Encyclopedia of software components

Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component

Virtual reality flight control display with six-degree-of-freedom controller and spherical orientation overlay

A virtual reality flight control system displays to the pilot the image of a scene surrounding a vehicle or pod having six degrees of freedom of acceleration or velocity control by the pilot and traveling through inertial space, the image itself including a superimposed figure providing the pilot an instant reference of orientation consisting of superimposed sets of geometric figures whose relative orientations provide the pilot an instantaneous feel or sense of orientation changes with respect to some fixed coordinate system. They include a first set of geometric figures whose orientations are fixed to the pilot's vehicle and a second set of geometric figures whose orientations are fixed with respect to a fixed or interstellar coordinate system. The first set of figures is a first set of orthogonal great circles about the three orthogonal axes of the flight vehicle or pod and centered at and surrounding the pilot's head, while the second set of figures is a second set of orthogonal great circles about the three orthogonal axes of a fixed or interstellar coordinate system, also centered at and surrounding the pilot's head

Encyclopedia of Software Components

Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component

A State of Mind: Determining Bad Faith in Trespasses to Oil and Gas: A Call to Courts to Apply a True Subjective Analysis to Determine Whether a Trespasser to an Oil and Gas Estate Trespasses in Good or Bad Faith

It has always been the law of trespass mesne profits to an oil and gas estate that a trespasser is liable for the value of the oil and gas that it has produced from the estate to which it trespasses. That value is determined after ascertaining whether the trespasser held an honest belief that he or she had the right to produce oil or gas from the estate upon which it trespassed. In those cases, the trespasser is said to have trespassed in good faith. Conversely, the trespasser acts in bad faith when it knowingly produces oil and gas without the right to do so. The rule is couched subjectively from the perspective of the trespasser and not from the view of a reasonable person in the same position as the trespasser

A State of Mind: Determining Bad Faith in Trespasses to Oil and Gas: A Call to Courts to Apply a True Subjective Analysis to Determine Whether a Trespasser to an Oil and Gas Estate Trespasses in Good or Bad Faith

It has always been the law of trespass mesne profits to an oil and gas estate that a trespasser is liable for the value of the oil and gas that it has produced from the estate to which it trespasses. That value is determined after ascertaining whether the trespasser held an honest belief that he or she had the right to produce oil or gas from the estate upon which it trespassed. In those cases, the trespasser is said to have trespassed in good faith. Conversely, the trespasser acts in bad faith when it knowingly produces oil and gas without the right to do so. The rule is couched subjectively from the perspective of the trespasser and not from the view of a reasonable person in the same position as the trespasser

Assessing regional patterns of juvenile salmon growth in the Salish Sea

Early marine juvenile growth in Pacific salmon is generally positively correlated with overall survival to reproductive age. In this study, regional patterns of juvenile salmon growth are being analyzed over a two-year period (2012-2013) in the Salish Sea and surrounding waters to better assess juvenile productivity, via growth, in the Salish Sea and surrounding waters to provide us insight into possible mechanisms regulating survival. Insulin-like growth factor-1 (IGF-1), a hormone used to assess instantaneous growth in fishes, including juvenile salmon, was measured in late June and early July of 2012 and 2013 in the Strait of Georgia, Johnstone Strait, Queen Charlotte Strait, and Puget Sound. Juvenile sockeye (Oncorhynchus nerka) and pink salmon (O. gorbuscha) were collected in 2012, whereas juvenile coho (O. kisutch), Chinook (O. tshawytscha), and chum salmon (O. keta) where obtained in both years. In 2012 IGF-1 levels were highest in pink salmon from the Gulf Islands and Puget Sound; this was a unique pattern among the 5 species of juvenile salmon sampled. Coho salmon IGF-1 levels were highest in samples from the Northern Strait of Georgia. Chinook salmon IGF-1 levels were significantly higher in the Strait of Georgia than Puget Sound. The only regions where IGF-1 values were consistently low for three of the four species were Queen Charlotte Strait and Johnstone Strait. Analyses of 2013 IGF-1 levels (juvenile coho, Chinook, chum and a low number of sockeye) are underway and scheduled plans to obtain samples in late June to early July of 2014 are in place

Acute physiological stress down-regulates mRNA expressions of growth-related genes in coho salmon

Growth and development in fish are regulated to a major extent by growth-related factors, such as liver-derived insulin-like growth factor (IGF) -1 in response to pituitary-secreted growth hormone (GH) binding to the GH receptor (GHR). Here, we report on the changes in the expressions of gh, ghr, and igf1 genes and the circulating levels of GH and IGF-1 proteins in juvenile coho salmon (Oncorhynchus kisutch) in response to handling as an acute physiological stressor. Plasma GH levels were not significantly different between stressed fish and prestressed control. Plasma IGF-1 concentrations in stressed fish 1.5 h post-stress were the same as in control fish, but levels in stressed fish decreased significantly 16 h post-stress. Real-time quantitative PCR (qPCR) analysis showed that ghr mRNA levels in pituitary, liver, and muscle decreased gradually in response to the stressor. After exposure to stress, hepatic igf1 expression transiently increased, whereas levels decreased 16 h post-stress. On the other hand, the pituitary gh mRNA level did not change in response to the stressor. These observations indicate that expression of gh, ghr, and igf1 responded differently to stress. Our results show that acute physiological stress can mainly down-regulate the expressions of growth-related genes in coho salmon in vivo. This study also suggests that a relationship between the neuroendocrine stress response and growth-related factors exists in fish.Peer reviewed: YesNRC publication: Ye

Global Conformational Dynamics of a Y-Family DNA Polymerase during Catalysis

High-resolution analysis of protein, and DNA conformational changes during DNA polymerization, established relationships between the enzymatic function and conformational dynamics of individual domains for a DNA polymerase

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A>T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data to identify 10 risk loci for fIIP. Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequencing studies of lung tissue to identify and characterize new fIIP risk loci.We performed genome-wide genotype imputation association analyses in 1616 non-Hispanic white (NHW) cases and 4683 NHW controls followed by validation and replication (878 cases, 2017 controls) genotyping and targeted gene expression in lung tissue. Following meta-analysis of the discovery and replication populations, we identified a novel fIIP locus in the HLA region of chromosome 6 (rs7887 P meta  = 3.7 × 10(-09)). Imputation of classic HLA alleles identified two in high linkage disequilibrium that are associated with fIIP (DRB1*15:01 P = 1.3 × 10(-7) and DQB1*06:02 P = 6.1 × 10(-8)). Targeted RNA-sequencing of the HLA locus identified 21 genes differentially expressed between fibrotic and control lung tissue (Q < 0.001), many of which are involved in immune and inflammatory response regulation. In addition, the putative risk alleles, DRB1*15:01 and DQB1*06:02, are associated with expression of the DQB1 gene among fIIP cases (Q < 1 × 10(-16)).We have identified a genome-wide significant association between the HLA region and fIIP. Two HLA alleles are associated with fIIP and affect expression of HLA genes in lung tissue, indicating that the potential genetic risk due to HLA alleles may involve gene regulation in addition to altered protein structure. These studies reveal the importance of the HLA region for risk of fIIP and a basis for the potential etiologic role of auto-immunity in fIIP.National Heart, Lung and Blood Institute R01-HL095393 R01-HL097163 P01-HL092870 RC2-HL101715 U01-HL089897 U01-HL089856 U01-HL108642 P50-HL089493