Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data

The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.

Reducing temperature sensitivity of gas measurement using chirped-modulated photoacoustic spectroscopy

Resonance frequency drift caused by a change in temperature greatly limits the application of high-Q resonators with high temperature sensitivity in photoacoustic (PA) gas detection systems. In this work, a chirp-wavelength combined modulation method was designed by incorporating a real-time frequency scanning in wavelength-modulated PA spectroscopy to reduce the influence of temperature changes on measurement. Theoretical analysis shows that the chirp rate depends on the precision requirements and the cutoff frequency of the cascaded low-pass filter. Trace acetylene measurement experiment at varying temperature verified that the proposed method can significantly reduce the temperature sensitivity within a preset temperature range. Thus, this method can effectively reduce the temperature sensitivity of a high-Q resonator for improving the measurement accuracy and detection limit in trace gas detection.

Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency

Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.

[Current status of hyperkalemia in dialysis patients in China]

Objective: To investigate the prevalence and associated factors of hyperkalemia in dialysis patients. Methods: Patients underwent hemodialysis (HD) and peritoneal dialysis (PD) from multi-center databases were recruited from January 2017 to December 2019, and those aged ≥18 years and with dialysis duration ≥3 months were included to analyze the prevalence and related factors of hyperkalemia. Results: A total of 12 364 patients were enrolled in the study, and 6 836 cases were men. The average age of the patients was (51±15) years. Among these patients, 4 230 cases underwent HD while 8 134 received PD. Hyperkalemia was detected in 20.7% (2 554/12 364) of the patients while hypokalemia was found in 17.0%(2 102/12 364) of the patients. Multivariate logistic regression showed that HD (OR=2.25, 95%CI: 1.54-3.30), diabetes mellitus (DM) (OR=1.65, 95%CI: 1.17-2.32), high body mass index (BMI) (OR=1.06, 95%CI: 1.03-1.09), high levels of serum albumin (OR=1.04, 95%CI: 1.01-1.07) and phosphorus (OR=3.12, 95%CI: 2.44-4.00), low levels of serum bicarbonate (OR=0.89, 95%CI: 0.87-0.92), triglycerides (OR=0.76, 95%CI: 0.68-0.85) and creatinine (OR=0.95, 95%CI: 0.90-0.99), usage of angiotensin converting enzyme inhibitor/Angiotensin Ⅱ receptor antagonist (ACEI/ARB, OR=1.38, 95%CI: 1.11-1.72) and beta-blocker (OR=1.32, 95%CI: 1.07-1.64) were associated with hyperkalemia. Conclusions: Hyperkalemia occurred in 20.7% of the dialysis patients. HD, DM, high BMI, high levels of serum albumin and phosphorus, low levels of serum bicarbonate, triglycerides and creatinine, use of ACEI/ARB were associated with hyperkalemia.

The association between vitamin D receptor FokI gene polymorphism and osteoporosis in postmenopausal women: a meta-analysis

OBJECTIVE

This study aimed to quantitatively summarize the evidence for vitamin D receptor (VDR) FokI gene polymorphism and osteoporosis risk in Caucasian and Asian postmenopausal women.

MATERIALS AND METHODS

The PubMed, EMBASE, Weipu, CNKI, and Wanfang databases were searched for eligible studies. Case-control studies containing available genotype frequencies for F/f were chosen, and the odds ratio (OR) with 95% confidence interval (CI) was used to assess the strength of this association.

RESULTS

In total, 3349 osteoporosis cases and 3202 controls were identified in our meta-analysis. In the stratified analysis, a significant association was observed between VDR FokI gene polymorphism and postmenopausal osteoporosis susceptibility in Asian subjects (additive model: OR = 1.529, 95% CI 1.053-2.219, p = 0.026; dominant model: OR 2.711, 95% CI 1.693-4.342 p < 0.001; co-dominant model: ff vs. FF, OR 2.796, 95% CI 1.439-5.433 p = 0.002), and we failed to find any significant relationship in Caucasian populations.

CONCLUSION

The present meta-analysis suggests that the VDR FokI genotype is associated with increased risk of osteoporosis in Asian women but not in Caucasian women. To draw comprehensive and true conclusions, further prospective studies with larger numbers of participants worldwide are needed to examine associations between VDR FokI polymorphism and osteoporosis.

Association of interleukin-6 promoter polymorphism with knee osteoarthritis: a meta-analysis

BACKGROUND

Osteoarthritis (OA) is the most common form of human polyarthritis. Many genetic factors have been implicated in OA. It was reported that a polymorphism in the gene of interleukin-6 (IL-6) was associated with OA of knee. The aim of this study was to determine whether functional IL-6 promoter -174G/C (rs1800795) polymorphisms confer susceptibility to knee OA.

METHODS

A meta-analysis was conducted on the association between the IL-6 polymorphism and knee OA. Electronic search at PubMed, EMBASE, Weipu database, and Wanfang database was conducted to select studies. Case-control studies containing available genotype frequencies of IL-6 -174G/C were chosen, and odds ratio (OR) with 95% confidence interval (CI) was used to assess the strength of this association.

RESULTS

A total of seven studies involving 6 464 subjects (knee OA 3 331 and controls 3 133) were considered in this study. The results suggested that the variant genotypes were not associated with knee OA risk in all genetic models (additive model: OR = 1.144, 95% CI 0.934-1.402, P = 0.194; recessive model: OR = 1.113, 95% CI 0.799-1.550, P = 0.526; dominant model: OR = 1.186, 95% CI 0.918-1.531, P = 0.191). A symmetric funnel plot, the Begg's test (P > 0.05), suggested that the data lacked publication bias.

CONCLUSIONS

This meta-analysis does not support the idea that rs1800795 genotype is associated with increased risk of knee OA. However, to draw comprehensive and more reliable conclusions, further prospective studies with larger numbers of participants worldwide are needed to examine the association between rs1800795 polymorphism and knee OA.

Antineoplastic mechanism of Octreotide action in human hepatoma

OBJECTIVES

To investigate whether apoptosis can be induced by Octreotide in human hepatoma cells in vitro and elucidate the antineoplastic mechanism of Octreotide in hepatoma.

METHODS

A cultured human hepatoma cell line, BEL-7402, was exposed to Octreotide and apoptosis was evaluated by cytochemical staining (Hochesst 33,258), transmission electron microscopy, agarose gel electrophoresis and flow cytometry (FCM).

RESULTS

After exposure to 0.2 microgram/ml Octreotide, apoptosis with nuclear chromatin condensation as well as fragmentation, cell shrinkage and the formation of apoptotic bodies was observed using cytochemical staining and transmission electron microscopy. A DNA ladder in agarose gel electrophoresis was also displayed. FCM showed that the apoptotic cell number rose with an increase in the concentration of Octreotide (0-2 micrograms/ml). There was a positive correlation between Octreotide concentration and apoptotic rate in BEL-7402 cells (r = 0.809, P < 0.05).

CONCLUSION

Apoptosis in human hepatoma cells can be induced by Octreotide, which may be related to the mechanism of antineoplastic action of Octreotide in hepatoma.

Autocolorization of three-dimensional radiological data

It requires skill, effort, and time to visualize desired anatomic structures from radiological data in three-dimensions. There have been many attempts at automating this process and making it less labor intensive. The technique we have developed is based on mutual information for automatic multi-modality image fusion (MIAMI Fuse, University of Michigan). The initial development of our technique has focused on the autocolorization of the liver, portal vein, and hepatic vein. A standard dataset in which these structures had been segmented and assigned colors was created from the full color Visible Human Female (VHF) and then optimally fused to the fresh CT Visible Human Female. This semi-automatic segmentation and coloring of the CT dataset was subjectively evaluated to be reasonably accurate. The transformation could be viewed interactively on the ImmersaDesk, in an immersive Virtual Reality (VR) environment. This 3D segmentation and visualization method marks the first step to a broader, standardized automatic structure visualization method for radiological data. Such a method, would permit segmentation of radiological data by canonical structure information and not just from the data's intrinsic dynamic range.

Manipulation of volumetric patient data in a distributed virtual reality environment

Due to increases in network speed and bandwidth, distributed exploration of medical data in immersive Virtual Reality (VR) environments is becoming increasingly feasible. The volumetric display of radiological data in such environments presents a unique set of challenges. The shear size and complexity of the datasets involved not only make them difficult to transmit to remote sites, but these datasets also require extensive user interaction in order to make them understandable to the investigator and manageable to the rendering hardware. A sophisticated VR user interface is required in order for the clinician to focus on the aspects of the data that will provide educational and/or diagnostic insight. We will describe a software system of data acquisition, data display, Tele-Immersion, and data manipulation that supports interactive, collaborative investigation of large radiological datasets. The hardware required in this strategy is still at the high-end of the graphics workstation market. Future software ports to Linux and NT, along with the rapid development of PC graphics cards, open the possibility for later work with Linux or NT PCs and PC clusters.

Radiological tele-immersion for next generation networks

Since the acquisition of high-resolution three-dimensional patient images has become widespread, medical volumetric datasets (CT or MR) larger than 100 MB and encompassing more than 250 slices are common. It is important to make this patient-specific data quickly available and usable to many specialists at different geographical sites. Web-based systems have been developed to provide volume or surface rendering of medical data over networks with low fidelity, but these cannot adequately handle stereoscopic visualization or huge datasets. State-of-the-art virtual reality techniques and high speed networks have made it possible to create an environment for clinicians geographically distributed to immersively share these massive datasets in real-time. An object-oriented method for instantaneously importing medical volumetric data into Tele-Immersive environments has been developed at the Virtual Reality in Medicine Laboratory (VRMedLab) at the University of Illinois at Chicago (UIC). This networked-VR setup is based on LIMBO, an application framework or template that provides the basic capabilities of Tele-Immersion. We have developed a modular general purpose Tele-Immersion program that automatically combines 3D medical data with the methods for handling the data. For this purpose a DICOM loader for IRIS Performer has been developed. The loader was designed for SGI machines as a shared object, which is executed at LIMBO's runtime. The loader loads not only the selected DICOM dataset, but also methods for rendering, handling, and interacting with the data, bringing networked, real-time, stereoscopic interaction with radiological data to reality. Collaborative, interactive methods currently implemented in the loader include cutting planes and windowing. The Tele-Immersive environment has been tested on the UIC campus over an ATM network. We tested the environment with 3 nodes; one ImmersaDesk at the VRMedLab, one CAVE at the Electronic Visualization Laboratory (EVL) on east campus, and a CT scan machine in UIC Hospital. CT data was pulled directly from the scan machine to the Tele-Immersion server in our Laboratory, and then the data was synchronously distributed by our Onyx2 Rack server to all the VR setups. Instead of permitting medical volume visualization at one VR device, by combining teleconferencing, tele-presence, and virtual reality, the Tele-Immersive environment will enable geographically distributed clinicians to intuitively interact with the same medical volumetric models, point, gesture, converse, and see each other. This environment will bring together clinicians at different geographic locations to participate in Tele-Immersive consultation and collaboration.

Wnt-1 regulation of connexin43 in cardiac myocytes

Gap junction channels composed of connexin43 (Cx43) are essential for normal heart formation and function. We studied the potential role of the Wnt family of secreted polypeptides as regulators of Cx43 expression and gap junction channel function in dissociated myocytes and intact hearts. Neonatal rat cardiomyocytes responded to Li(+), which mimics Wnt signaling, by accumulating the effector protein beta-catenin and by inducing Cx43 mRNA and protein markedly. Induction of Cx43 expression was also observed in cardiomyocytes cocultured with Rat-2 fibroblasts or N2A neuroblastoma cells programmed to secrete bioactive Wnt-1. By transfecting a Cx43 promoter-reporter gene construct into cardiomyocytes, we demonstrated that the inductive effect of Wnt signaling was transcriptionally mediated. Enhanced expression of Cx43 increased cardiomyocyte cell coupling, as determined by Lucifer Yellow dye transfer and by calcium wave propagation. Conversely, in a transgenic cardiomyopathic mouse model that exhibits ventricular arrhythmias and gap junctional remodeling, beta-catenin and Cx43 expression were downregulated concordantly. In response to Wnt signaling, the accumulating Cx43 colocalized with beta-catenin in the junctional membrane; moreover, forced expression of Cx43 in cardiomyocytes reduced the transactivation potential of beta-catenin. These findings demonstrate that Wnt signaling is an important modulator of Cx43-dependent intercellular coupling in the heart, and they support the hypothesis that dysregulated signaling contributes to altered impulse propagation and arrhythmia in the myopathic heart.

Specific loss of protein kinase activities in senescent erythrocytes

Rabbit erythrocytes of progressively increasing age were isolated using an avidin-biotin affinity technique and the activity of protein kinases and other enzymes was analyzed in cytosols and membranes from the isolated cells. The activities of cytosolic protein kinase C (PKC), cAMP-dependent kinase (PKA), and casein kinase type I and II (CKI and II) were all found to undergo an age-dependent decrease of twofold to fourfold over the 8-week lifespan of the cells. Membrane-associated tyrosine kinase showed little or no decrease, but membrane-associated CKI showed a dramatic eightfold decrease over the 8-week period. By contrast, various cytosolic enzymes, including lactate dehydrogenase, phosphoglycerate kinase, pyruvate kinase, and acid phosphatase, showed no change in activity over the same time period. Density-separated human erythrocytes showed qualitatively similar decreases in cytosolic protein kinase activities in the densest fractions, which contain the oldest cells. Our results show that aging erythrocytes undergo progressive loss of protein kinases that may adversely affect various cellular processes. The age-dependent loss of kinase activity reported here is one of the most striking manifestations of erythrocyte senescence yet to be reported.

Phosphatidylinositol 3-kinase activity in murine erythroleukemia cells during DMSO-induced differentiation

We have used murine erythroleukemia cells (MEL cells) to investigate the role of phosphatidylinositol 3-kinase (PI 3-kinase) in erythroid differentiation. When treated with dimethyl sulfoxide (DMSO), MEL cells grown on a fibronectin matrix become committed to erythroid differentiation asynchronously, with 90% of cells becoming committed by Day 3 of treatment. We found that during the first 3 days of DMSO treatment MEL cells showed a twofold increase in total PI 3-kinase activity and a fourfold increase in the highly phosphorylated PI 3-kinase product, PIP3. At the same time there was no change in the content of p85, the PI 3-kinase regulatory subunit. After Day 3, PI 3-kinase activity declined, in parallel with a disappearance of p85 antigen from the cells. Inclusion of the PI 3-kinase inhibitor Wortmannin in the culture medium resulted in an inhibition of cellular PI 3-kinase activity and a delay in DMSO-induced erythroid differentiation. These data suggest that PI 3-kinase may play a critical role during commitment of MEL cells to erythroid differentiation.

[Protective effects of prostacyclin on acute necrotizing pancreatitis and its renal damage in rats]

In a rat model with acute necrotizing pancreatitis (ANP), the administration of exogenous prostacyclin (PGI2) significantly increased the pancreatic and renal blood flow, brought the level of 6-keto-PGF1 alpha to TXB2 in renal vein blood back to normal, reduced the severity of pancreatic and renal histolcagic damage, decreased the mortality, and prolonged survival time. The study showed that exogenous PGI2 can increase pancreatic blood flow in rats with ANP, help to prevent ANP, and protect from renal damage following ANP.

Fast algorithm for exact rendering of space-filling molecular models with shadows

An algorithm for accurate rendering of space-filling molecular models with shadows is presented. The intensity of light and cast shadows are computed to generate realistic pictures. Arbitrary numbers of light sources, which may be at infinite or finite distances can be applied. Hidden-surface removal, lighting, and shadowing are presented in detail.