A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer

Estrogen receptor (ER)-negative breast cancer shows a higher incidence in women of African ancestry compared to women of European ancestry. In search of common risk alleles for ER-negative breast cancer, we combined genome-wide association study (GWAS) data from women of African ancestry (1,004 ER-negative cases and 2,745 controls) and European ancestry (1,718 ER-negative cases and 3,670 controls), with replication testing conducted in an additional 2,292 ER-negative cases and 16,901 controls of European ancestry. We identified a common risk variant for ER-negative breast cancer at the TERT-CLPTM1L locus on chromosome 5p15 (rs10069690: per-allele odds ratio (OR) = 1.18 per allele, P = 1.0 × 10(-10)). The variant was also significantly associated with triple-negative (ER-negative, progesterone receptor (PR)-negative and human epidermal growth factor-2 (HER2)-negative) breast cancer (OR = 1.25, P = 1.1 × 10(-9)), particularly in younger women (<50 years of age) (OR = 1.48, P = 1.9 × 10(-9)). Our results identify a genetic locus associated with estrogen receptor negative breast cancer subtypes in multiple populations.     

Cosmological Black Holes and the Direction of Time

Macroscopic irreversible processes emerge from fundamental physical laws of reversible character. The source of the local irreversibility seems to be not in the laws themselves but in the initial and boundary conditions of the equations that represent the laws. In this work we propose that the screening of currents by black hole event horizons determines, locally, a preferred direction for the flux of electromagnetic energy. We study the growth of black hole event horizons due to the cosmological expansion and accretion of cosmic microwave background radiation, for different cosmological models. We propose generalized McVittie co-moving metrics and integrate the rate of accretion of cosmic microwave background radiation onto a supermassive black hole over cosmic time. We find that for flat, open, and closed Friedmann cosmological models, the ratio of the total area of the black hole event horizons with respect to the area of a radial co-moving space-like hypersurface always increases. Since accretion of cosmic radiation sets an absolute lower limit to the total matter accreted by black holes, this implies that the causal past and future are not mirror symmetric for any spacetime event. The asymmetry causes a net Poynting flux in the global future direction; the latter is in turn related to the ever increasing thermodynamic entropy. Thus, we expose a connection between four different “time arrows”: cosmological, electromagnetic, gravitational, and thermodynamic.     

Human gut microbiome viewed across age and geography

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.     

The human footprint in the carbon cycle of temperate and boreal forests

Temperate and boreal forests in the Northern Hemisphere cover an area of about 2 x 10(7) square kilometres and act as a substantial carbon sink (0.6-0.7 petagrams of carbon per year). Although forest expansion following agricultural abandonment is certainly responsible for an important fraction of this carbon sink activity, the additional effects on the carbon balance of established forests of increased atmospheric carbon dioxide, increasing temperatures, changes in management practices and nitrogen deposition are difficult to disentangle, despite an extensive network of measurement stations. The relevance of this measurement effort has also been questioned, because spot measurements fail to take into account the role of disturbances, either natural (fire, pests, windstorms) or anthropogenic (forest harvesting). Here we show that the temporal dynamics following stand-replacing disturbances do indeed account for a very large fraction of the overall variability in forest carbon sequestration. After the confounding effects of disturbance have been factored out, however, forest net carbon sequestration is found to be overwhelmingly driven by nitrogen deposition, largely the result of anthropogenic activities. The effect is always positive over the range of nitrogen deposition covered by currently available data sets, casting doubts on the risk of widespread ecosystem nitrogen saturation under natural conditions. The results demonstrate that mankind is ultimately controlling the carbon balance of temperate and boreal forests, either directly (through forest management) or indirectly (through nitrogen deposition).     

Identifying composite crosscutting concerns with scatter-based graph clustering

Identifying composite crosscutting concerns(CCs) is a research task and challenge of aspect mining.In this paper,we propose a scatter-based graph clustering approach to identify composite CCs.Inspired by the state-of-the-art link analysis tech-niques,we propose a two-state model to approximate how CCs tangle with core modules.According to this model,we obtain scatter and centralization scores for each program element.Espe-cially,the scatter scores are adopted to select CC seeds.Further-more,to identify composite CCs,we adopt a novel similarity measurement and develop an undirected graph clustering to group these seeds.Finally,we compare it with the previous work and illustrate its effectiveness in identifying composite CCs.     

Deficiency of hyccin, a newly identified membrane protein, causes hypomyelination and congenital cataract

We describe a new autosomal recessive white matter disorder ('hypomyelination and congenital cataract') characterized by hypomyelination of the central and peripheral nervous system, progressive neurological impairment and congenital cataract. We identified mutations in five affected families, resulting in a deficiency of hyccin, a newly identified 521-amino acid membrane protein. Our study highlights the essential role of hyccin in central and peripheral myelination.     

Ultra-broadband semiconductor laser

The fundamental mechanism behind laser action leads in general only to narrowband, single-wavelength emission. Several approaches for achieving spectrally broadband laser action have been put forward, such as enhancing the optical feedback in the wings of the gain spectrum, multi-peaked gain spectra, and the most favoured technique at present, ultrashort pulse excitation. Each of these approaches has drawbacks, such as a complex external laser cavity configuration, a non-flat optical gain envelope function, or an inability to operate in continuous mode, respectively. Here we present a monolithic, mid-infrared 'supercontinuum' semiconductor laser that has none of these drawbacks. We adopt a quantum cascade configuration, where a number of dissimilar intersubband optical transitions are made to cooperate in order to provide broadband optical gain from 5 to 8 microm wavelength. Laser action with a Fabry-Pérot spectrum covering all wavelengths from 6 to 8 microm simultaneously is demonstrated with this approach. Lasers that emit light over such an extremely wide wavelength range are of interest for applications as varied as terabit optical data communications or ultra-precision metrology and spectroscopy.     

Separable processing of consonants and vowels

There are two views about the nature of consonants and vowels. One view holds that they are categorically distinct objects that play a fundamental role in the construction of syllables in speech production. The other view is that they are convenient labels for distinguishing between peak (vowel) and non-peak (consonant) parts of a continuous stream of sound that varies in sonority (roughly the degree of openness of the vocal apparatus during speech), or that they are summary labels for bundles of feature segments. Taking the latter view, consonants and vowels do not have an independent status in language processing. Here we provide evidence for the possible categorical distinction between consonants and vowels in the brain. We report the performance of two Italian-speaking aphasics who show contrasting, selective difficulties in producing vowels and consonants. Their performance in producing individual consonants is independent of the sonority value and feature properties of the consonants. This pattern of results suggests that consonants and vowels are processed by distinct neural mechanisms, thereby providing evidence for their independent status in language production.     

New gene functions in megakaryopoiesis and platelet formation

Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function.