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Motivation: It has been proposed that clustering clinical markers, such as blood test results, can be used to stratify patients. However, the robustness of clusters formed with this approach to data pre-processing and clustering algorithm choices has not been evaluated, nor has clustering reproducibility. Here, remade use of the NHANES survey to compare clusters generated with various combinations of pre-processing and clustering algorithms, and tested their reproducibility in two separate samples. Method: Values of 44 biomarkers and 19 health/life style traits were extracted from the National Health and Nutrition Examination Survey (NHANES). The 1999-2002 survey was used for training, while data from the 2003-2006 survey was tested as a validation set. Twelve combinations of pre-processing and clustering algorithms were applied to the training set. The quality of the resulting clusters was evaluated both by considering their properties and by comparative enrichment analysis. Cluster assignments were projected to the validation set (using an artificial neural network) and enrichment in health/life style traits in the resulting clusters was compared to the clusters generated from the original training set. Results: The clusters obtained with different pre-processing and clustering combinations differed both in terms of cluster quality measures and in terms of reproducibility of enrichment with health/life style properties. Z-score normalization, for example, dramatically improved cluster quality and enrichments, as compared to unprocessed data, regardless of the clustering algorithm used. Clustering diabetes patients revealed a group of patients enriched with retinopathies. This could indicate that routine laboratory tests can be used to detect patients suffering from complications of diabetes, although other explanations for this observation should also be considered. Conclusions: Clustering according to classical clinical biomarkers is a robust process, which may help in patient stratification. However, optimization of the pre-processing and clustering process may be still required. [ABSTRACT FROM AUTHOR]

Objective: Postpartum hemoglobin (Hb) levels may impact maternal and breast-fed newborn well being and health. Yet, the sources of variation in maternal postpartum Hb levels are poorly understood. We set to investigate whether age has an effect on postpartum Hb levels, and if this effect is similar in different ethnic groups . Study design: The birth records of over 200,000 births in a tertiary medical center were scanned for the first and second births to Jewish and Bedouin mothers in Israel. Age trends in Hb levels were analyzed using linear and bi-linear models. Confounding factors were eliminated by testing the significance of the preferred model in homogenous sub-populations. Results: In Jewish Israeli mothers, postpartum hemoglobin level follow a bi-linear trend, peaking at the age of 27-31 years, both during the first and second births. In Israeli Bedouin mothers, a linear decline is observed through all ages. Conclusion: These results suggest an ethnic difference in the age trends of postpartum Hb levels. Clinically, significant changes may occur between the ages of 27 and 30 years. [ABSTRACT FROM AUTHOR]

Abiotic stresses are a primary cause of crop loss worldwide. The convergence of stress signalling pathways to a common set of transcription factors suggests the existence of upstream regulatory genes that control plant responses to multiple abiotic stresses. To identify such genes, data from published Arabidopsis thaliana abiotic stress microarray analyses were combined with our presented global analysis of early heat stress-responsive gene expression, in a relational database. A set of Multiple Stress ( MST) genes was identified by scoring each gene for the number of abiotic stresses affecting expression of that gene. ErmineJ over-representation analysis of the MST gene set identified significantly enriched gene ontology biological processes for multiple abiotic stresses and regulatory genes, particularly transcription factors. A subset of MST genes including only regulatory genes that were designated ‘ Multiple Stress Regulatory’ ( MSTR) genes, was identified. To validate this strategy for identifying MSTR genes, mutants of the highest-scoring MSTR gene encoding the circadian clock protein CCA1, were tested for altered sensitivity to stress. A double mutant of CCA1 and its structural and functional homolog, LATE ELONGLATED HYPOCOTYL, exhibited greater sensitivity to salt, osmotic and heat stress than wild-type plants. This work provides a reference data set for further study of MSTR genes. [ABSTRACT FROM AUTHOR]

Background: Hip fractures are costly and common in older adults, but there is limited understanding of how treatment patterns and outcomes might differ between countries. Methods: We performed a retrospective serial cross‐sectional cohort study of adults aged ≥66 years hospitalized with hip fracture between 2011 and 2018 in the US, Canada, England, the Netherlands, Taiwan, and Israel using population‐representative administrative data. We examined mortality, hip fracture treatment approaches (total hip arthroplasty [THA], hemiarthroplasty [HA], internal fixation [IF], and nonoperative), and health system performance measures, including hospital length of stay (LOS), 30‐day readmission rates, and time‐to‐surgery. Results: The total number of hip fracture admissions between 2011 and 2018 ranged from 23,941 in Israel to 1,219,696 in the US. In 2018, 30‐day mortality varied from 3% (16% at 1 year) in Taiwan to 10% (27%) in the Netherlands. With regards to processes of care, the proportion of hip fractures treated with HA (range 23%–45%) and THA (0.2%–10%) differed widely across countries. For example, in 2018, THA was used to treat approximately 9% of patients in England and Israel but less than 1% in Taiwan. Overall, IF was the most common surgery performed in all countries (40%–60% of patients). IF was used in approximately 60% of patients in the US and Israel, but only 40% in England. In 2018, rates of nonoperative management ranged from 5% of patients in Taiwan to nearly 10% in England. Mean hospital LOS in 2018 ranged from 6.4 days (US) to 18.7 days (England). The 30‐day readmission rate in 2018 ranged from 8% (in Canada and the Netherlands) to nearly 18% in England. The mean days to surgery in 2018 ranged from 0.5 days (Israel) to 1.6 days (Canada). Conclusions: We observed substantial between‐country variation in mortality, surgical approaches, and health system performance measures. These findings underscore the need for further research to inform evidence‐based surgical approaches. [ABSTRACT FROM AUTHOR]

Objectives: The KPC-producing Klebsiella pneumoniae (KPC-KP) clonal group (CG) 258 has disseminated throughout Israeli post-acute care hospitals (PACHs). The objectives of the study were (i) to describe the evolution and (ii) to understand the dissemination modes of CG 258 in the PACH system in Israel.Methods: KPC-KP surveillance cultures isolates were collected in Israeli PACHs in three national point-prevalence surveys: 2008, 2011 and 2013. CG 258 was identified by pilv-l PCR. WGS was performed for CG 258 isolates from 9 of 14 PACHs and data extracted for core-genome MLST (cgMLST) and for capsule polysaccharide gene cluster analysis.Results: The proportional representation of CG 258 among the KPC-KP isolates increased from 72 of 104 isolates (69.2%) in 2008 to 113 of 133 isolates (85%) in 2011 ( P  =   0.004 for 2008 versus 2011) and remained high in 2013 [56 of 67 isolates (83.6%)]. All isolates were related to CG 258 clade 2. cgMLST phylogenetic analysis showed relative convergence in the 2008 survey, with increasing diversification in the subsequent surveys. A predominantly institutional dissemination pattern was observed only in centre F from southern Israel. A predominantly regional dissemination pattern was observed in the two PACHs in Jerusalem. The other PACHs were characterized by a combined institutional and generalized pattern, with the majority of isolates clustering within the same PACH and survey.Conclusions: CG 258 clade 2 has retained its predominance despite increased diversification. Although interchanging of CG 258 strains occurred between most PACHs, local spread is the leading cause of its dissemination. [ABSTRACT FROM AUTHOR]

Key Points: Question: How do treatment patterns and outcomes for older patients presenting with acute myocardial infarction differ for low- vs high-income individuals across 6 countries. Findings: In this study of 289 376 patients aged 66 years or older hospitalized with ST-segment elevation myocardial infarction (STEMI) and 843 046 hospitalized with non-STEMI across 6 health systems, adjusted 30-day and 1-year mortality rates were higher for low-income patients, whereas rates of cardiac catheterization and percutaneous coronary interventions were lower. High-income patients also had shorter length of stay and lower rates of readmissions. Meaning: These results suggest that income-based disparities were present even in countries with universal health insurance and robust social safety net systems. Importance: Differences in the organization and financing of health systems may produce more or less equitable outcomes for advantaged vs disadvantaged populations. We compared treatments and outcomes of older high- and low-income patients across 6 countries. Objective: To determine whether treatment patterns and outcomes for patients presenting with acute myocardial infarction differ for low- vs high-income individuals across 6 countries. Design, Setting, and Participants: Serial cross-sectional cohort study of all adults aged 66 years or older hospitalized with acute myocardial infarction from 2013 through 2018 in the US, Canada, England, the Netherlands, Taiwan, and Israel using population-representative administrative data. Exposures: Being in the top and bottom quintile of income within and across countries. Main Outcomes and Measures: Thirty-day and 1-year mortality; secondary outcomes included rates of cardiac catheterization and revascularization, length of stay, and readmission rates. Results: We studied 289 376 patients hospitalized with ST-segment elevation myocardial infarction (STEMI) and 843 046 hospitalized with non-STEMI (NSTEMI). Adjusted 30-day mortality generally was 1 to 3 percentage points lower for high-income patients. For instance, 30-day mortality among patients admitted with STEMI in the Netherlands was 10.2% for those with high income vs 13.1% for those with low income (difference, −2.8 percentage points [95% CI, −4.1 to −1.5]). One-year mortality differences for STEMI were even larger than 30-day mortality, with the highest difference in Israel (16.2% vs 25.3%; difference, −9.1 percentage points [95% CI, −16.7 to –1.6]). In all countries, rates of cardiac catheterization and percutaneous coronary intervention were higher among high- vs low-income populations, with absolute differences ranging from 1 to 6 percentage points (eg, 73.6% vs 67.4%; difference, 6.1 percentage points [95% CI, 1.2 to 11.0] for percutaneous intervention in England for STEMI). Rates of coronary artery bypass graft surgery for patients with STEMI in low- vs high-income strata were similar but for NSTEMI were generally 1 to 2 percentage points higher among high-income patients (eg, 12.5% vs 11.0% in the US; difference, 1.5 percentage points [95% CI, 1.3 to 1.8 ]). Thirty-day readmission rates generally also were 1 to 3 percentage points lower and hospital length of stay generally was 0.2 to 0.5 days shorter for high-income patients. Conclusions and Relevance: High-income individuals had substantially better survival and were more likely to receive lifesaving revascularization and had shorter hospital lengths of stay and fewer readmissions across almost all countries. Our results suggest that income-based disparities were present even in countries with universal health insurance and robust social safety net systems. This serial cross-sectional cohort study compares whether treatment patterns and outcomes for patients presenting with acute myocardial infarction differ for low- vs high-income individuals across 6 countries. [ABSTRACT FROM AUTHOR]

Background: Appropriate and timely diagnosis is one of the most important milestones in effective migraine care and is affected by public awareness, access to medical care, health care systems, and physicians' knowledge. We assessed the variability in migraine diagnosis rates in different communities under universal national health coverage in Israel. Methods: In this population-based retrospective, observational, cohort study, adult (≥18 years) migraine patients were identified in the computerized database of the southern district of the Clalit Health Services Health Maintenance Organization (HMO) based on recorded diagnosis and/or purchase of specific anti-migraine acute medication (triptans). Migraine prevalence in 2018 was calculated in the entire study population and in different municipalities. We utilized a standardized (age and gender) mortality ratio (SMR) approach for comparison among the municipalities. Results: In 2018, a total of 29,938 migraine patients were identified out of 391,528 adult HMO members, with an overall prevalence (per 10,000) of migraine of 764.64 (7.65%), 1143.34 (11.43%) for women, and 374.97 (3.75%) for men. Among the municipalities, adjusted prevalence (per 10,000) ranged from 386.15 (3.86%) to 1320.60 (13.21%). The female-to-male ratio ranged from 1.8:1 to 5.1:1. Prevalence rates were positively associated with the socioeconomic status of the municipalities (Spearman rho = 0.472, P = 0.031). Conclusions: High variability in the prevalence of diagnosed migraine suggests underdiagnosis. Resources for awareness and educational programs should be directed to low diagnosed prevalence communities. [ABSTRACT FROM AUTHOR]

Herpes zoster (HZ) represents a serious health problem in the general population due to its abundance and complications. Stroke and acute myocardial infarction are well-documented short-term complications of HZ, primarily due to vasculopathy in the cerebral and coronary arteries. However, no major study to date has specifically demonstrated that HZ is a long-term risk factor for all Major Adverse Cardiac and Cerebrovascular Events (MACCE). A retrospective cohort study was conducted analyzing the association between HZ and MACCE. We compared HZ patients diagnosed between 2001 and 2018 and a matched control group. The model was stratified according to matched pairs and adjusted for age, socioeconomic status, history of dyslipidemia, and prior myocardial infarction (MI). Association between HZ exposure and stroke was assessed through a multivariable Cox regression analysis. The study included 41,930 patients, with 20,965 patients in each group. The risk of MACCE was 19% higher among HZ patients in the first year of follow up (P < 0.001). Antiviral treatment did not positively affect long-term survival among HZ patients (P < 0.001). These results suggest that HZ is a marker of long-term vascular risk. Additional studies will be needed to further evaluate this risk, the impact of HZ vaccination on such risk, and potential mitigation strategies. [ABSTRACT FROM AUTHOR]

The quantum computer game ‘Schrödinger cat and hounds’ is the quantum extension of the well-known classical game fox and hounds. Its main objective is to teach the unique concepts of quantum mechanics in a fun way. ‘Schrödinger cat and hounds’ demonstrates the effects of superposition, destructive and constructive interference, measurements and entanglement. More advanced concepts, like particle–wave duality and decoherence, can also be taught using the game as a model. The game that has an optimal solution in the classical version, can have many different solutions and a new balance of powers in the quantum world. Game-aided lectures were given to high-school students which showed that it is a valid and entertaining teaching platform. [ABSTRACT FROM AUTHOR]

Background: Understanding migraine epidemiology and its burden is crucial for planning health policies and interventions at the local level as well as at the global level. National policies in Israel rely on global estimations and not on local data since local epidemiologic studies had not previously been performed. In this study, we evaluated the epidemiology of migraine in the southern district of Israel using the electronic medical records database of the largest Israeli health maintenance organization (HMO). Methods: In this population-based, retrospective, observational cohort study, adult migraine patients were identified in the computerized database of the southern district of the Clalit Health Services HMO (total population, 0.75 million). Patients were identified based on recorded diagnosis (International Classification of Diseases, Ninth Revision) and/or claims for specific anti-migraine medication (triptans) between 2000 and 2018. A 1:2 age-, gender-, and primary care clinic–matched control group was used for evaluation of comorbidities. Results: In 2018, a total of 29,938 patients with migraine were identified out of 391,528 adult HMO members. Most of the patients were women (75.8%), and the mean ± standard deviation age at diagnosis was 36.94 ± 13.61 years. The overall prevalence of migraine (per 10,000) was 764.64 (7.65%), 1143.34 (11.43%) for women and 374.97 (3.75%) for men. The highest prevalence was observed in patients aged 50 to 60 years and 40 to 50 years (1143.98 [11.44%] and 1019.36 [10.19%], respectively), and the lowest prevalence was among patients aged 18 to 30 years and > 70 years (433.45 [4.33%] and 398.49 [3.98%], respectively). Conclusions: This is the first large-scale epidemiologic study of migraine prevalence in Israel. Compared to international estimations, migraine appears to be underdiagnosed in the southern district of Israel. [ABSTRACT FROM AUTHOR]

Simple Summary: Occult blood in stool is the screening modality of choice for colorectal cancer in most countries. Only a small percentage of patients with positive results of this test will have colorectal cancer. In the present study, we wanted to determine risk factors for having colorectal cancer among patients with positive fecal testing. We found that age, anemia, family history of colorectal cancer, and previous colorectal cancer are factors for having colorectal cancer among those with positive fecal testing. The practical implication of the findings of the present study is that people who have positive fecal testing and one of the found risk factors should be prioritized for colonoscopy scheduling. (1) Background: Fecal occult blood test (FOBT) is the modality of choice in most countries for colorectal cancer (CRC) screening. We aimed to investigate the risk factors for CRC among patients with a positive FOBT in real life. (2) Methods: This was a retrospective study that included patients who tested positive for FOBT. Data regarding the comorbidities and laboratories were collected and compared between CRC and non-CRC groups. (3) Results: Positive FOBT was found among 45,500 (5.36%) subjects and CRC was found in 1502 (3.3%). CRC patients were older, age 62.7 ± 7.15 years compared with 59.33 ± 7.3 years (p < 0.001), and had significantly higher rates of hypertension (48.4% vs. 44.7%, p = 0.002), iron-deficiency anemia (20.6% vs. 16.4, p < 0.001), family history of CRC (7.3% vs. 5.1%, p < 0.001), and previous CRC (6.5% vs. 0.3%, p < 0.001). Lower levels of hemoglobin, iron, and ferritin were found in the CRC group. Age, family history of CRC, and previous CRC were found to be significant risk factors for diagnosis of CRC after positive FOBT with OR of 1.057, 1.4, and 15.9, respectively. (4) Conclusions: Iron-deficiency anemia, family history of CRC, previous colorectal cancer, and low hemoglobin, iron, and ferritin levels should direct physicians to give high priority to colonoscopy scheduling. [ABSTRACT FROM AUTHOR]

Summary: Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat‐tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts.We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica.The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress‐ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat‐responsive orthologs, display a lower basal and higher heat‐induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV‐B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod‐insensitive, early‐flowering phenotype.We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle. [ABSTRACT FROM AUTHOR]

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease. We aimed to investigate the potential similarities and differences regarding the disease among Arabs and Jews. Retrospective study included all patients older than 18 years with NAFLD diagnosis according to ICD-10 codes. Data regarding demographics, comorbidities, and outcomes were retrieved using the MdClone platform from “Clalit” in Israel. Data concerning 34,090 Arab patients and 173,500 Jewish patients with NAFLD were included. Arab patients were significantly younger at diagnosis (35.0 ± 13 years vs. 43.6 ± 15 years, p < 0.001) and had higher rates of obesity and diabetes mellitus (69.5% vs. 56.5% and 27.0% vs. 22.7%, p < 0.001, respectively). Arab patients had higher rates of cirrhosis and portal hypertension-related complications (2.5% vs. 2.0%, p < 0.001), esophageal varices (0.9% vs. 0.5%, p < 0.001), spontaneous bacterial peritonitis (0.3% vs. 0.1%, p < 0.001), and hepatorenal syndrome (0.3% vs. 0.1%, p < 0.001). There was no significant difference in the prevalence of hepatocellular carcinoma between study groups (0.4% vs. 0.5%, p = 0.156). Liver transplantation was performed in 0.2% of Arab NAFLD patients compared to 0.07% of Jewish NAFLD patients (p < 0.001). Lower rates of all-cause mortality were found among the Arab NAFLD patients versus Jewish NAFLD patients (7.7% versus 11.5%, p < 0.001). According to the Cox regression model, Arab ethnicity is a risk factor for death with OR of 1.36. Significant differences regarding comorbidities, complications, liver transplantations rates, and all-cause mortality were found among NAFLD patients of different ethnicities, hence specific population need specific consideration in prevention, early diagnosis and follow up. [ABSTRACT FROM AUTHOR]

Two genes encoding Arabidopsis (Arabidopsis thaliana) DEAD-box RNA helicases were identified in a functional genomics screen as being down-regulated by multiple abiotic stresses. Mutations in either gene caused increased tolerance to salt, osmotic, and heat stresses, suggesting that the helicases suppress responses to abiotic stress. The genes were therefore designated STRESS RESPONSE SUPPRESSOR1 (STRSTI; At1g31970) and STRS2 (At5g08620). In the strs mutants, salt, osmotic, and cold stresses in- duced enhanced expression of genes encoding the transcriptional activators DREB1A/CBF3 and DREB2A and a downstream DREB target gene, RD29A. Under heat stress, the strs mutants exhibited enhanced expression of the heat shock transcription factor genes, HSF4 and HSF7, and the downstream gene HEAT SHOCK PROTEIN1O1. Germination of mutant seed was hyposensitive to the phytohormone abscisic acid (ABA), but mutants showed up-regulated expression of genes encoding ABA- dependent stress-responsive transcriptional activators and their downstream targets. In wild-type plants, STRSI and STRS2 expression was rapidly down-regulated by salt, osmotic, and heat stress, but not cold stress. STRS expression was also reduced by ABA, but salt stress led to reduced STRS expression in both wild-type and ABA-deficient mutant plants. Taken together, our results suggest that STRS1 and STRS2 attenuate the expression of stress-responsive transcriptional activators and function in ABA-dependent and ABA-independent abiotic stress signaling networks. [ABSTRACT FROM AUTHOR]

The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), bla CTX-M gene allele, and mobile genetic elements (MGEs) surrounding it. Out of the 287 bovine- and 104 community-derived ESBL-producing E. coli isolates, 44 and 26 isolates were subjected to NGS, respectively. Both populations exhibited a diverse but distinct clonal structure with predominance of several sequence types (STs); two clones, ST-10/167 ( n  = 13) and ST-38 ( n  = 8), were present. cgMLST analysis of these clones revealed that the majority of isolates exhibited phylogenetic distance (PD) of >178 gene difference from their closest isolate, with the exception of five isolates that exhibited PD of <24 gene difference, including two bovine- to three community-derived isolates. Hence, clonal transmission of ESBL-producing E. coli between cattle and the community, although uncommon, is likely to have occurred. The bla CTX-M-15 gene was identified in 52/70 (74%) isolates from both cattle and the community and was surrounded by MGEs that were composed mostly of either the Tn 3 or IS 1380 families. Thus, MGEs are likely to play an important role in the exchange of resistance genes. [ABSTRACT FROM AUTHOR]

As challenges to food security increase, the demand for lead genes for improving crop production is growing. However, genetic screens of plant mutants typically yield very low frequencies of desired phenotypes. Here, we present a powerful computational approach for selecting candidate genes for screening insertion mutants. We combined ranking of Arabidopsis thaliana regulatory genes according to their expression in response to multiple abiotic stresses (Multiple Stress [ MST] score), with stress-responsive RNA co-expression network analysis to select candidate multiple stress regulatory ( MSTR) genes. Screening of 62 T- DNA insertion mutants defective in candidate MSTR genes, for abiotic stress germination phenotypes yielded a remarkable hit rate of up to 62%; this gene discovery rate is 48-fold greater than that of other large-scale insertional mutant screens. Moreover, the MST score of these genes could be used to prioritize them for screening. To evaluate the contribution of the co-expression analysis, we screened 64 additional mutant lines of MST-scored genes that did not appear in the RNA co-expression network. The screening of these MST-scored genes yielded a gene discovery rate of 36%, which is much higher than that of classic mutant screens but not as high as when picking candidate genes from the co-expression network. The MSTR co-expression network that we created, Ara STressRegNet is publicly available at . This systems biology-based screening approach combining gene ranking and network analysis could be generally applicable to enhancing identification of genes regulating additional processes in plants and other organisms provided that suitable transcriptome data are available. [ABSTRACT FROM AUTHOR]

Background: The probable influence of genes and the environment on sex determination in Nile tilapia suggests that it should be regarded as a complex trait. Detection of sex determination genes in tilapia has both scientific and commercial importance. The main objective was to detect genes and microRNAs that were differentially expressed by gender in early embryonic development. Results: Artificial fertilization of Oreochromis niloticus XX females with either sex-reversed ΔXX males or genetically-modified YY ‘supermales’ resulted in all-female and all-male embryos, respectively. RNA of pools of all-female and all-male embryos at 2, 5 and 9 dpf were used as template for a custom Agilent eArray hybridization and next generation sequencing. Fifty-nine genes differentially expressed between genders were identified by a false discovery rate of p < 0.05. The most overexpressed genes were amh and tspan8 in males, and cr/20β-hsd, gpa33, rtn4ipl and zp3 in females (p < 1 × 10−9). Validation of gene expression using qPCR in embryos and gonads indicated copy number variation in tspan8, gpa33, cr/20β-hsd and amh. Sequencing of amh identified a male-specific duplication of this gene, denoted amhy, differing from the sequence of amh by a 233 bp deletion on exonVII, hence lacking the capability to encode the protein motif that binds to the transforming growth factor beta receptor (TGF-β domain). amh and amhy segregated in the mapping family in full concordance with SD-linked marker on LG23 signifying the QTL for SD. We discovered 831 microRNAs in tilapia embryos of which nine had sexually dimorphic expression patterns by a false discovery rate of p < 0.05. An up-regulated microRNA in males, pma-mir-4585, was characterized with all six predicted target genes including cr/20β-hsd, down-regulated in males. Conclusions: This study reports the first discovery of sexually differentially expressed genes and microRNAs at a very early stage of tilapia embryonic development, i.e. from 2 dpf. Genes with sexually differential expression patterns are enriched for copy number variation. A novel male-specific duplication of amh, denoted amhy, lacking the TGF-β domain was identified and mapped to the QTL region on LG23 for SD, thus indicating its potential role in SD. [ABSTRACT FROM AUTHOR]