Pairwise Correlation Analysis Research Articles

A model incorporating serum C3 complement levels may be useful for diagnosing biliary atresia in infants

IntroductionCorrectly identifying patients with biliary atresia (BA), while avoiding invasive diagnostic methods is challenging. The purpose of this study was to determine the value of serum immune indicators for distinguishing BA from other causes of cholestasis in infants. Patients and methodsThe data of infants with a surgical/histological diagnosis of BA and those with other causes of cholestatic jaundice were retrospectively analyzed. Patients were divided into a BA group and a cholestasis control (CC) group. Biochemical parameters, major lymphocyte subsets, immunoglobin and C3 and C4 complement levels were compared between the groups. ResultsA total of 129 infants with BA and 63 with other causes of cholestasis (CC control group) with a median age of 2.2 months were included in the analysis. The levels of CD3+ T cells, CD3+CD4+ T cells, and premature T cells and the levels of C3 and C4 were all significantly higher in the BA group compared to the CC group (all P<0.05). Pair-wise correlation analyses indicated that C3 and C4 had a significant positive correlation with γ-GT in the BA group, but not in the CC group. Five indices were found to be significantly associated with BA: stool color, globulin, γ-GT, C3 and C4. A model incorporating stool color, gamma-glutamyl transpeptidase level, and C3 level exhibited an area under the ROC curve (AUC) of 0.93, and a sensitivity of 93% and specificity of 83% for the diagnosis of BA. ConclusionsModels incorporating serum C3 levels may be useful for accurately diagnosing BA in infants.

AB0263 THE LEVEL OF 7-HYDROXY METHOTREXATE IN BLOOD CELLS IN PATIENTS WITH RHEUMATOID ARTHRITIS DIRECTLY CORRELATES WITH THE LEVEL OF POLYGLUTAMATES OF METHOTREXATE

Background:7-hydroxy Methotrexate (7-hydroxy-MTX) is a phase I metabolite of MTX, which is converted by hepatic aldehyde oxidases. It is known that 7-hydroxy MTX can reduce the effectiveness of methotrexate, which is associated with increased excretion of methotrexate due to a decrease in polyglutamation and binding to enzymes [1].Objectives:To analyze the level of 7-hydroxy-MTX in peripheral blood cells in order to study the correlation of the level of this metabolite with the level of polyglutamates of methotrexate (MTXPGs).Methods:The prospective study included 65 patients aged 53±11 years, 50 women, 13 men, diagnosed with RA, according to the ACR/EULAR 2020 criteria, methotrexate (MTX) naiive. The duration of the disease was 7,5[4;24] months. All patients were administrated MTX subcutaneously at a dose of 10-15 mg/m2. The visits were carried out at weeks 0, 4, 12, 24 and 36, at all visits samples were taken for the content of MTXPGs with 1,2,3 and 4 glutamate residues and 7-hydroxy MTX separately in red blood cells mass (RBC) and mononuclear cells (MO). The mononuclear fraction was isolated by layering on verografin-ficoll. All patients received folic acid at a standard dose of 5 mg 24 hours after parenteral MTX administration. Samples were collected no earlier than 36 hours after MTX administration. All patients had normal renal function. Disease activity was assessed using the DAS28 index calculated by C-reactive protein.Results:The average concentration of 7-hydroxy MTX is shown in Table 1.Table 1.Level of 7-hydroxy MTX in erythrocytes and mononuclear cells, nmol/L, Median [25; 75 quartiles]7-hydroxy MTX level in:4 weeks12 weeks24 weeks36 weeksRBC18,5[3,1;61,5]10,2[3,6;50,8]10,3[1,7;36,8]7,2[0,1;25,3]MO0,8[0,1;15,2]4,0[0,1;42,2]3,5[0,1;8,1]0,4[0,1;8,9]The level of 7-hydroxy-MTX directly correlated with the level of MTXPGs 1-4, and summary MTXPG in both RBC and MO. Analysis of pairwise correlations according to Pearson showed that: after 4, 12 and 36 weeks, the level of 7-hydroxy-MTX did not correlate with the value of DAS28. After 24 weeks of therapy, the level of 7-hydroxy-MTX in RBC was inversely correlated with DAS28 of the disease (p=0.043).Conclusion:The preliminary results indicate a positive correlation between the level of 7-hydroxy-MTX and MTXPGs in RBC and MO. In this regard, the concentration of 7-hydroxy-MTX can be used as a prognostic marker for MTX therapy in the absence of opportunities in clinical centers to measure the entire line of MTXPGs in RBC and MO. Since the data obtained are somewhat at odds with the few literary sources, it is necessary to conduct further research on this fact.

A novel approach for in vitro fungicide screening and the sensitivity of Monilinia populations from peach orchards in Turkey to respiratory inhibitor fungicides

Brown rot caused by Monilinia fructicola and M. laxa can result in considerable losses in peach production worldwide. Respiratory Inhibitors (RIs) have been used to control the disease in Turkey and worldwide. However, resistance against RIs may have been developing in Monilinia populations in Turkey. The sensitivity level of the total of 128 isolates of Monilinia fructicola and M. laxa from peach fruits in Turkey were tested against certain RIs: azoxystrobin, boscalid, and commercially used signum (26,7% boscalid, 6,7% pyraclostrobin). Fungal growth from both mycelia and conidia was evaluated as fungicide response phenotypes. A new approach was developed to define the sensitivity levels of the isolates. The mean IC50 values of each fungicide on representative collection from each species were used as discriminatory doses in view of both phenotypes. The whole collection was scanned at discriminatory doses and the relative growth (RG) of each isolate was obtained. The distribution of RG data sets in the quantile ranges was considered to define sensitivity levels of the isolates against each fungicide. Resistance levels for mycelial and conidial growth assays varied within and between the species against the three RIs. According to the pairwise correlation analyses between responses of the species to the fungicides, the significant correlation indicating a cross-resistance was only found between boscalid and signum on conidial growth assays for M. fructicola. This study represents in vitro fungicide responses of a large population of Monilinia pathogens from peach in Turkey for the first time which will help to reconsider disease control strategies and suggests a fungicide sensitivity definition be used in all in vitro fungicide assays as a common and comparable strategy at the global stage.

Planarian stem cells specify fate yet retain potency during the cell cycle.

Planarian whole-body regeneration is enabled by stem cells called neoblasts. At least some neoblasts are individually pluripotent. Neoblasts are also heterogeneous, with subpopulations of specialized neoblasts having different specified fates. Fate specification in neoblasts is regulated by fate-specific transcription factor (FSTF) expression. Here, we find that FSTF expression is common in neoblast S/G2/M cell-cycle phases but less common in G1. We find that specialized neoblasts can divide to produce progeny with asymmetric cell fates, suggesting that they could retain pluripotency. Furthermore, no known neoblast class was present in all neoblast colonies, suggesting that pluripotency is not the exclusive property of any known class. We tested this possibility with single-cell transplantations, which indicate that at least some specialized neoblasts are likely clonogenic. On the basis of these findings, we propose a model for neoblast pluripotency in which neoblasts can undergo specialization during the cell cycle without loss of potency.

Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm.

Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber core germplasm (CG) consisting of 94 resequenced lines was evaluated for PM resistance in four trials across three years (2013, 2014, and 2016). These trials were performed on adult plants in the field with natural infection. Using genome-wide association study (GWAS), 13 loci (pmG1.1, pmG1.2, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1, and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7. Among these loci, ten were mapped to chromosomal intervals where QTLs had been reported in previous studies, while, three (pmG2.1, pmG3.1, and pmG4.1) were novel. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in four trials. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, candidate genes located in the QTL intervals were predicted. SNPs in these candidate genes were analyzed between haplotypes of highly resistant (HR) and susceptible (HS) CG lines, which were defined based on combing disease index data of all trials. Furthermore, candidate genes (Csa5G622830 and CsGy5G015660) reported in previous studies for PM resistance and cucumber orthologues of several PM susceptibility (S) genes (PMR5, PMR-6, and MLO) that are colocalized with certain QTLs, were analyzed for their potential contribution to the QTL effect on both PM and DM in the CG population. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for both PM and DM resistance, which can be exploited in cucumber breeding.

Elucidating the complementarity of resting-state networks derived from dynamic [18F]FDG and hemodynamic fluctuations using simultaneous small-animal PET/MRI

Functional connectivity (FC) and resting-state network (RSN) analyses using functional magnetic resonance imaging (fMRI) have evolved into a growing field of research and have provided useful biomarkers for the assessment of brain function in neurological disorders. However, the underlying mechanisms of the blood oxygen level-dependant (BOLD) signal are not fully resolved due to its inherent complexity. In contrast, [18F]fluorodeoxyglucose positron emission tomography ([18F]FDG-PET) has been shown to provide a more direct measure of local synaptic activity and may have additional value for the readout and interpretation of brain connectivity. We performed an RSN analysis from simultaneously acquired PET/fMRI data on a single-subject level to directly compare fMRI and [18F]FDG-PET-derived networks during the resting state. Simultaneous [18F]FDG-PET/fMRI scans were performed in 30 rats. Pairwise correlation analysis, as well as independent component analysis (ICA), were used to compare the readouts of both methods. We identified three RSNs with a high degree of similarity between PET and fMRI-derived readouts: the default-mode-like network (DMN), the basal ganglia network and the cerebellar-midbrain network. Overall, [18F]FDG connectivity indicated increased integration between different, often distant, brain areas compared to the results indicated by the more segregated fMRI-derived FC. Additionally, several networks exclusive to either modality were observed using ICA. These networks included mainly bilateral cortical networks of a limited spatial extent for fMRI and more spatially widespread networks for [18F]FDG-PET, often involving several subcortical areas.This is the first study using simultaneous PET/fMRI to report RSNs subject-wise from dynamic [18F]FDG tracer delivery and BOLD fluctuations with both independent component analysis (ICA) and pairwise correlation analysis in small animals. Our findings support previous studies, which show a close link between local synaptic glucose consumption and BOLD-fMRI-derived FC. However, several brain regions were exclusively attributed to either [18F]FDG or BOLD-derived networks underlining the complementarity of this hybrid imaging approach, which may contribute to the understanding of brain functional organization and could be of interest for future clinical applications.

MRI index lesion radiomics and machine learning for detection of extraprostatic extension of disease: a multicenter study

ObjectivesTo build a machine learning (ML) model to detect extraprostatic extension (EPE) of prostate cancer (PCa), based on radiomics features extracted from prostate MRI index lesions.MethodsConsecutive MRI exams of patients undergoing radical prostatectomy for PCa were retrospectively collected from three institutions. Axial T2-weighted and apparent diffusion coefficient map images were annotated to obtain index lesion volumes of interest for radiomics feature extraction. Data from one institution was used for training, feature selection (using reproducibility, variance and pairwise correlation analyses, and a correlation-based subset evaluator), and tuning of a support vector machine (SVM) algorithm, with stratified 10-fold cross-validation. The model was tested on the two remaining institutions’ data and compared with a baseline reference and expert radiologist assessment of EPE.ResultsIn total, 193 patients were included. From an initial dataset of 2436 features, 2287 were excluded due to either poor stability, low variance, or high collinearity. Among the remaining, 14 features were used to train the ML model, which reached an overall accuracy of 83% in the training set. In the two external test sets, the SVM achieved an accuracy of 79% and 74% respectively, not statistically different from that of the radiologist (81–83%, p = 0.39–1) and outperforming the baseline reference (p = 0.001–0.02).ConclusionsA ML model solely based on radiomics features demonstrated high accuracy for EPE detection and good generalizability in a multicenter setting. Paired to qualitative EPE assessment, this approach could aid radiologists in this challenging task.Key Points• Predicting the presence of EPE in prostate cancer patients is a challenging task for radiologists.• A support vector machine algorithm achieved high diagnostic accuracy for EPE detection, with good generalizability when tested on multiple external datasets.• The performance of the algorithm was not significantly different from that of an experienced radiologist.

Financial Inclusion and Youth Agriculture Involvement in Tanzania: A Case of Misenyi District, Kagera Region.

The paper investigated the effects of financial inclusion on youth agriculture involvement in Tanzania. Specifically the study was conducted in Kagera region, Misenyi district with the specific objectives of examining the effects of branch penetration, credit penetration, deposit penetration, interest rate and finding out the effects of education on financial service usage and youth agriculture involvement. The study was supported by the institution theory. Data were collected using questionnaires and they were analysed using linear regression with the helpof SPSS software. Descriptive statistics, pairwise correlation and regression analysis was used to present the findings and the results indicated that a huge level of financial inclusion is needed to achieve a sizable effect on agricultural involvement. This is due to the minimal effect magnitudes on the dependent variable resulting from financial inclusion variables. Financial inclusion and agricultural involvement policies need to consider women and middle-aged individuals, deposit penetration need to be explored and credit penetration need to be extended to maximize its effects on agricultural involvement.

Bioinformatics Analyses Reveals a Comprehensive Landscape of CXC Chemokine Family Functions in Non-Small Cell Lung Cancer

Backgrounds. Lung cancer is a major source of tumor-related death each year with non-small cell lung cancer (NSCLC) being a prevalent subtype. The metastasis from NSCLC to the brain usually imposes many neuron disorders. Previous studies have suggested that communications among cancer cells and interstitial cells are essential in tumorigenesis and are influenced by chemokines. In the tumor microenvironment, CXC chemokines can participate in the shifting of immune cells and manage tumor cell condition, thus affecting the progression of cancer and patient destinies. However, the expression and values of CXC chemokine family in NSCLC have not been systematically illustrated using public databases. Methods. UALCAN, STRING, ONCOMINE, GeneMANIA, cBioPortal, GEPIA, TISIDB, TRRUST, TIMER, Kaplan-Meier Plotter, and R software were utilized in this study. Results. Based on the TIMER and UACLCAN databases, in LUAD patients, the expression levels of CXCL10, CXCL13, and CXCL14 were significantly elevated while the transcriptional levels of CXCL2/3/4/7/12/16 were significantly reduced; in LUSC patients, the expression levels of CXCL6/10/13/14 were significantly elevated while the expression levels of CXCL2/3/4/5/7/11/12/16/17 were significantly reduced. We found remarkable relevance between the pathological stages of LUAD patients and the expressions of CXCL8 (positive) and CXCL17 (negative). Similarly, there are significant correlations between the pathological stages of LUSC patients and the expressions of CXCL1/2/6/17. In LUAD, patients with low expression levels of CXCL1/4/7/8 and patients with high expression levels of CXCL12/14/16 were associated with a significantly better prognosis. But in LUSC, all correlations between chemokines and prognosis are statistically insignificant. Pairwise expression correlation analysis among CXC chemokines shows that there are 7 significant correlations (between CXCL1 and CXCL2, between CXCL1 and CXCL3, between CXCL1 and CXCL8, between CXCL2 and CXCL3, between CXCL4 and CXCL7, between CXCL9 and CXCL10, and between CXCL9 and CXCL11) in LUAD and 4 significant correlations (between CXCL1 and CXCL8, between CXCL2 and CXCL3, between CXCL4 and CXCL7, and between CXCL10 and CXCL11) in LUSC. Significant correlations between the expressions of CXC chemokines and the infiltration of six common types of immune cells were also discovered in both LUAD and LUSC. Conclusions. We provided a comprehensive landscape of the CXC chemokine family in LUAD and LUSC using the bioinformatics method and found differences between LUSC and LUAD in the field of CXC chemokines. Our study may help validate and identify known novel immunotherapeutic targets and prognostic biomarkers.

Evaluation of Acromegaly patients with sleep disturbance related symptoms.

Background and Objectives:It is known that the prevalence of obstructive sleep apnea (OSA) is increased in acromegaly. Craniofacial anomalies, macroglossia, and thickening of the laryngeal wall caused by the increase in soft tissue in these patients lead to OSA. Also, the increase in growth hormone can trigger central apnea by causing a decrease in respiratory drive. Determining the polysomnographic characteristics of acromegaly patients is important to reveal the effect of these mechanisms.Methods:The demographic and polysomnographic characteristics of 33 acromegaly patients who underwent polysomnography (PSG) with suspicion of sleep disorders between 2011 and 2018 in the sleep laboratory of our hospital were retrospectively analyzed. One of the patients was excluded from the analysis because PSG was performed in the postoperative period. The remaining 32 patients with active acromegaly were grouped according to their gender and the presence of OSA and compared with statistical methods in terms of polysomnographic and clinical features.Results:OSA (AHI>5) was detected in 78.1% of 32 active acromegaly patients (18 females, 14 males) who underwent PSG with suspicion of sleep-disordered breathing. Moderate-severe OSA (62.5%) was found in most patients, and there was no difference between the sexes in terms of OSA detection rate and OSA severity. Respiratory events appear to be predominantly obstructive hypopneas. Also, the polysomnographic features of female and male acromegaly patients with OSA were found to be similar. It is seen that the OSA group is similar to the group with simple snoring in terms of body mass index (BMI), but is statistically significantly older (p=0,007). A positive correlation was found between age and AHI in pairwise correlation analysis (r:0,426 p:0,015, respectively).Conclusion:Considering that the prevalence of OSA in the population is approximately 5%, our results show that the risk of OSA in acromegaly increases, and obstructive pathways are effective in this increase. The probability of OSA occurrence and polysomnographic features between the genders are similar. Although the median BMI of the patients with and without OSA was similar, the median age was higher in the group with OSA, middle-aged acromegaly patients should be evaluated in terms of OSA even if there is no obvious obesity.

Comparison of Proteomics Profiles Between Xenografts Derived from Cell Lines and Primary Tumors of Thyroid Carcinoma.

Patient-consistent xenograft model is a challenge for all cancers but particularly for thyroid cancer, which shows some of the greatest genetic divergence between human tumors and cell lines. In this study, proteomic profiles of tumor tissues from patients, included anaplastic thyroid carcinoma (ATC) and papillary thyroid carcinoma, and xenografts (8305C, 8505C, FRO, BAPAP and IHH4) were obtained using HPLC-tandem mass spectrometry and compared based on all proteins detected (3,961), cancer-related proteins and druggable proteins using pairwise Pearson's correlation analysis. The human tissue showed low proteomic similarity to the ATC cell lines (8305C, r = 0.344-0.416; 8505C, 0.47-0.579; FRO, 0.267-0.307) and to PTC cell lines (BCPAP, 0.303-0.468; IHH4, 0.262-0.509). Human tissue showed the following similarity to cell lines at the level of 135 cancer-related pathways. The ATC cell lines contained 47.4% of the cancer-related pathways (19.26%-33.33%), while the PTC cell lines contained 40% (BCPAP, 25.93%; IHH4, 28.89%). In patient tumor tissues, 44-60 of 76 and 52-53 of 93 druggable proteins were identified in ATC and PTC tumors, respectively. Ten and 29 druggable proteins were not identified in any of the ATC and PTC xenografts, respectively. We provide a reference for CDX selecting in in vivo studies of thyroid cancer.

Notum palmitoleoyl-protein carboxylesterase regulates Fas cell surface death receptor-mediated apoptosis via the Wnt signaling pathway in colon adenocarcinoma

ABSTRACT Colon adenocarcinoma (COAD) is one of the most common types of malignancy and accounts for >3 million deaths worldwide each year. The present study aimed to evaluate the role of notum palmitoleoyl-protein carboxylesterase (NOTUM) in in vivo and in vitro, and to identify the relationship between NOTUM and the apoptosis of COAD. Moreover, the present study aimed to investigate whether NOTUM regulated Fas cell surface death receptor (FAS)-mediated apoptosis was affected by the Wnt signaling pathway. Gene expression profiling interactive analysis (GEPIA) was used to predict the potential function of NOTUM. Western blotting and reverse transcription-quantitative PCR were conducted to detect the protein and mRNA expression levels of NOTUM in different tissues or cell lines. The occurrence and development of COAD was detected after NOTUM knockdown lentivirus administration. The apoptosis of COAD was also observed. SKL2001 was applied to examine whether the role of NOTUM was regulated by Wnt. GEPIA analysis demonstrated that NOTUM expression in COAD tumor tissue was higher compared with in normal tissues. Pair-wise gene correlation analysis identified a potential relationship between NOTUM and Wnt. NOTUM protein and mRNA expression levels in colon carcinoma tissues and RKO cells were increased. NOTUM knockdown lentivirus serves a role in inhibiting COAD development by reducing tumor proliferation, reducing tumor size, and increasing the level of apoptosis in vitro and in vivo. Moreover, NOTUM could increase apoptosis in COAD, which was regulated by FAS, and SKL2001 blocked the progress of apoptosis after NOTUM regulation by NOTUM knockdown lentivirus in vitro and in vivo. Collectively, the present results suggested that NOTUM may be able to regulate the apoptosis of COAD, and that Wnt may be the down-stream target signaling of NOTUM in apoptosis.

Correlation of patients’ demographics and clinical symptoms with temporomandibular disorders

ABSTRACT Objective To investigate the correlation between basic characteristics and clinical features of patients with temporomandibular disorders (TMD). Methods The R language statistical tool was used to analyze the clinical information of 500 TMD patients, i.e., age, sex, joint noises, mouth opening pattern, and pain symptoms, as well as the results of the mandibular push-back test. A pairwise correlation analysis of each clinical feature was carried out. Results The highest incidence of TMD was observed in the age group of 20 to 30 years (240/500). Around 2/3 of the patients showed pain symptoms. Abnormal mouth opening patterns, joint noises, and temporomandibular joint synovitis (TMJS) were observed in 48.4, 65.4, and 34% of patients, respectively. Conclusion Joint click and the corrected deviation of the mouth opening pattern are signs of early-stage TMD, whereas limited mouth opening and TMJS are indicators of progressive stage and complicated TMD.

Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS.

Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci for DM resistance in a core germplasm (CG) of cucumber lines that represent diverse origins and ecotypes. Phenotypic data on responses to DM infection were collected in four field trials across three years, 2014, 2015, and 2016. With the resequencing data of these CG lines, GWAS for DM resistance was performed and detected 18 loci that were distributed on all the seven cucumber chromosomes. Of these 18 loci, only six (dmG1.4, dmG4.1, dmG4.3, dmG5.2, dmG7.1, and dmG7.2) were detected in two experiments, and were considered as loci with a stable effect on DM resistance. Further, 16 out of the 18 loci colocalized with the QTLs that were reported in previous studies and two loci, dmG2.1 and dmG7.1, were novel ones identified only in this study. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, several candidate genes were identified as potential causal genes underlying the stable and novel loci, including Csa1G575030 for dmG1.4, Csa2G060360 for dmG2.1, Csa4G064680 for dmG4.1, Csa5G606470 for dmG5.2, and Csa7G004020 for dmG7.1. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for DM resistance. The potential of using these CG lines for future allele-mining of candidate genes was discussed in the context of breeding cucumber with resistance to DM.

Plasma homocysteine levels in patients with keratoconus

BackgroundTo compare the plasma levels of homocysteine between patients with keratoconus and healthy subjects.MethodsThirty‐three keratoconus patients, and 47 age‐gender matched healthy subjects were included in this prospective study. The plasma level of homocysteine, folic acid, and vitamin B12 was assessed using the chemiluminescence immunometric method. According to the manufacturer's instructions, the normal plasma level of homocysteine, vitamin B12 and folic acid was accepted as ≤ 13 μm/L, 191–663-pg/mL, and 4.6–18.7-ng/mL respectively. Mann–Whitney U and Spearman's correlation tests were used for pairwise comparisons and correlation analysis, respectively.ResultsThere was a statistically significant difference between keratoconus patients and healthy subjects in terms of mean plasma level of homocysteine (15.02 ± 8.01 μm/l in keratoconus patients versus 12.62 ± 8.17 μm/l in healthy subjects, p = 0.01). However, the mean plasma level of either vitamin B12 (263.78 ± 107.2-pg/ml in keratoconus patients versus 264.78 ± 94.2-pg/ml in healthy subjects, p = 0.3), or folic acid (5.98 ± 3.2-ng/ml in keratoconus patients versus 6.72 ± 3.1-ng/ml in healthy subjects, p = 0.1) were not statistically significantly different between two groups. A negative correlation was found between plasma homocysteine level and central corneal thickness (p < 0.001). A positive correlation was found between plasma homocysteine level and steepest keratometry (p = 0.004) and average Sim‐K (p = 0.002).ConclusionsThe increased plasma level of homocysteine in keratoconus patients may either arise from a consequence of biochemical events such as oxidative stress, or it may contribute to the pathogenesis or progression of keratoconus by chelating copper, which is an important co‐factor of lysyl oxidase enzyme taking place in corneal collagen crosslinking.

Antimicrobial Use Indices-The Value of Reporting Antimicrobial Use in Multiple Ways Using Data From Canadian Broiler Chicken and Turkey Farms.

We have previously described the importance of using multiple indicators for reporting national farm-level antimicrobial use (AMU) information, but the distribution of flock-level AMU and how these indicators relate to each other has not yet been fully explored. Using farm-level surveillance data (2013–2019), for broiler chickens (n = 947 flocks) and turkeys (n = 427), this study aims to (1) characterize flock-level AMU and identify high users, (2) identify appropriate AMU indicators and biomass denominator [population correction unit (PCU) vs. kg weight at pre-slaughter], and (3) make recommendations on the application to veterinarian-producer and national-level reporting. Diverse AMU patterns were identified in broiler chickens (156 patterns) and turkeys (68 patterns); of these, bacitracin, reported by 25% of broiler chicken and 19% of turkey producers, was the most frequently occurring pattern. Depending on the indicator chosen, variations in reported quantity of use, temporal trends and relative ranking of the antimicrobials changed. Quantitative AMU analysis yielded the following results for broiler chickens: mean 134 mg/PCU; 507 number (n) of Canadian (CA) defined daily doses (DDDvet) per 1,000 chicken-days and 18 nDDDvetCA/PCU. Analysis in turkey flocks yielded the following: mean 64 mg/PCU, 99 nDDDvetCA/1,000 turkey-days at risk and 9 nDDDvetCA/PCU. Flocks were categorized based on the percentiles of the mg/PCU distribution: “medium” to “low” users (≤75th percentile) and “high” users (>75th percentile). The odds of being a high user in both broiler chickens and turkeys were significantly increased: if water medications were used, and if trimethoprim-sulfonamides, bacitracins, and tetracyclines were used. Pairwise correlation analysis showed moderate correlation between mg/PCU and the nDDDvetCA/1,000 animal days at risk and between mg/PCU and nDDDvetCA/PCU. Significantly high correlation between nDDDvetCA/1,000 animal days at risk and nDDDvetCA/PCU was observed, suggestive that either of these could be used for routine monitoring of trends in AMU. One source of discrepancy between the indicators was the antimicrobial. Understanding the choice of parameter input and effects on reporting trends in AMU will inform surveillance reporting best practices to help industry understand the impacts of their AMU reduction strategies and to best communicate the information to veterinarians, their producers, and other stakeholders.

Regularized S-Map Reveals Varying Bacterial Interactions.

There is a growing awareness that bacterial interactions follow a highly nonlinear pattern in reality. However, it is challenging to track the varying bacterial interactions using pairwise correlation analysis, which fails to explore their potential effects on the behavior of microbes. Here, we utilized a regularized sequential locally weighted global linear map (S-map) to capture the varying interspecific interactions from the time series data of a bacterial community under exposure to nitrite. Our results show that bacterial interactions are highly variable and that asymmetric interactions dominate the interaction pattern in a community. Furthermore, we propose a Jacobian coefficient-based statistical method to predict the harmony level of a bacterial community at each successive ecosystem state. The results show that the bacterial community exhibits a higher harmony level in nitrite-treated samples than in the control group. We show that the community harmony level is positively associated with the specific endogenous respiration rates and biofilm formation of the culture. In addition, the community tends to process lower diversity and structural stability under zero- and high-nitrite stresses. We demonstrate that the harmony level, rather than structural stability, is a useful index for unveiling the underlying mechanism of bacterial performance. Overall, the regularized S-map can help us to understand bacterial interactions in ecosystems more accurately than previous approaches.IMPORTANCE It has long been acknowledged that bacterial interactions play important roles in community structure and function. Revealing the interaction variability can allow an understanding of how bacteria respond to perturbation and why bacterial community performance changes. Such information should improve our skills in engineering bacterial communities (e.g., in a wastewater treatment plant) and achieve better removal performance and lower energy consumption.

Genome-wide association analysis of opioid use disorder: A novel approach using clinical data

BackgroundOpioid use disorder (OUD) represents a large and pervasive global public health challenge. Previous genetic studies have demonstrated the significant heritability of OUD and identified several single-nucleotide polymorphisms (SNPs) associated with its prevalence. MethodsIn this paper, we conducted a genome-wide association analysis on opioid use disorder that leveraged genetic and clinical data contained in a biobank of 21,310 patients of European ancestry. We identified 1039 cases of opioid use disorder based on diagnostic codes from nearly 16 million encounters in electronic health records (EHRs). ResultsWe discovered one novel OUD-associated locus on chromosome 4 that was significant at a genome-wide threshold (p = 2.40 × 10−8). Heritability analysis suggested that common SNPs explained 0.06 (se 0.02, p = 0.0065) of the phenotypic variation in OUD. When we restricted controls to those with previous opioid prescriptions, we were able to further strengthen the original signal and discovered another significant locus on chromosome 16. Pair-wise genetic correlation analysis yielded strong positive correlations between OUD and two other major substance use disorders, alcohol and nicotine, with the strongest correlation between nicotine and opioid use disorder (genetic correlation 0.65, se = 0.19, p = 0.00048), suggesting a significant shared genetic component across different substance disorders. ConclusionsThis pragmatic, clinically-focused approach may supplement more traditional methods to facilitate identification of new genetic underpinnings of OUD and related disorders.

COLEC12 regulates apoptosis of osteosarcoma through Toll-like receptor 4-activated inflammation.

ObjectiveTo investigate the role of COLEC12 in osteosarcoma and observe the relationship between COLEC12 knockdown and the inflammation of osteosarcoma. Then, further explore whether the process is regulated by TLR4.MethodGEPIA and TCGA systems were used to predict the potential function of COLEC12. Western blot and RT‐PCR were used to analyze the protein expression, or mRNA level, of COLEC12 in different tissue or cell lines. The occurrence and development of osteosarcoma were observed by using COLEC12 knockdown lentivirus. The inflammation indexes of osteosarcoma, in vitro and in vivo, were explored. TLR4 knockdown lentivirus was applied to the relationship between COLEC12 and TLR4.ResultsCOLEC12 expression in SARC tumor tissue was higher than in normal, and a high expression of COLEC12 in SARC patients had a worse prognostic outcome. Pairwise gene correlation analysis revealed a potential relationship between COLEC12 and TLR4. The COLEC12 expression and mRNA level in the tumor or Saos‐2 cells were increased. COLEC12 knockdown lentivirus could inhibit osteosarcoma development, in vivo and vitro, through reducing tumor volume and weight, weakening tumor proliferation, migration, and invasion, and enhancing apoptosis. Furthermore, COLEC12 knockdown could increase inflammation of osteosarcoma, in vivo and in vitro, through inducing myeloperoxidase (MPO), TLR4, NF‐κB, and C3, and expression of related inflammatory factors. Finally, TLR4 knockdown lentivirus inhibits the progress of inflammation after COLEC12 regulation, in vivo and vitro.ConclusionCOLEC12 may be able to regulate apoptosis and inflammation of osteosarcoma, and TLR4 may be the downstream target factor of COLEC12 in inflammation.

Abstract 1673: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

Abstract Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, which could impact the capacity of PDXs for faithful modeling of patient treatment response. Such results contrast with reports that have observed genomic fidelity of PDX models with respect to the originating patient tumors and from early to late passages by direct DNA measurements (DNA sequencing or SNP arrays). Here we resolve these contradicting observations by systematically evaluating CNA changes and the genes they affect during engraftment and passaging in a large, internationally collected set of PDX models, comparing both RNA and DNA-based approaches. The data collected, as part of the U.S. National Cancer Institute (NCI) PDXNet (PDX Development and Trial Centers Research Network) Consortium and EurOPDX consortium, comprises 1548 patient (PT) and PDX datasets (1451 unique samples) from 509 models derived from American, European and Asian cancer patients, spanning across 16 tumor types. By assessing copy number changes by pairwise (PT-PDX or PDX-PDX) correlation and residual analysis to control for systematic biases, our study demonstrates that prior reports of systematic copy number divergence between PTs and PDXs are incorrect, and confirms the high retention of copy number during PDX engraftment and passaging. Moreover, only a small proportion of models show large CNA discordance between the samples, suggesting that the variations observed in PDX are mainly due to rare clonal selection of individual tumors rather than murine pressures. This large scale data analysis also reveals several other findings that clarify the evolutionary process in PDXs. We do observe larger deviations between PT-PDX than in PDX-PDX comparisons, likely due to dilution of PT signal by human stromal cells. Interestingly, we found that a major contributor to the differences between PDX samples is lineage-specific drift associated with splitting of tumors into fragments during PDX propagation. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models, suggesting the lack of systematic copy number evolution driven by the PDX mouse host. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multi-region tumor samples or intra-patient samples. Thus concerns about the genetic stability of the PDX system are likely to be less important than the spatial heterogeneity of solid tumors themselves. This result is consistent with our results on lineage effects during passaging, which indicate that intratumoral spatial evolution is the major reason for genetic drift. Our in-depth tracking of CNAs throughout PDX engraftment and passaging confirms that tumors engrafted and passaged in PDX models maintain a high degree of molecular fidelity to the original patient tumors and their suitability for pre-clinical drug testing. This work also finely enumerates the copy number profiles in hundreds of publicly available models, which will enable researchers to assess the suitability of each for individualized treatment studies. Citation Format: Xing Yi Woo, Jessica Giordano, Anuj Srivastava, Zi-Ming Zhao, Michael W. Lloyd, Roebi de Bruijn, Yun-Suhk Suh, Jong-Il Kim, Han-Kwang Yang, Charles Lee, Dennis A. Dean, Brandi Davis-Dusenbery, Yvonne A. Evrard, James H. Doroshow, Alana L. Welm, Bryan Welm, Michael T. Lewis, Bingliang Fang, Jack A. Roth, Funda Meric-Bernstam, Meenhard Herlyn, Michael Davies, Li Ding, Shunqiang Li, Ramaswamy Govindan, Claudio Isella, Jeffrey A. Moscow, Livio Trusolino, Annette Byrne, Jos Jonkers, Carol J. Bult, Enzo Medico, Jeffrey H. Chuang, PDXNET consortium &amp; EurOPDX consortium. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1673.