Higher-Order Angular Galaxy Correlations in the SDSS: Redshift and Color Dependence of non-Linear Bias

We present estimates of the N-point galaxy, area-averaged, angular correlation functions $\bar{\omega}_{N}$($\theta$) for $N$ = 2,...,7 for galaxies from the fifth data release of the Sloan Digital Sky Survey. Our parent sample is selected from galaxies with $18 \leq r < 21$, and is the largest ever used to study higher-order correlations. We subdivide this parent sample into two volume limited samples using photometric redshifts, and these two samples are further subdivided by magnitude, redshift, and color (producing early- and late-type galaxy samples) to determine the dependence of $\bar{\omega}_{N}$($\theta$) on luminosity, redshift, and galaxy-type. We measure $\bar{\omega}_{N}$($\theta$) using oversampling techniques and use them to calculate the projected, $s_{N}$. Using models derived from theoretical power-spectra and perturbation theory, we measure the bias parameters $b_1$ and $c_2$, finding that the large differences in both bias parameters ($b_1$ and $c_2$) between early- and late-type galaxies are robust against changes in redshift, luminosity, and $\sigma_8$, and that both terms are consistently smaller for late-type galaxies. By directly comparing their higher-order correlation measurements, we find large differences in the clustering of late-type galaxies at redshifts lower than 0.3 and those at redshifts higher than 0.3, both at large scales ($c_2$ is larger by $\sim0.5$ at $z > 0.3$) and small scales (large amplitudes are measured at small scales only for $z > 0.3$, suggesting much more merger driven star formation at $z > 0.3$). Finally, our measurements of $c_2$ suggest both that $\sigma_8 < 0.8$ and $c_2$ is negative.Comment: 46 pages, 19 figures, Accepted to Ap

Invest to Save: Report and Recommendations of the NSF-DELOS Working Group on Digital Archiving and Preservation

Digital archiving and preservation are important areas for research and development, but there is no agreed upon set of priorities or coherent plan for research in this area. Research projects in this area tend to be small and driven by particular institutional problems or concerns. As a consequence, proposed solutions from experimental projects and prototypes tend not to scale to millions of digital objects, nor do the results from disparate projects readily build on each other. It is also unclear whether it is worthwhile to seek general solutions or whether different strategies are needed for different types of digital objects and collections. The lack of coordination in both research and development means that there are some areas where researchers are reinventing the wheel while other areas are neglected. Digital archiving and preservation is an area that will benefit from an exercise in analysis, priority setting, and planning for future research. The WG aims to survey current research activities, identify gaps, and develop a white paper proposing future research directions in the area of digital preservation. Some of the potential areas for research include repository architectures and inter-operability among digital archives; automated tools for capture, ingest, and normalization of digital objects; and harmonization of preservation formats and metadata. There can also be opportunities for development of commercial products in the areas of mass storage systems, repositories and repository management systems, and data management software and tools.

Mimicry of Pre–B Cell Receptor Signaling by Activation of the Tyrosine Kinase Blk

During B lymphoid ontogeny, assembly of the pre–B cell receptor (BCR) is a principal developmental checkpoint at which several Src-related kinases may play redundant roles. Here the Src-related kinase Blk is shown to effect functions associated with the pre-BCR. B lymphoid expression of an active Blk mutant caused proliferation of B progenitor cells and enhanced responsiveness of these cells to interleukin 7. In mice lacking a functional pre-BCR, active Blk supported maturation beyond the pro–B cell stage, suppressed VH to DJH rearrangement, relieved selection for productive heavy chain rearrangement, and stimulated κ rearrangement. These alterations were accompanied by tyrosine phosphorylation of immunoglobulin β and Syk, as well as changes in gene expression consistent with developmental maturation. Thus, sustained activation of Blk induces responses normally associated with the pre-BCR

Genomic Classifier Augments the Role of Pathological Features in Identifying Optimal Candidates for Adjuvant Radiation Therapy in Patients With Prostate Cancer: Development and Internal Validation of a Multivariable Prognostic Model.

Purpose Despite documented oncologic benefit, use of postoperative adjuvant radiotherapy (aRT) in patients with prostate cancer is still limited in the United States. We aimed to develop and internally validate a risk-stratification tool incorporating the Decipher score, along with routinely available clinicopathologic features, to identify patients who would benefit the most from aRT. Patient and Methods Our cohort included 512 patients with prostate cancer treated with radical prostatectomy at one of four US academic centers between 1990 and 2010. All patients had ≥ pT3a disease, positive surgical margins, and/or pathologic lymph node invasion. Multivariable Cox regression analysis tested the relationship between available predictors (including Decipher score) and clinical recurrence (CR), which were then used to develop a novel risk-stratification tool. Our study adhered to the Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis guidelines for development of prognostic models. Results Overall, 21.9% of patients received aRT. Median follow-up in censored patients was 8.3 years. The 10-year CR rate was 4.9% vs. 17.4% in patients treated with aRT versus initial observation ( P \u3c .001). Pathologic T3b/T4 stage, Gleason score 8-10, lymph node invasion, and Decipher score \u3e 0.6 were independent predictors of CR (all P \u3c .01). The cumulative number of risk factors was 0, 1, 2, and 3 to 4 in 46.5%, 28.9%, 17.2%, and 7.4% of patients, respectively. aRT was associated with decreased CR rate in patients with two or more risk factors (10-year CR rate 10.1% in aRT v 42.1% in initial observation; P = .012), but not in those with fewer than two risk factors ( P = .18). Conclusion Using the new model to indicate aRT might reduce overtreatment, decrease unnecessary adverse effects, and reduce risk of CR in the subset of patients (approximately 25% of all patients with aggressive pathologic disease in our cohort) who benefit from this therapy

Impact of the SPOP Mutant Subtype on the Interpretation of Clinical Parameters in Prostate Cancer.

Purpose: Molecular characterization of prostate cancer, including The Cancer Genome Atlas, has revealed distinct subtypes with underlying genomic alterations. One of these core subtypes, SPOP (speckle-type POZ protein) mutant prostate cancer, has previously only been identifiable via DNA sequencing, which has made the impact on prognosis and routinely used risk stratification parameters unclear. Methods: We have developed a novel gene expression signature, classifier (Subclass Predictor Based on Transcriptional Data), and decision tree to predict the SPOP mutant subclass from RNA gene expression data and classify common prostate cancer molecular subtypes. We then validated and further interrogated the association of prostate cancer molecular subtypes with pathologic and clinical outcomes in retrospective and prospective cohorts of 8,158 patients. Results: The subclass predictor based on transcriptional data model showed high sensitivity and specificity in multiple cohorts across both RNA sequencing and microarray gene expression platforms. We predicted approximately 8% to 9% of cases to be SPOP mutant from both retrospective and prospective cohorts. We found that the SPOP mutant subclass was associated with lower frequency of positive margins, extraprostatic extension, and seminal vesicle invasion at prostatectomy; however, SPOP mutant cancers were associated with higher pretreatment serum prostate-specific antigen (PSA). The association between SPOP mutant status and higher PSA level was validated in three independent cohorts. Despite high pretreatment PSA, the SPOP mutant subtype was associated with a favorable prognosis with improved metastasis-free survival, particularly in patients with high-risk preoperative PSA levels. Conclusion: Using a novel gene expression model and a decision tree algorithm to define prostate cancer molecular subclasses, we found that the SPOP mutant subclass is associated with higher preoperative PSA, less adverse pathologic features, and favorable prognosis. These findings suggest a paradigm in which the interpretation of common risk stratification parameters, particularly PSA, may be influenced by the underlying molecular subtype of prostate cancer

Environment Constrains Fitness Advantages of Division of Labor in Microbial Consortia Engineered for Metabolite Push or Pull Interactions

Fitness benefits from division of labor are well documented in microbial consortia, but the dependency of the benefits on environmental context is poorly understood. Two synthetic Escherichia coli consortia were built to test the relationships between exchanged organic acid, local environment, and opportunity costs of different metabolic strategies. Opportunity costs quantify benefits not realized due to selecting one phenotype over another. The consortia catabolized glucose and exchanged either acetic or lactic acid to create producer-consumer food webs. The organic acids had different inhibitory properties and different opportunity costs associated with their positions in central metabolism. The exchanged metabolites modulated different consortial dynamics. The acetic acid-exchanging (AAE) consortium had a “push” interaction motif where acetic acid was secreted faster by the producer than the consumer imported it, while the lactic acid-exchanging (LAE) consortium had a “pull” interaction motif where the consumer imported lactic acid at a comparable rate to its production. The LAE consortium outperformed wild-type (WT) batch cultures under the environmental context of weakly buffered conditions, achieving a 55% increase in biomass titer, a 51% increase in biomass per proton yield, an 86% increase in substrate conversion, and the complete elimination of by-product accumulation all relative to the WT. However, the LAE consortium had the trade-off of a 42% lower specific growth rate. The AAE consortium did not outperform the WT in any considered performance metric. Performance advantages of the LAE consortium were sensitive to environment; increasing the medium buffering capacity negated the performance advantages compared to WT

In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different

RATIONALE: Sputum and bronchoalveolar lavage fluid (BALF) are often obtained to elucidate the lower airway microbiota in adults. Acquiring sputum samples from children is difficult and obtaining samples via bronchoscopy in children proves challenging due to the need for anesthesia and specialized procedural expertise; therefore nasopharyngeal (NP) swabs are often used as surrogates when investigating the pediatric airway microbiota. In adults, the airway microbiota differs significantly between NP and BALF samples however, minimal data exist in children. OBJECTIVES: To compare NP and BALF samples in children undergoing clinically indicated bronchoscopy. METHODS: NP and BALF samples were collected during clinically indicated bronchoscopy. Bacterial DNA was extracted from 72 samples (36 NP/BALF pairs); the bacterial V1-V3 region of the 16S rRNA gene was amplified and sequenced on the Illumina Miseq platform. Analysis was performed using mothur software. RESULTS: Compared to NP samples, BALF had increased richness and diversity. Similarity between paired NP and BALF (intra-subject) samples was greater than inter-subject samples (P = 0.0006). NP samples contained more Actinobacteria (2.2% vs 21%; adjusted P = 1.4 × 10-6 ), while BALF contained more Bacteroidetes (29.5% vs 3.2%; adjusted P = 1.2 × 10-9 ). At the genus level several differences existed, however Streptococcus abundance was similar in both sample types (NP 37.3% vs BAL 36.1%; adjusted P = 0.8). CONCLUSION: Our results provide evidence that NP samples can be used to distinguish differences between children, but the relative abundance of organisms may differ between the nasopharynx and lower airway in pediatric patients. Studies utilizing NP samples as surrogates for the lower airway should be interpreted with caution

Unbiased clustering estimates with the DESI fibre assignment

The Emission Line Galaxy survey made by the Dark Energy Spectroscopic Instrument (DESI) survey will be created from five passes of the instrument on the sky. On each pass, the constrained mobility of the ends of the fibres in the DESI focal plane means that the angular-distribution of targets that can be observed is limited. Thus, the clustering of samples constructed using a limited number of passes will be strongly affected by missing targets. In two recent papers, we showed how the effect of missing galaxies can be corrected when calculating the correlation function using a weighting scheme for pairs. Using mock galaxy catalogues we now show that this method provides an unbiased estimator of the true correlation function for the DESI survey after any number of passes. We use multiple mocks to determine the expected errors given one to four passes, compared to an idealised survey observing an equivalent number of randomly selected targets. On BAO scales, we find that the error is a factor 2 worse after one pass, but that after three or more passes, the errors are very similar. Thus we find that the fibre assignment strategy enforced by the design of DESI will not affect the cosmological measurements to be made by the survey, and can be removed as a potential risk for this experiment.Comment: 11 pages, 8 figure

Median fin function during the escape response of bluegill sunfish (Lepomis macrochirus). I: Fin-ray orientation and movement

The fast-start escape response is critically important to avoid predation, and axial movements driving it have been studied intensively. Large median dorsal and anal fins located near the tail have been hypothesized to increase acceleration away from the threat, yet the contribution of flexible median fins remains undescribed. To investigate the role of median fins, C-start escape responses of bluegill sunfish (Lepomis macrochirus) were recorded by three high-speed, high-resolution cameras at 500framess–1 and the 3-D kinematics of individual dorsal and anal fin rays were analyzed. Movement and orientation of the fin rays relative to the body axis were calculated throughout the duration of the C-start. We found that: (1) timing and magnitude of angular displacement varied among fin rays based on position within the fin and (2) kinematic patterns support the prediction that fin rays are actively resisting hydrodynamic forces and transmitting momentum into the water. We suggest that regions within the fins have different roles. Anterior regions of the fins are rapidly elevated to increase the volume of water that the fish may interact with and transmit force into, thus generating greater total momentum. The movement pattern of all the fin rays creates traveling waves that move posteriorly along the length of the fin, moving water as they do so. Flexible posterior regions ultimately act to accelerate this water towards the tail, potentially interacting with vortices generated by the caudal fin during the C-start. Despite their simple appearance, median fins are highly complex and versatile control surfaces that modulate locomotor performance.Organismic and Evolutionary Biolog