The case for open computer programs

Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail.     

Into the mind of a fly

Where do animal behaviours come from and are they controlled by genes? This is the fundamental question posed by the field of neurogenetics. Pioneering work from the 1960s in Seymour Benzer's laboratory demonstrated for the first time that Drosophila melanogaster fruitflies could be mutated to obtain animals with insomnia, learning disabilities and homosexual courtship behaviours.     

Influence of soil water availability on competition among leafy spurge ( Euphorbia Esula ) and grasses

Some perturbations differentially influence invasive plant and grass production. For example, growth regulator herbicides and biological control agents can dramatically reduce leafy spurge production while having little or no influence on grass production, and overgrazing can reduce grass production while not substantially influencing leafy spurge production because cattle typically ingest little or no leafy spurge. To predict how grass production will respond to a perturbation that influences only leafy spurge and to predict how leafy spurge production will respond to a perturbation that affects only grasses, competitive relationships must be understood. Seeding mixtures of leafy spurge and 2 grasses were planted in experiments and grown for 127 days to determine whether different water application regimes influenced competition among these 3 species. Competition became less intense as the number of water applications increased. If this finding holds true under field conditions, then it indicates that competition is less intense in years and locations with numerous precipitation events. Competitive interactions (i.e., competition coefficients) were less variable when water was applied more frequently, but the ability of models to account for variation in plant weight (i.e., r 2 ) was not influenced by the frequency of water application. This suggests that models will predict invasive plant and grass biomass with equal accuracy in years with few or many precipitation events. Competitive effects were similar regardless of grass species, which suggests that grasses might be considered collectively in predicting response to perturbations in the field.     

Geographic variation in pelage color of pi?on mice ( Peromyscus truei ) in the northern Great Basin and environs

Cluster analyses of values for hue, value, and chroma (based on Munsell soil-color charts) obtained at 6 points on pelages of 202 adult pion mice ( Peromyscus truei ) from the northern Great Basin and environs produced dendrograms with specimens grouped into 5 clusters. In most instances distribution of specimens forming clusters reflected those published for nominal races. In instances in which previous distributions of nominal races were not supported and for specimens previously unclassified, geographic distribution of groups of color morphs was logical and suggested avenues for additional research on geographic variation in the species.     

A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL)

The importance of individual microRNAs (miRNAs) has been established in specific cancers. However, a comprehensive analysis of the contribution of miRNAs to the pathogenesis of any specific cancer is lacking. Here we show that in T-cell acute lymphoblastic leukemia (T-ALL), a small set of miRNAs is responsible for the cooperative suppression of several tumor suppressor genes. Cross-comparison of miRNA expression profiles in human T-ALL with the results of an unbiased miRNA library screen allowed us to identify five miRNAs (miR-19b, miR-20a, miR-26a, miR-92 and miR-223) that are capable of promoting T-ALL development in a mouse model and which account for the majority of miRNA expression in human T-ALL. Moreover, these miRNAs produce overlapping and cooperative effects on tumor suppressor genes implicated in the pathogenesis of T-ALL, including IKAROS (also known as IKZF1), PTEN, BIM, PHF6, NF1 and FBXW7. Thus, a comprehensive and unbiased analysis of miRNA action in T-ALL reveals a striking pattern of miRNA-tumor suppressor gene interactions in this cancer.     

Melanin-concentrating hormone is the cognate ligand for the orphan G-protein-coupled receptor SLC-1.

The underlying causes of obesity are poorly understood but probably involve complex interactions between many neurotransmitter and neuropeptide systems involved in the regulation of food intake and energy balance. Three pieces of evidence indicate that the neuropeptide melanin-concentrating hormone (MCH) is an important component of this system. First, MCH stimulates feeding when injected directly into rat brains; second, the messenger RNA for the MCH precursor is upregulated in the hypothalamus of genetically obese mice and in fasted animals; and third, mice lacking MCH eat less and are lean. MCH antagonists might, therefore, provide a treatment for obesity. However, the development of such molecules has been hampered because the identity of the MCH receptor has been unknown until now. Here we show that the 353-amino-acid human orphan G-protein-coupled receptor SLC-1 expressed in HEK293 cells binds MCH with sub-nanomolar affinity, and is stimulated by MCH to mobilize intracellular Ca2+ and reduce forskolin-elevated cyclic AMP levels. We also show that SLC-1 messenger RNA and protein is expressed in the ventromedial and dorsomedial nuclei of the hypothalamus, consistent with a role for SLC-1 in mediating the effects of MCH on feeding.     

论专家证人渎职责任

在传统的做法中，基于证人豁免原则的保护，作为专家证人出庭作证的专业人士在审判中所提供的证言不受追究。而专家证人玩忽职守责任的理论又非常具有说服力，因此在实际中，出现了对传统的背离。一种关于专家证人渎职责任的理论可能正在形成。     

A sensory source for motor variation

Suppose that the variability in our movements is caused not by noise in the motor system itself, nor by fluctuations in our intentions or plans, but rather by errors in our sensory estimates of the external parameters that define the appropriate action. For tasks in which precision is at a premium, performance would be optimal if no noise were added in movement planning and execution: motor output would be as accurate as possible given the quality of sensory inputs. Here we use visually guided smooth-pursuit eye movements in primates as a testing ground for this notion of optimality. In response to repeated presentations of identical target motions, nearly 92% of the variance in eye trajectory can be accounted for as a consequence of errors in sensory estimates of the speed, direction and timing of target motion, plus a small background noise that is observed both during eye movements and during fixations. The magnitudes of the inferred sensory errors agree with the observed thresholds for sensory discrimination by perceptual systems, suggesting that the very different neural processes of perception and action are limited by the same sources of noise.