Measuring our universe from galaxy redshift surveys

Galaxy redshift surveys have achieved significant progress over the last couple of decades. Those surveys tell us in the most straightforward way what our local universe looks like. While the galaxy distribution traces the bright side of the universe, detailed quantitative analyses of the data have even revealed the dark side of the universe dominated by non-baryonic dark matter as well as more mysterious dark energy (or Einstein's cosmological constant). We describe several methodologies of using galaxy redshift surveys as cosmological probes, and then summarize the recent results from the existing surveys. Finally we present our views on the future of redshift surveys in the era of Precision Cosmology.Comment: 82 pages, 31 figures, invited review article published in Living Reviews in Relativity, http://www.livingreviews.org/lrr-2004-

Assays to Detect β-Tubulin Codon 200 Polymorphism in Trichuris trichiura and Ascaris lumbricoides

The soil-transmitted helminths Ascaris lumbricoides and Trichuris trichiura are gastrointestinal nematodes causing many disabilities in tropical parts of the developing world. Control programs, such as “The Focussing Resources on Effective School Health” (FRESH) Partnership, have been implemented to remove human soil-transmitted nematodes through large-scale use of benzimidazole anthelmintic drugs for school-aged children in developing countries. The benzimidazole drugs albendazole and mebendazole are commonly used as a single annual treatment in areas where the burden is high. In veterinary nematodes, repeated use of these anthelmintics has selected for resistant populations. Resistance to benzimidazoles is commonly associated with a single amino acid substitution from phenylalanine to tyrosine in the β-tubulin gene at position 200. In this study, we have developed pyrosequencing assays for codon 200 in A. lumbricoides and T. trichiura to screen for this single nucleotide polymorphism (SNP) in β-tubulin. The 200Tyr SNP was detected at low frequency in T. trichiura from non-treated people from Kenya and at high frequency in T. trichiura from treated people from Panama. The presence of the resistance-associated SNP may play a role in the sometimes low and variable efficacy of benzimidazole anthelmintics against T. trichiura

Stabilization of dense Antarctic water supply to the Atlantic Ocean overturning circulation

The lower limb of the Atlantic overturning circulation is resupplied by the sinking of dense Antarctic Bottom Water (AABW) that forms via intense air–sea–ice interactions next to Antarctica, especially in the Weddell Sea. In the last three decades, AABW has warmed, freshened and declined in volume across the Atlantic Ocean and elsewhere, suggesting an ongoing major reorganization of oceanic overturning. However, the future contributions of AABW to the Atlantic overturning circulation are unclear. Here, using observations of AABW in the Scotia Sea, the most direct pathway from the Weddell Sea to the Atlantic Ocean, we show a recent cessation in the decline of the AABW supply to the Atlantic overturning circulation. The strongest decline was observed in the volume of the densest layers in the AABW throughflow from the early 1990s to 2014; since then, it has stabilized and partially recovered. We link these changes to variability in the densest classes of abyssal waters upstream. Our findings indicate that the previously observed decline in the supply of dense water to the Atlantic Ocean abyss may be stabilizing or reversing and thus call for a reassessment of Antarctic influences on overturning circulation, sea level, planetary-scale heat distribution and global climate

Location-Specific Responses to Thermal Stress in Larvae of the Reef-Building Coral Montastraea faveolata

The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations.To test the hypothesis that larval transcription profiles reflect location-specific responses to thermal stress, symbiont-free gametes from three to four colonies of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico, fertilized, and raised under mean and elevated (up 1 to 2 degrees C above summer mean) temperatures. These locations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among 1,310 unigenes were simultaneously characterized using custom cDNA microarrays, allowing investigation of gene expression patterns among larvae generated from wild populations under stress. Results show both conserved and location-specific variation in key processes including apoptosis, cell structuring, adhesion and development, energy and protein metabolism, and response to stress, in embryos of a reef-building coral.These results provide first insights into location-specific variation in gene expression in the face of gene flow, and support the hypothesis that coral host genomes may house adaptive potential needed to deal with changing environmental conditions

Long-term outcomes for neoadjuvant versus adjuvant chemotherapy in early breast cancer: meta-analysis of individual patient data from ten randomised trials

Background Neoadjuvant chemotherapy (NACT) for early breast cancer can make breast-conserving surgery more feasible and might be more likely to eradicate micrometastatic disease than might the same chemotherapy given after surgery. We investigated the long-term benefits and risks of NACT and the influence of tumour characteristics on outcome with a collaborative meta-analysis of individual patient data from relevant randomised trials. Methods We obtained information about prerandomisation tumour characteristics, clinical tumour response, surgery, recurrence, and mortality for 4756 women in ten randomised trials in early breast cancer that began before 2005 and compared NACT with the same chemotherapy given postoperatively. Primary outcomes were tumour response, extent of local therapy, local and distant recurrence, breast cancer death, and overall mortality. Analyses by intention-to-treat used standard regression (for response and frequency of breast-conserving therapy) and log-rank methods (for recurrence and mortality). Findings Patients entered the trials from 1983 to 2002 and median follow-up was 9 years (IQR 5–14), with the last follow-up in 2013. Most chemotherapy was anthracycline based (3838 [81%] of 4756 women). More than two thirds (1349 [69%] of 1947) of women allocated NACT had a complete or partial clinical response. Patients allocated NACT had an increased frequency of breast-conserving therapy (1504 [65%] of 2320 treated with NACT vs 1135 [49%] of 2318 treated with adjuvant chemotherapy). NACT was associated with more frequent local recurrence than was adjuvant chemotherapy: the 15 year local recurrence was 21·4% for NACT versus 15·9% for adjuvant chemotherapy (5·5% increase [95% CI 2·4–8·6]; rate ratio 1·37 [95% CI 1·17–1·61]; p=0·0001). No significant difference between NACT and adjuvant chemotherapy was noted for distant recurrence (15 year risk 38·2% for NACT vs 38·0% for adjuvant chemotherapy; rate ratio 1·02 [95% CI 0·92–1·14]; p=0·66), breast cancer mortality (34·4% vs 33·7%; 1·06 [0·95–1·18]; p=0·31), or death from any cause (40·9% vs 41·2%; 1·04 [0·94–1·15]; p=0·45). Interpretation Tumours downsized by NACT might have higher local recurrence after breast-conserving therapy than might tumours of the same dimensions in women who have not received NACT. Strategies to mitigate the increased local recurrence after breast-conserving therapy in tumours downsized by NACT should be considered—eg, careful tumour localisation, detailed pathological assessment, and appropriate radiotherapy

Peak nasal inspiratory flow; normal range in adult population

AIMS: Measurement of Peak Nasal Inspiratory Flow (PNIF) seems to be a cheap, simple, easily performed method to assess nasal patency. The purpose of this study is to establish normative PNIF data for a healthy adult population and provide charts relating PNIF normal values with age, height and sex in adults. METHODS AND RESULTS: Repeated measurements of PNIF were performed in 170 volunteers. In total, 137 of these fulfilled the study criteria (66 females and 50 males) and all of them were non-smokers, non-asthmatic, without nose and paranasal sinuses problems, with ages ranging from 16 to 84 years. Data were statistically analysed and tables were produced relating PNIF to age, sex and height. There was no interaction of sex with age or height. There was considerable residual variability of PNIF between individuals not explained by any of the variables studied. CONCLUSIONS: We conclude that PNIF could be a useful method to study nasal patency in both primary and secondary care to aid diagnosis of nasal disease. The study provides normative data for a Caucasian population. Further variables need to be explored to predict expected PNIF values more accurately

Does peak nasal inspiratory flow relate to peak expiratory flow?

AIMS: Measurement of Peak Nasal Inspiratory Flow (PNIF) seems to be a cheap and easily performed method to assess nasal patency. As demonstrated in a previous work, PNIF is influenced by SEX, AGE and HEIGHT. However there is a large degree of between-patient variability in PNIF levels. The purpose of this analysis is to determine whether the measurement of the pulmonary ventilatory capacity, by mean of Peak Expiratory Flow (PEF), enables more precise determination of PNIF. METHODS AND RESULTS: Repeated measurements of PNIF and PEF were performed in 112 volunteers. 100 of these fulfilled the study criteria (55 females and 45 males) and all of them were non-smokers, non-asthmatic, without nose and paranasal sinuses problems, with ages ranging from 15 to 71 years. Statistical analysis was undertaken to determine whether a relationship existed between PNIF and age, sex and height, but which also considered PEF. The data from both experiments were analysed together. In both groups there is a clear tendency for PNIF to increase with PEF. As clearly demonstrated in this work the value of PEF is informative in predicting PNIF and that the larger the value of PEF, the larger the value of PNIF. CONCLUSIONS: PNIF is a useful method to study nasal patency in both primary and secondary care to aid diagnosis of nasal disease, but low values of PNIF have to be confirmed by a study of the PEF as PNIF low values may be an expression of low ventilatory activity rather than an expression of nasal obstruction