Big Data, Predictive Analytics, and Quality Improvement in Kidney Transplantation: A Proof of Concept

We sought proof of concept of a Big Data Solution incorporating longitudinal structured and unstructured patient-level data from electronic health records (EHR) to predict graft loss (GL) and mortality. For a quality improvement initiative, GL and mortality prediction models were constructed using baseline and follow-up data (0-90 days posttransplant; structured and unstructured for 1-year models; data up to 1 year for 3-year models) on adult solitary kidney transplant recipients transplanted during 2007-2015 as follows: Model 1: United Network for Organ Sharing (UNOS) data; Model 2: UNOS & Transplant Database (Tx Database) data; Model 3: UNOS, Tx Database & EHR comorbidity data; and Model 4: UNOS, Tx Database, EHR data, Posttransplant trajectory data, and unstructured data. A 10% 3-year GL rate was observed among 891 patients (2007-2015). Layering of data sources improved model performance; Model 1: area under the curve (AUC), 0.66; (95% confidence interval [CI]: 0.60, 0.72); Model 2: AUC, 0.68; (95% CI: 0.61-0.74); Model 3: AUC, 0.72; (95% CI: 0.66-077); Model 4: AUC, 0.84, (95 % CI: 0.79-0.89). One-year GL (AUC, 0.87; Model 4) and 3-year mortality (AUC, 0.84; Model 4) models performed similarly. A Big Data approach significantly adds efficacy to GL and mortality prediction models and is EHR deployable to optimize outcomes.

[Effects of different techniques on removal of vapor lock in the apical region of curved canals: a cone-beam computed tomography study]

OBJECTIVE

To compare the effect of four different techniques on removal of vapor lock in the apical region of curved root canals.

METHODS

Forty simulated resin root canals with 45° curvature were prepared using WaveOne Primary, then the apical foramen were sealed with soft wax. The teeth were divided randomly into 4 groups thereafter (n=10). Contract solution was injected into the canals using a 30 G side-vented needle and scanned with cone-beam CT (CBCT) to identify the volume of the vapor lock. Four different techniques including photon-induced photoacoustic streaming (PIPS) laser-activated irrigation, gutta-percha cone technique, ultrasonic irrigation, and sonic irrigation were used to remove the vapor locks in the root canals. The residual volume of the vapor lock was identified again using CBCT scanning data. Accordingly, the reduction rates of the vapor lock were calculated. Furthermore, the initial and residual vapor lock length was calculated. The data were analyzed by using the One-way ANOVA analysis and Kruskal-Wallis H test at a significance level of P<0.05.

RESULTS

There was no significant difference in the initial vapor lock volume (P>0.05). Residual volume of the vapor lock for PIPS laser-activated irrigation was 0 mm(3), and that for gutta-percha cone technique was (0.02±0.07) mm3, significantly lower than those of ultrasonic and sonic irrigation, the values being (0.20±0.09) mm(3) and (0.23±0.06) mm(3) (P<0.001), respectively. The reduction rates of the vapor lock of PIPS laser-activated irrigation and gutta-percha cone technique were 100.00% (100.00%, 100.00%) and 100.00% (77.66%, 100.00%), respectively, significantly higher than those of ultrasonic irrigation [70.37% (56.41%, 91.43%)] and sonic irrigation [63.54% (51.47%, 74.00%), P<0.001]. The length of the residual vapor lock for PIPS laser-activated irrigation was 0 mm, and that for gutta-percha cone technique was (0.15±0.47) mm, significantly lower than those of ultrasonic and sonic irrigation, values being (2.21±0.09) mm and (2.34±0.08) mm (P<0.001), respectively. The length of the residual vapor locks in the ultrasonic and sonic group remained approximately the same as the distance between the working tip and the apical foramen.

CONCLUSION

PIPS laser activated irrigation and gutta-percha cone technique could remove the vapor lock from the apical region of curved canals effectively.

Antisense locked nucleic acids targeting agrA inhibit quorum sensing and pathogenesis of community-associated methicillin-resistant Staphylococcus aureus

AIM

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is commonly associated with nonnosocomial skin and soft tissue infections due to its virulence, which is mainly controlled by the accessory gene regulator (agr) quorum sensing (QS) system. In this study (KFF)₃ K peptide-conjugated locked nucleic acids (PLNAs) targeting agrA mRNA were developed to inhibit agr activity and arrest the pathogenicity of CA-MRSA.

METHODS AND RESULTS

Two PLNAs were designed, and synthesized, after predicting the secondary structure of agrA mRNA. The influence on bacterial growth was tested using a growth curve assay. RT-qPCR, haemolysis assay, lactate dehydrogenase release assay and chemotaxis assay were used to evaluate the effects of the PLNAs on inhibiting agr QS. A mouse skin infection model was employed to test the protective effect of the PLNAs in vivo. None of the PLNAs were found to be bacteriostatic or bactericidal in vitro. However, one PLNA, PLNA34, showed strong ability to suppress expression of agrA and the effector molecule RNAIII in USA300 LAC strain. Furthermore, PLNA34 inhibited the expression of virulence genes that are upregulated by agr, including hla, psmα, psmβ and pvl. The haemolytic activity of the supernatants from PLNA34-treated bacteria was also dramatically reduced, as well as the capacity to lyse and recruit neutrophils. Moreover, PLNA34 showed high levels of protection in the CA-MRSA mouse skin infection model.

CONCLUSIONS

The anti-agrA PLNA34 can effectively inhibit the agr QS and suppress CA-MRSA pathogenicity.

SIGNIFICANCE AND IMPACT OF THE STUDY

agrA is a promising target for the development of antisense oligonucleotides to block agr QS.

Genome-Wide Analysis of RNA Secondary Structure

Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNA-binding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo. These data sets provide new glimpses into the RNA universe. Analyses of RNA structuromes in HIV, yeast, Arabidopsis, and mammalian cells and tissues have revealed regulatory effects of RNA structure on messenger RNA (mRNA) polyadenylation, splicing, translation, and turnover. Application of new methods for genome-wide identification of mRNA modifications, particularly methylation and pseudouridylation, has shown that the RNA "epitranscriptome" both influences and is influenced by RNA structure. In this review, we describe newly developed genome-wide RNA structure-probing methods and synthesize the information emerging from their application.

A Pilot Metabolic Profiling Study of Patients With Neonatal Jaundice and Response to Phototherapy

Phototherapy has been widely used in treating neonatal jaundice, but detailed metabonomic profiles of neonatal jaundice patients and response to phototherapy have not been characterized. Our aim was to depict the serum metabolic characteristics of neonatal jaundice patients relative to controls and changes in response to phototherapy. A (1) H nuclear magnetic resonance (NMR)-based metabonomic approach was employed to study the metabolic profiling of serum from healthy infants (n = 25) and from infants with neonatal jaundice (n = 30) pre- and postphototherapy. The acquired data were processed by multivariate principal component analysis (PCA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA). The PLS-DA and OPLS-DA model identified nine metabolites capable of distinguishing patients from controls. In addition, 28 metabolites such as β-glucose, α-glucose, valine, and pyruvate changed in response to phototherapy. This study offers useful information on metabolic disorders in neonatal jaundice patients and the effects of phototherapy on lipids, amino acid, and energy metabolism.

CpG island evolution in the mammalian DHRS4 gene cluster and its role in the regulation of gene transcription

The dehydrogenase/reductase (SDR family) member 4 (DHRS4) gene is copied during mammalian evolution; therefore, while only one DHRS4 gene is expressed in the mouse genome, the gene cluster consists of two (DHRS4 and DHRS4L1) and three (DHRS4, DHRS4L2, and DHRS4L1) copies in chimpanzees and humans, respectively. In this study, we explored the possible regulatory mechanism of the DHRS4 gene cluster in mammalian evolution by analyzing the promoter sequence, methylation of CpG islands, and RNA expression of the DHRS4 gene cluster in mice, chimpanzees, and humans by bioinformatics prediction, bisulfite sequencing PCR, and real-time reverse transcriptase-PCR. The results indicated that the DHRS4 gene was actively expressed in the three model species. The RNA level of DHRS4L1 was much lower than those of DHRS4 and DHRS4L2, and expressed lower homologous sequence identity to DHRS4 and DHRS4L2. DHRS4L2, the latest evolutionary copy of the DHRS4 gene in mammals, received a high promoter prediction score, and was the only copy of the DHRS4 gene cluster presenting hypermethylated CpG islands in the promoter region. An analysis of the relationship between the promoter characteristics and RNA expression of the DHRS4 gene cluster indicated that the development of CpG islands, in addition to the promoter sequence, during mammalian evolution could modulate the dose compensatory regulation of the copy number-varied DHRS4 gene cluster.

[Characterization of ovarian adrenal rest tumors in children and adolescent females with congenital adrenal hyperplasia due to 21-hydroxylase deficiency]

OBJECTIVE

To summarize the characterization of ovarian adrenal rest tumors (OART) in children and adolescent females with congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD).

METHOD

We have diagnosed 4 cases of CAH 21-OHD with OART in the recent 5 years in pediatric endocrinology unit of the first affiliated hospital of Sun Yat-Sen University. Clinical characterizations were summarized, including symptoms, growth patterns and bone age advancements, serum steroid concentrations, imaging results and the follow-up data.

RESULT

The 4 cases of OART accounted for 2.5 % of the CAH 21-OHD girls, which was much lower than the detection rate, 29.5%, of testicular ART in our patient group during the same period. The 4 cases included 3 salt wasters and 1 with simple virilizm. OART were diagnosed at the age of 8.9 years, 15.8 years, 21.4 years and 9.3 years, respectively. Before the diagnosis of OART, their daily hydrocortisone doses reached 16 mg/(m(2)·d)to 24 mg/(m(2)·d). The patients presented with deteriorated acne, deepened voice, amenorrhea (2 cases), accelerated growth and advanced bone age, ΔBA/ΔCA reached 1.2(during GnRHa treatment)and 2.0. Their serum adrenal steroids increased significantly and hyperplasia of adrenal glands were found in all patients. The diagnosis could be confirmed before the operation in only 1 case. The diagnosis could not be made until the planned sub-total adrenalectomy in the other 3 cases. The follow-up periods of OART were 4.8, 4.7, 3.8 and 2.7 years, respectively. Removal of OART resulted in symptoms relief at least partialy and lowered daily hydrocortisone doses, 14 to 19 mg/(m(2)·d).

CONCLUSION

The detection rate of OART was much lower than testicular ART. Before the diagnosis of OART, the patients presented with deteriorated virilescence, accelerated growth and advanced bone age, elevated serum adrenal steroids and hyperplasia of adrenal glands. Removal of the OART resulted in symptoms relief at least partialy.

Improved image-quality consistency in coronary CT angiography using a test-bolus-based individually tailored contrast medium injection protocol

AIM

To develop and validate a test bolus (TB)-based quantitative model to create an individualised contrast medium injection protocol for use at coronary computed tomography angiography (CCTA) to improve patient-to-patient uniformity of intracoronary attenuation.

MATERIALS AND METHODS

In the model-building phase, 175 patients who underwent CCTA using a traditional contrast medium injection protocol were recruited. A personalised injection equation was proposed according to the relationship between aortic enhancement and the haemodynamic parameters obtained from the TB. In the model-validation phase, a target aortic enhancement of 350 HU was set. Two hundred and fifteen additional CCTA examinations were performed using the proposed personalised injection model. Comparisons of inter-individual variability between the traditional and the proposed personalised injection protocol were performed.

RESULTS

In the model-building phase, a high positive correlation between aortic enhancement and the haemodynamic parameters obtained from the TB was found. As a result, a personalised injection equation was determined using linear regression. In the model-validation phase, the average aortic enhancement was 350.5 HU, without significant differences from the preset level. Using the TB-based personalised injection protocol, inter-individual variability of aortic enhancement was significantly reduced (71.8 versus 38.9 HU, p<0.001) and patients who were scanned at 100 kVp had a reduction in the average contrast medium flow rate from 4.1 to 3.2 ml/s (p<0.001).

CONCLUSIONS

The proposed TB-based injection protocol can achieve a desired preset and stable aortic enhancement.

Cancer therapy in the necroptosis era

Necroptosis is a caspase-independent form of regulated cell death executed by the receptor-interacting protein kinase 1 (RIP1), RIP3, and mixed lineage kinase domain-like protein (MLKL). Recently, necroptosis-based cancer therapy has been proposed to be a novel strategy for antitumor treatment. However, a big controversy exists on whether this type of therapy is feasible or just a conceptual model. Proponents believe that because necroptosis and apoptosis use distinct molecular pathways, triggering necroptosis could be an alternative way to eradicate apoptosis-resistant cancer cells. This hypothesis has been preliminarily validated by recent studies. However, some skeptics doubt this strategy because of the intrinsic or acquired defects of necroptotic machinery observed in many cancer cells. Moreover, two other concerns are whether or not necroptosis inducers are selective in killing cancer cells without disturbing the normal cells and whether it will lead to inflammatory diseases. In this review, we summarize current studies surrounding this controversy on necroptosis-based antitumor research and discuss the advantages, potential issues, and countermeasures of this novel therapy.

Microphthalmia-associated transcription factor/T-box factor-2 axis acts through Cyclin D1 to regulate melanocyte proliferation

OBJECTIVES

Control of cell proliferation is critical for accurate cell differentiation and tissue formation, during development and regeneration. Here, we have analysed the role of microphthalmia-associated transcription factor MITF and its direct target, T-box factor TBX2, in regulating proliferation of mammalian neural crest-derived melanocytes.

MATERIALS AND METHODS

Immunohistochemistry was used to examine spatial and temporal expression of TBX2 in melanocytes in vivo. RNAi and cell proliferation analysis were used to investigate functional roles of TBX2. Furthermore, quantitative RT-PCR, western blot analysis and flow cytometry were used to further scrutinize molecular mechanisms underlying TBX2-dependent cell proliferation.

RESULTS

TBX2 was found to be co-expressed with MITF in melanocytes of mouse hair follicles. Specific Tbx2 knockdown in primary neural crest cells led to inhibition MITF-positive melanoblast proliferation. Tbx2 knockdown in melan-a cells led to reduction in Cyclin D1 expression and G1-phase cell cycle arrest. TBX2 directly activated Ccnd1 transcription by binding to a specific sequence in the Ccnd1 promoter, and the defect in cell proliferation could be rescued partially by overexpression of Cyclin D1 in Tbx2 knockdown melanocytes.

CONCLUSIONS

Results suggest that the Mitf-Tbx2-Cyclin D1 pathway played an important role in regulation of melanocyte proliferation, and provided novel insights into the complex physiology of melanocytes.