Cross-prediction-powered inference

While reliable data-driven decision-making hinges on high-quality labeled data, the acquisition of quality labels often involves laborious human annotations or slow and expensive scientific measurements. Machine learning is becoming an appealing alternative as sophisticated predictive techniques are being used to quickly and cheaply produce large amounts of predicted labels; e.g., predicted protein structures are used to supplement experimentally derived structures, predictions of socioeconomic indicators from satellite imagery are used to supplement accurate survey data, and so on. Since predictions are imperfect and potentially biased, this practice brings into question the validity of downstream inferences. We introduce cross-prediction: a method for valid inference powered by machine learning. With a small labeled dataset and a large unlabeled dataset, cross-prediction imputes the missing labels via machine learning and applies a form of debiasing to remedy the prediction inaccuracies. The resulting inferences achieve the desired error probability and are more powerful than those that only leverage the labeled data. Closely related is the recent proposal of prediction-powered inference [A. N. Angelopoulos, S. Bates, C. Fannjiang, M. I. Jordan, T. Zrnic, Science 382, 669-674 (2023)], which assumes that a good pretrained model is already available. We show that cross-prediction is consistently more powerful than an adaptation of prediction-powered inference in which a fraction of the labeled data is split off and used to train the model. Finally, we observe that cross-prediction gives more stable conclusions than its competitors; its CIs typically have significantly lower variability.

Association of Systemic Vascular Resistance Analog and Cardiovascular Outcomes: The Heart and Soul Study

Background Systemic vascular resistance (SVR) is an integral component of the hemodynamic profile. Previous studies have demonstrated a close correlation between an estimated SVR analog (eSVR) based on echocardiographic methods and SVR by direct hemodynamic measurement. However, the prognostic impact of eSVR remains unestablished. Methods and Results Study participants with established coronary artery disease from the Heart and Soul Study formed this study cohort. We defined Doppler-derived eSVR as the ratio of systolic blood pressure to left ventricular outflow tract velocity time integral. Study participants were separated based on baseline eSVR tertile: <5.6, 5.6 to <6.9, and ≧6.9. An elevated eSVR was defined as an eSVR in the third tertile (≧6.9). Follow-up eSVR was calculated at the fifth year of checkup. Cardiovascular outcomes included heart failure, major cardiovascular events, and all-cause death. Among the 984 participants (67±11 years old, 82% men), subjects with the highest baseline eSVR tertile were the oldest, with the highest systolic blood pressure and lowest left ventricular outflow tract velocity time integral. A higher eSVR was associated with increased risk of heart failure, major cardiovascular events, and death. The hazard ratio for major cardiovascular events was 1.38 (95% CI, 1.02-1.86, P=0.03) for subjects with the highest eSVR tertile compared with the lowest. In addition, those with a persistently elevated eSVR during follow-up had the most adverse outcomes. Conclusions An elevated eSVR, derived by the ratio of systolic blood pressure and left ventricular outflow tract velocity time integral, was more closely correlated with cardiovascular events than systolic blood pressure alone. Repeatedly elevated eSVR was associated with more adverse outcomes.

The reaction of Criegee intermediates with formamide and its implication to atmospheric aerosols

The reactions of Criegee intermediates (CIs) play an important role in the formation of secondary organic aerosols that have negative effect on visibility, human health, and global climate. New particle formation (NPF) can contribute to more than half of the aerosols in terms of their number concentration. Here, the reactions of CIs with formamide (FA) in the gas-phase and at the air/water interface were investigated using quantum chemistry calculation and Born-Oppenheimer molecular dynamic simulations. The results show that the reaction mechanism of CIs with FA is similar to that with formic acid, and the formation of hydroperoxymethyl formimidate (P4) is the most favorable pathway both in the gas-phase and at the air/water interface. Moreover, the potential contribution of the products to NPF was also evaluated by means of the molecular dynamic simulations. The results indicate that the product (P4) can participate in the SA-based NPF and water molecules are beneficial to enhance the NPF. The exploration will provide insight into the reaction of CIs with amide and the effect of the Criegee chemistry on the atmospheric aerosols.

Theoretical study of the reaction mechanism between Criegee intermediates and hydroxyl radicals in the presence of ammonia and amine

Criegee intermediates (CIs), formed in the ozonolysis process of unsaturated hydrocarbons, play an important role in the formation of OH radicals, sulfuric acid, and aerosols. In this study, quantum chemical calculations were carried out to investigate the mechanism for the reaction of Criegee intermediates [involving CH₂OO, CH₃CHOO and (CH₃)₂COO] with OH radicals at the level of CCSD(T)/jun-cc-pVTZ//M06-2X/6-311 + G(2d,2p). A third component, such as water, ammonia, or amines, was introduced to the reaction of CIs with OH to evaluate their catalytic effect. The results show that the OH addition is the favorable channel among four channels involving cis-H abstraction, trans-H abstraction and O abstraction. The third component has a positively catalytic effect on the trans-H abstraction and O abstraction pathways. Moreover, for the trans-H abstraction of CH₃CHOO and (CH₃)₂COO with OH, ammonia and amine exhibit more effectively catalytic ability than water. Furthermore, Born-Oppenheimer molecular dynamic simulation results show that the addition of third component to CIs and hydrogen abstraction from the third component by OH occur simultaneously.

Hsa-miR-196a2 polymorphism increases the risk of acute lymphoblastic leukemia in Chinese children

Acute lymphoblastic leukemia (ALL) is a major cause of mortality and morbidity in childhood, and the causes of ALL are not completely understood. microRNAs (miRNAs) regulate various biological processes including organ development, cell growth regulation, cell differentiation, apoptosis, and tumorigenesis. We performed a case-control study with 570 childhood ALL cases and 673 cancer-free controls to investigate the association between hsa-miR-196a2 rs11614913 T>C polymorphism and ALL risk. The bioinformatics was used to estimate the potential target of hsa-miR-196a2. In the present study, the hsa-miR-196a2 variant TC heterozygote, and CC/TC genotypes were found to be associated with a significantly increased childhood ALL risk, compared with the TT wild-type homozygote (adjusted OR=1.50, 95% CI=1.15-1.95 for TC and OR=1.40, 95% CI=1.09-1.79 for CC/TC). Further, the difference was pronounced in younger (≤6) subjects or parental non-drinker. The significance of the increased risk is more obvious than the higher treatment branch. Additionally, we found that the rs11614913 TC genotype can increase B-phenotype ALL risk (OR=1.37, 95% CI=1.07-1.76). Finally, combination of three bioinformatics approaches revealed that HOXC8 may be the target gene of hsa-miR-196a2. Taken together, our finding suggested that hsa-miR-196a2 rs11614913 T>C may increase the risk of childhood ALL. Large studies with the function of hsa-miR-196a2 are needed in the further study.

Effect of interleukin-17A and interleukin-17F gene polymorphisms on the risk of gastric cancer in a Chinese population

We selected six tagged single-nucleotide polymorphisms (SNPs) in the IL-17A and IL-17F genes, and evaluated the relationship between the six common SNPs and H. pylori infection, tobacco smoking and subsites of gastric cancer in gastric cancer patients. Genotyping of IL-17A (rs2275913, rs3748067 and rs3819025) and IL-17A (rs763780, rs9382084, and rs12203582) was performed in a 384-well plate format on the MassARRAY® platform. An unconditional multiple logistical regression model was performed to determine the association between IL-17A and IL-17F genetic variations and gastric cancer risk. Unconditional logistic regression analysis showed that subjects carrying the rs2275913AA and rs3748067 TT genotypes were 1.70 and 3.45 times more likely to develop gastric cancer. Furthermore, rs2275913 and rs3748067 genetic variants significantly interacted with H. pylori infection on the risk of gastric cancer. The interaction between rs3748067 and rs9382084 genetic variants and tobacco smoking trend was significant. In addition, rs2275913, rs3748067 and rs9382084 genetic variants were only associated with non-cardia gastric cancer. The findings suggest that the rs2275913, rs3748067 and rs9382084 polymorphisms increase the risk of gastric cancer, and they interact with H. pylori infection, tobacco smoking and subsites of gastric cancer. These findings could be helpful in identifying individuals at increased risk for developing gastric cancer.

A common polymorphism in pre-microRNA-146a is associated with lung cancer risk in a Korean population

INTRODUCTION

MicroRNAs (miRs) play important roles in the development and progression of human cancers. MiR-146a down-regulates epidermal growth factor receptor and the nuclear factor-κB regulatory kinase interleukin-1 receptor-associated kinase 1 genes that play important roles in lung carcinogenesis. This study was conducted to evaluate the association between rs2910164C>G, a functional polymorphism in the pre-miR-146a, and lung cancer risk.

MATERIAL AND METHODS

The rs2910164C>G genotypes were determined in 1094 patients with lung cancer and 1100 healthy controls who were frequency matched for age and gender.

RESULTS

The rs2910164 CG or GG genotype was associated with a significantly decreased risk for lung cancer compared to that of the CC genotype (adjusted odds ratio=0.80, 95% confidence interval=0.66-0.96, P=0.02). When subjects were stratified according to smoking exposure (never, light and heavy smokers), the effect of the rs2910164C>G genotype on lung cancer risk was significant only in never smokers (adjusted odds ratio=0.66, 95% confidence interval=0.45-0.96, P=0.03, under a dominant model for the C allele) and decreased as smoking exposure level increased (Ptrend<0.001). In line with this result, the level of miR-146a expression in the tumor tissues was significantly higher in the GG genotype than in the CC or CG genotype only in never-smokers (P=0.02).

CONCLUSIONS

These findings suggest that the rs2910164C>G in pre-miR-146a may contribute to genetic susceptibility to lung cancer, and that miR-146a might be involved in lung cancer development.

Association of the rs6235 variant in the proprotein convertase subtilisin/kexin type 1 (PCSK1) gene with obesity and related traits in a Taiwanese population

One particularly interesting single nucleotide polymorphism (SNP), rs6235 (encoding an S690T substitution), in the proprotein convertase subtilisin/kexin type 1 (PCSK1) gene has been widely associated with obesity in several European cohorts. The present study was intended to investigate the association between the PCSK1 rs6235 SNP and the prevalence of overweight or obesity, or obesity-related metabolic traits in a Taiwanese population. A total of 964 Taiwanese subjects with general health examinations were analyzed. Our data revealed no association of PCSK1 rs6235 with the risk of obesity or overweight in the complete subjects. However, the PCSK1 rs6235 SNP exhibited a significant association with overweight among the male subjects (P=0.03), but not among the female subjects. Furthermore, the carriers of GG variant had a significantly higher waist circumference than those with the CC variant (82.5 ± 11.5 vs. 81.2 ± 10.2 cm; P=0.01) and those with the CG variant (82.5 ± 11.5 vs. 81.4 ± 10.4 cm; P=0.021). In addition, the carriers of GG variant had a higher diastolic blood pressure than those with the CC variant (81.9 ± 14.2 vs. 80.3 ± 12.9 mm Hg; P=0.023). Our study indicates that the PCSK1 rs6235 SNP may contribute to the risk of overweight in men and predict obesity-related metabolic traits such as waist circumference and diastolic blood pressure in Taiwanese subjects.

Association between MTHFR C677T polymorphism and depression: An updated meta-analysis of 26 studies

BACKGROUND

Previous studies concerning the association between the 5,10-methylenetetrahydrofolate reductase (MTHFR) C677T gene polymorphism and depression have provided inconclusive findings. A meta-analysis was therefore performed to investigate a more reliable estimate.

METHODS

This meta-analysis recruited 26 published studies which were selected by a search of electronic databases up to January 2013, including 4992 depression cases and 17,082 controls. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association between MTHFR C677T polymorphism and depression susceptibility using random effect models.

RESULTS

Meta-analyses results suggested that MTHFR C677T polymorphism contributed to the increased depression risk in overall populations (for T vs. C: OR=1.19, 95%CI=1.07-1.32; for TT+CT vs. CC: OR=1.15, 95%CI=1.01-1.31; for TT vs. CC: OR=1.42, 95%CI=1.16-1.75; for TT vs. CT+CC: OR=1.38, 95%CI=1.16-1.63). Subgroup analysis by ethnicity indicated an association in Asian populations (for T vs. C: OR=1.36, 95%CI=1.11-1.66; for TT+CT vs. CC: OR=1.32, 95%CI=1.03-1.69; for TT vs. CC: OR=1.88, 95%CI=1.26-2.79; for TT vs. CT+CC: OR=1.76, 95%CI=1.30-2.38); and a marginal association in White populations (for TT vs. CT+CC: OR=1.15, 95%CI=1.01-1.31). However, the association between the MTHFR C677T polymorphism and depression was not observed in the elderly.

CONCLUSION

The MTHFR C677T polymorphism was associated with an increased risk of depression, especially in Asian populations. However, there was no evidence indicating a correlation in the elderly.

Studying the effects of polycyclic aromatic hydrocarbons on peripheral arterial disease in the United States

PURPOSE

Polycyclic aromatic hydrocarbons are a group of prevalent pollutants which are produced by incomplete combustion of organic materials such as coal, fuel, tobacco smoking and food cooking. The associations between exposures to polycyclic aromatic hydrocarbons (PAHs) and peripheral arterial disease (PAD) have not been well studied.

METHODS

We used the 2001-2004 National Health and Nutrition Examination Survey (NHANES) to investigate the associations between eight monohydroxy urinary metabolites of four PAHs and PAD.

RESULTS

In a logistic regression model, subjects within the middle and highest tertiles of fluorene metabolites, 2-hydroxyfluorene (2-FLUO) and 3-hydroxyfluorene (3-FLUO), and phenanthrene metabolites, 1-hydroxyphenanthrene (1-PHEN) and 2-hydroxyphenanthrene (2-PHEN), had significantly higher prevalence of PAD as compared to subjects within the lowest tertile after adjusting for cigarette smoking, diabetes mellitus and other covariates (For 2-FLUO, the 3rd tertile: OR=2.22, 95% CI=1.13-4.37, p for trend=0.02; For 3-FLUO, the 3rd tertile: OR=2.36, 95% CI: 1.16-4.77, p for trend=0.02; For 1-PHEN, the 3rd tertile: OR=1.84, 95% CI: 1.01-3.37, p for trend=0.04; For 2-PHEN, the 3rd tertile: OR=1.76, 95% CI: 1.07-2.88, p for trend=0.03).

CONCLUSIONS

Our findings suggest that exposure to PAHs may increase the risk of PAD. Further studies are necessary to explore the associations between PAHs and PAD.

Association of interleukin-18 gene polymorphisms with the outcomes of hepatitis C virus infection in high-risk Chinese Han population

Interleukin 18 (IL-18) gene polymorphisms have been reported to be associated with the outcomes of hepatitis C virus (HCV) infection in Americans, Indians and Europeans. We aimed to investigate whether the association can be replicated in Chinese Han population. Three IL-18 variants, -656G>T, -137G>C and +105A>C, were genotyped in three independent Han cohorts consisting of 552 cases and 784 controls. By using logistic regression analysis and multiple testing, haplotype GCC were associated with a protection from susceptibility to HCV. After stratified analysis, both the carriage of -137C allele in the older or hemodialysis subgroup and the carriage of +105C allele in the younger subgroup were found to be significantly associated with a decreased risk of HCV susceptibility. By using logistic regression analysis and multiple testing for the resolution of HCV infection, our study showed that +105C allele and haplotype GGC displayed a negative effect on HCV persistence. After stratified analysis, a significantly decreased risk for HCV persistence was found in +105C allele in the subgroups of young, male or female, drug user or hemodialysis and HCV-1 or HCV mixed genotype. No significant association was observed between -656G>T and the outcomes of HCV infection. Our results demonstrated that the carriage of -137C allele, +105C allele, haplotype -656G/-137C/+105C and haplotype -656G/-137G/+105C of IL-18 gene may contribute to better outcomes of HCV infection in high-risk Chinese Han population.

Methylenetetrahydrofolate reductase C677T mutation in patients with alopecia areata in Turkish population

OBJECTIVE

Methylene-tetrahydrofolate reductase (MTHFR) is a key enzyme regulating folate metabolism and it is thought to influence DNA methylation and nucleic acid synthesis. Mutations in the MTHFR gene have been associated with several autoimmune disorders in previous studies. Alopecia areata (AA) is considered to be a tissue-specific autoimmune disease as the hair follicle has been targeted and antibodies to their own hair follicle structures have been developed. Since there is a common shared pathway between AA and other autoimmune disorders, we aimed to investigate a possible association between the MTHFR gene C677T mutation and AA susceptibility in the Turkish population.

METHODS

The study included 136 patients affected by AA and 130 healthy controls. Genomic DNA was isolated and genotyped using a polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) assay for the MTHFR gene C677T mutation.

RESULTS

The distributions of genotype and allele frequencies of MTHFR gene C677T mutation were statistically different between AA patients and the control group (p=0.036 and p=0.011, respectively). High differences were also observed when the patients and controls were compared according to CC versus CT+TT (p=0.012). CT+TT genotypes and T allele of MTHFR gene C677T mutation were found to be a susceptibility factor for AA in the Turkish population.

CONCLUSION

The results suggest that MTHFR gene C677T mutation may have an effect on the risk of alopecia areata in the Turkish population. This is the first study reporting the association between the MTHFR (C677T) genotype and AA.

Prognostic value of epidermal growth factor receptor in patients with gastric cancer: a meta-analysis

BACKGROUND

The epidermal growth factor receptor (EGFR) plays important roles in the development of gastric cancer. This study aims to analyze the prognostic value of EGFR in patients with gastric cancer.

METHODS

A meta-analysis is performed by searching Cochrane Library, PubMed, EMBASE and Science Direct databases from Jan 1970 to May 2013. Data are extracted from studies evaluating the survival of gastric cancer patients with either positive or negative EGFR expression. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) are calculated.

RESULTS

Totally 1600 cases of gastric cancer patients from five studies are subjected to final analysis. The HR of post-operational survival of patients with positive EGFR expression is 1.16 (95% CI: 0.94-1.43) as compared with those with negative expression, indicating that positive EGFR expression does not significantly predict the poor survival of gastric cancer.

CONCLUSIONS

EGFR expression is not an independent predictor for the survival of gastric cancer patients.

Higher glycemic index and glycemic load diet is associated with increased risk of esophageal squamous cell carcinoma: a case-control study

Several studies have indicated the association between intake of foods high in dietary glycemic index (GI) and glycemic load (GL) with an increased risk of digestive tract cancers. We hypothesized that GI and GL may be associated with risk of esophageal squamous cell carcinoma (ESCC) in a high-risk population in Iran. In total, we interviewed 47 cases with incident of ESCC and 96 frequency-matched hospital controls, then calculated the average dietary GI and GL via a validated food frequency questionnaire. Dietary GL was calculated as a function of GI, carbohydrate content, and frequency of intake of certain foods. Dietary GI and GL levels were significantly higher among the ESCC cases compared with the controls (P < .05). After adjustment for potential confounders, those in the highest tertile of dietary GI had 2.95 times higher risk of ESCC compared with those in the lowest (95% confidence interval, 1.68-3.35; P for trend = .002). In addition, being in the highest tertile of dietary GL was positively associated with an ESCC risk (odds ratio, 3.49; 95% confidence interval, 2.98-4.41; P for trend = .001). Findings of the present study indicate that diets with high GI and GL might have potentially unfavorable effects on ESCC risk and suggest a possible role for excess circulating insulin and related insulin-like growth factor 1 in esophageal cancer development.

The effect of HLA on immunological response to hepatitis B vaccine in healthy people: a meta-analysis

BACKGROUND AND AIM

Evidence is accumulating that several markers in the human leukocyte antigen (HLA) region have been associated with decreased or increased antibody response to hepatitis B vaccine in different individuals. This meta-analysis is to assess the associations of HLA class II DRB1 and DQB1 alleles with immunologic response to hepatitis B vaccine in healthy people.

METHODS

A systematic review of cohort studies in healthy people was performed. We searched databases for relevant studies that were published in English or Chinese up to February 17, 2012. Odds ratios (ORs) with corresponding 95% confidence intervals (CIs) of HLA alleles response to hepatitis B vaccine were pooled by using of a fixed-effects or random-effects model depending on absence or presence of significant heterogeneity. All statistical tests were two-sided.

RESULTS

Fifteen studies were included in this meta-analysis after scanning 774 potentially relevant articles. A total of 2308 subjects (including 1215 responders, 873 nonresponders and 220 control populations) were included. For DRB1 alleles, pooled ORs showed that three HLA variants, DRB1*01, DRB1*1301 and DRB1*15 were associated with a significant increase antibody response to hepatitis B vaccine, their pooled ORs were 2.73, 5.94 and 2.29 respectively. While DRB1 *03 (DRB1*0301), DRB1*04, DRB1*07 and DRB1*1302 were opposite, their pooled ORs were 0.55(0.42), 0.57, 0.24 and 0.25 respectively. And for DQB1 alleles, pooled ORs showed that DQB1*05 (DQB1*0501), DQB1*06, DQB1*0602 were associated with a significant increase antibody response to hepatitis B vaccine. Their merger ORs were 1.85, 2.35, 2.34 and 3.32 respectively. While DQB1*02 (pooled OR=0.27) was adverse. Sensitivity and specificity analysis of HLA alleles showed that DRB1*1301and DQB1*0602 had high specificity (94.2% and 90.1%) but low sensitivity (25.1% and 26.3%), respectively.

CONCLUSION

It was suggested that specific HLA class II alleles (DRB1 and DQB1) were associated with antibody response to HepB.

Diagnosis and management of Alzheimer's disease: past, present and future ethical issues

There is great interest in the ethical issues associated with Alzheimer's disease (AD) and related dementias given the prevalence of AD and the evolving neuroscience landscape in matters of diagnoses and therapeutics. Much of the ethics discussion arises in the tension between the principle of not doing harm (principle of non-maleficence) in this vulnerable population and the development of effective treatments (principle of beneficence). Autonomy and capacity issues are also numerous, wide-ranging, and concern (1) day to day affairs such as driving safely and spending money wisely, (2) life-time events such as designating a legal representative in case of incapacity, making a will, (3) consenting to treatment and diagnostic procedures, (4) participating in research. The latter issue is particularly thorny and illustrates well the complexity of tackling concerns related to capacity. The impetus to protect AD patients has partly led to ethics regulation and policies making research on inapt patients more difficult because of stringent requirements for signed informed consent or for showing the value of the research to this specific patient population. New issues are arising that relate to earlier diagnosis using biomarkers and (possibly soon) the use of drugs that modify disease progression. We here summarize and discuss the different ethical issues associated with AD from a historical perspective, with emphasis on diagnostic and treatments issues.