the steroid-resistant proteinuria and progressive glomerular damage characteristic of this disorder. Further correlation of intragraft IL-8 and angiotensinogen gene expression with clinical status will provide opportunities for innovative therapeutic trials.

In this study, we elucidated the differential expression of a set of local molecular factors in ectatic cone area of the cornea to uncover a functional cause for focal corneal weakening characteristic of the keratoconus (KC) disease. All human corneal samples were collected after approval of Institutional Ethics Committee and informed consent. Keratoconus patients were classified based on clinical parameters, topographical features, and structural deformity. Epithelial cells were collected from KC patients (n = 66) undergoing corneal cross-linking procedures from cone apex and periphery. Nonectatic refractive surgery patients (n = 23) served as controls. The ratio of epithelial gene expression in cone and periphery of each eye was estimated by quantitative PCR and correlated with clinical data. Similar cone versus periphery analysis was done from the KC stroma and from KC patients with Bowman's layer (BL) breach observed by anterior segment optical coherence tomography (OCT). Epithelium from the cone apex of KC patients had elevated levels of inflammatory factors TNF-α, IL-6, and matrix metalloproteinase 9 (MMP-9) but reduced Lysyl oxidase (LOX) and Collagen IVA1, which also demonstrated correlation with corneal curvature and deformity parameters. Stromal gene expression from KC patients showed trends similar to epithelium. Epithelium collected from the cone apex of BL breached KC patients showed significantly elevated MMP-9, TNF-α, and IL-6 levels but reduced IL-10, tissue inhibitor of metalloproteinases 1 (TIMP-1), and Collagen IVA1 expression. This study provides the first evidence that altered corneal epithelial and stromal expression of specific genes at the corneal cone apex drives focal structural weakness in KC.