A fast algorithm for the constrained multiple sequence alignment problem

Given n strings S1, S2, ..., Sn, and a pattern string P, the constrained multiple sequence alignment (CMSA) problem is to find an optimal multiple alignment of S1, S2, ..., Sn such that the alignment contains P, i.e. in the alignment matrix there exists a sequence of columns each entirely composed of symbol P[k] for every k, where P[k] is the kth symbol in P, 1 ≤ k ≤ |P|, and in the sequence, a column containing P[i] appears before the column containing P[j] for all i,j, i < j. The problem is motivated from the problem of comparing multiple sequences that share a common structure, or sequence pattern. There are O(2ns1s2...snr)-time dynamic programming algorithms for the problem, where s1,s2, ...,sn and r are, respectively, the lengths of the input strings and the pattern string. Feasibility of these algorithms in practice is limited when the number of sequences is large, or the sequences are long because of the impractically long time required by these algorithms. We present a new algorithm with worst-case time complexity also O(2ns1s2...snr), but the algorithm avoids redundant computations in existing dynamic programming solutions. Experiments on both randomly generated strings and real data show that this algorithm is much faster than the existing algorithms. We present an analysis that explains the speed-up obtained in our experiments by our algorithm over the naive dynamic programming algorithm for constrained multiple sequence alignment of protein sequences. The speed-up is more significant when pattern is long, or n is large. For example in the case of constrained pairwise sequence alignment (the CMSA problem with n=2) when the pattern is sufficiently long for strings S1 and S2, the asymptotic time complexity is observed to be O(s1s2) instead of O(s1s2r). Main ideas in our algorithm can also be used in other constrained sequence alignment problems

Global Breast Cancer: The Lessons to Bring Home

Breast cancer is the most common cancer affecting women globally. This paper discusses the current progress in breast cancer in Western countries and focuses on important differences of this disease in low- and middle-income countries (LMCs). It introduces several arguments for applying caution before globalizing some of the US-adopted practices in the screening and management of the disease. Finally, it suggests that studies of breast cancer in LMCs might offer important insights for a more effective management of the problem both in developing as well as developed countries

Reliability of follicle-stimulating hormone measurements in serum

BACKGROUND: Follicle-stimulating hormone (FSH), a member of gonadotropin family, is critical for follicular maturation and ovarian steroidogenesis. Serum FSH levels are known to fluctuate during different phases of menstrual cycle in premenopausal women, and increase considerably after the menopause as a result of ovarian function cessation. There is little existing evidence to guide researchers in estimating the reliability of serum FSH measurements. The objective of this study was to assess the reliability of FSH measurement using stored sera from an ongoing prospective cohort – the NYU Women's Health Study. METHODS: Sixty healthy women (16 premenopausal, 44 postmenopausal), who donated at least two blood samples at approximately 1-year intervals were studied. An immunoradiometric assay using a sandwich monoclonal antibodies technique was used to measure FSH levels in serum. RESULTS: The reliability of a single log-transformed FSH measurement, as determined by the intraclass correlation coefficient, was 0.70 for postmenopausal women (95% confidence interval (CI), 0.55–0.82) and 0.09 for premenopausal women (95% CI, 0–0.54). CONCLUSIONS: These results suggest that a single measurement is sufficient to characterize the serum FSH level in postmenopausal women and could be a useful tool in epidemiological research. For premenopausal women, however, the reliability coefficient was low, suggesting that a single determination is insufficient to reliably estimate a woman's true average serum FSH level and repeated measurements are desirable

Preliminary Evaluation of Nonlinear Effects on TCA Flutter

The objective of this study is to investigate the effect of nonlinear aerodynamics, especially at high angles-of-attack with leading-edge separation, on the TCA flutter properties at transonic speeds. In order to achieve that objective, flutter simulations with Navier-Stokes CFD must be performed. To this end, time-marching Navier-Stokes solutions are computed for the TCA wing/body configuration at high angles-of-attack in transonic flight regimes. The approach is to perform non-linear flutter calculations on the TCA at two angles-of-attack, the first one being a case with attached flow (a=2.8 degrees) and the second one being a high angle-of-attack case with a wing leading edge vortex (a=12.11 degrees). Comparisons of the resulting histories and frequency damping information for both angles-of-attack will evaluate the impact of high-alpha aerodynamics on flutter

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy

Dietary whole grain consumption has been postulated to have metabolic benefits. The purpose of this study was to compare a pregnancy diet containing 75% of total carbohydrates as refined grains with a diet of 75% of total carbohydrates as whole grains for pregnancy outcomes and effects on the microbiome. Gestational weight gain, glucose tolerance and newborn outcomes were measured on 248 enrolled compliant women from whom a subset of 103 women consented to give 108 vaginal and 109 anal swabs. The data presented here are limited to the patients from whom the vaginal and anal swabs were obtained in order to study the microbiome. A microbiome—16SrRNA survey—was characterized in these samples. Samples and measurements were obtained at the first obstetrical visit, before beginning a prescribed diet (T1—baseline) and after 17–32\ua0weeks on the prescribed diet (T3). Food frequency questionnaires and total plasma alkylresorcinols were used as a measure of whole grain consumption. There were no dietary differences in maternal weight gain, birth weight, or glucose tolerance test. Mothers consuming the whole grains diet showed a trend of gestational decrease in vaginal bacterial alpha diversity, with increasing Lactobacillus-dominance. No significant difference was observed for the anal microbiome. The results suggest that diet modulations of the vaginal microbiome during gestation may have important implications for maternal and neonatal health and in the intergenerational transfer of maternal microbiome. Trial registration: ClinicalTrials.gov Identifier: NCT03232762

Evaluation of Maternal and Fetal Outcomes in the Adolescents Pregnancy

Objective: In this study, our aim is to compare discussing maternal and fetal problems non-adolescent pregnancy with maternal and fetal problems in adolescent pregnancy that seen in hospital. Methods: 15-19 years of age (50 patients) and 20-23 years (96 patients) who gave birth at the Gynaecologi­cal and Obstetric Clinic under the Faculty of Medicine of Dicle University between January 2015-October 2015 were retrospectively evaluated. Age at birth, parity, blood pressure, pulse, gestational age, complications at birth, cesarean section indications, maternal biochemical pa­rameters, patients with preeclampsia and preterm birth, maternal and fetal complications were recorded. Results: Total number of births between January 2015- October 2015 were 1715 patients in our clinic. 62 of them (3.6%) were observed in the adolescent group. Maternal blood transfusion needs were found to be significantly higher in the adolescent group (p=0.004). Fetal abnor­malities and fetal intensive care needs were found to be significantly higher in the adolescent group (p=0.014, p=0.018). Conclusion: Adolescent pregnancies were high-risk pregnancies in terms of maternal anemia and blood transfusion requirements and because of adverse perina­tal outcomes. Therefore, to reduce the adolescent preg­nancy and to minimize perinatal complications should be done more extensive studies

Acute lower gastrointestinal bleeding: predictive factors and clinical outcome for the patients who needed first-time mesenteric conventional angiography

PURPOSE:We aimed to investigate patients with lower gastrointestinal bleeding who presented to the emergency department requiring initial conventional angiography. We report risk-stratified and mesenteric conventional angiography outcomes.METHODS:We retrospectively reviewed patients with lower gastrointestinal bleeding between 2001 and 2012. We included all consecutive patients with clinical lower gastrointestinal bleeding with a requirement of further angiography and possible embolization. Patients who had prior interventions or surgery were excluded.RESULTS:A total of 88 patients (35 women, 53 men) with a median age of 71 years (range, 23–99 years) were included in the analysis. Conventional angiography was positive and endovascular treatment was intended in 35 patients. Once the source of bleeding was found angiographically, endovascular treatment had a technical success rate of 90.3% and clinical success rate of 71.4%. Overall early rebleeding rate (30 days) was 13.6%.CONCLUSION:Identifying the source of lower gastrointestinal bleeding remains to be a clinical and angiographic challenge. Although we did not observe an association between mortality and clinical success, increased early rebleeding rates were associated with higher mortality rates

Characterization of a genomic signature of pregnancy identified in the breast.

The objective of this study was to comprehensively compare the genomic profiles in the breast of parous and nulliparous postmenopausal women to identify genes that permanently change their expression following pregnancy. The study was designed as a two-phase approach. In the discovery phase, we compared breast genomic profiles of 37 parous with 18 nulliparous postmenopausal women. In the validation phase, confirmation of the genomic patterns observed in the discovery phase was sought in an independent set of 30 parous and 22 nulliparous postmenopausal women. RNA was hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays containing probes to 54,675 transcripts, scanned and the images analyzed using Affymetrix GCOS software. Surrogate variable analysis, logistic regression, and significance analysis of microarrays were used to identify statistically significant differences in expression of genes. The false discovery rate (FDR) approach was used to control for multiple comparisons. We found that 208 genes (305 probe sets) were differentially expressed between parous and nulliparous women in both discovery and validation phases of the study at an FDR of 10% and with at least a 1.25-fold change. These genes are involved in regulation of transcription, centrosome organization, RNA splicing, cell-cycle control, adhesion, and differentiation. The results provide initial evidence that full-term pregnancy induces long-term genomic changes in the breast. The genomic signature of pregnancy could be used as an intermediate marker to assess potential chemopreventive interventions with hormones mimicking the effects of pregnancy for prevention of breast cancer

Characterization of a genomic signature of pregnancy identified in the breast.

The objective of this study was to comprehensively compare the genomic profiles in the breast of parous and nulliparous postmenopausal women to identify genes that permanently change their expression following pregnancy. The study was designed as a two-phase approach. In the discovery phase, we compared breast genomic profiles of 37 parous with 18 nulliparous postmenopausal women. In the validation phase, confirmation of the genomic patterns observed in the discovery phase was sought in an independent set of 30 parous and 22 nulliparous postmenopausal women. RNA was hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays containing probes to 54,675 transcripts, scanned and the images analyzed using Affymetrix GCOS software. Surrogate variable analysis, logistic regression, and significance analysis of microarrays were used to identify statistically significant differences in expression of genes. The false discovery rate (FDR) approach was used to control for multiple comparisons. We found that 208 genes (305 probe sets) were differentially expressed between parous and nulliparous women in both discovery and validation phases of the study at an FDR of 10% and with at least a 1.25-fold change. These genes are involved in regulation of transcription, centrosome organization, RNA splicing, cell-cycle control, adhesion, and differentiation. The results provide initial evidence that full-term pregnancy induces long-term genomic changes in the breast. The genomic signature of pregnancy could be used as an intermediate marker to assess potential chemopreventive interventions with hormones mimicking the effects of pregnancy for prevention of breast cancer

Genetically inferred birthweight, height, and puberty timing and risk of osteosarcoma

INTRODUCTION: Several studies have linked increased risk of osteosarcoma with tall stature, high birthweight, and early puberty, although evidence is inconsistent. We used genetic risk scores (GRS) based on established genetic loci for these traits and evaluated associations between genetically inferred birthweight, height, and puberty timing with osteosarcoma. METHODS: Using genotype data from two genome-wide association studies, totaling 1039 cases and 2923 controls of European ancestry, association analyses were conducted using logistic regression for each study and meta-analyzed to estimate pooled odds ratios (ORs) and 95% confidence intervals (CIs). Subgroup analyses were conducted by case diagnosis age, metastasis status, tumor location, tumor histology, and presence of a known pathogenic variant in a cancer susceptibility gene. RESULTS: Genetically inferred higher birthweight was associated with an increased risk of osteosarcoma (OR =1.59, 95% CI 1.07-2.38, P = 0.02). This association was strongest in cases without metastatic disease (OR =2.46, 95% CI 1.44-4.19, P = 9.5 ×10-04). Although there was no overall association between osteosarcoma and genetically inferred taller stature (OR=1.06, 95% CI 0.96-1.17, P = 0.28), the GRS for taller stature was associated with an increased risk of osteosarcoma in 154 cases with a known pathogenic cancer susceptibility gene variant (OR=1.29, 95% CI 1.03-1.63, P = 0.03). There were no significant associations between the GRS for puberty timing and osteosarcoma. CONCLUSION: A genetic propensity to higher birthweight was associated with increased osteosarcoma risk, suggesting that shared genetic factors or biological pathways that affect birthweight may contribute to osteosarcoma pathogenesis