Classifying the unknown: discovering novel gravitational-wave detector glitches using similarity learning

The observation of gravitational waves from compact binary coalescences by LIGO and Virgo has begun a new era in astronomy. A critical challenge in making detections is determining whether loud transient features in the data are caused by gravitational waves or by instrumental or environmental sources. The citizen-science project \emph{Gravity Spy} has been demonstrated as an efficient infrastructure for classifying known types of noise transients (glitches) through a combination of data analysis performed by both citizen volunteers and machine learning. We present the next iteration of this project, using similarity indices to empower citizen scientists to create large data sets of unknown transients, which can then be used to facilitate supervised machine-learning characterization. This new evolution aims to alleviate a persistent challenge that plagues both citizen-science and instrumental detector work: the ability to build large samples of relatively rare events. Using two families of transient noise that appeared unexpectedly during LIGO's second observing run (O2), we demonstrate the impact that the similarity indices could have had on finding these new glitch types in the Gravity Spy program

Implication of the overlap representation for modelling generalized parton distributions

Based on a field theoretically inspired model of light-cone wave functions, we derive valence-like generalized parton distributions and their double distributions from the wave function overlap in the parton number conserved s-channel. The parton number changing contributions in the t-channel are restored from duality. In our construction constraints of positivity and polynomiality are simultaneously satisfied and it also implies a model dependent relation between generalized parton distributions and transverse momentum dependent parton distribution functions. The model predicts that the t-behavior of resulting hadronic amplitudes depends on the Bjorken variable x_Bj. We also propose an improved ansatz for double distributions that embeds this property.Comment: 15 pages, 8 eps figure

Light-ion production in the interaction of 96 MeV neutrons with silicon

Double-differential cross sections for light-ion (p, d, t, He-3 and alpha) production in silicon, induced by 96 MeV neutrons are reported. Energy spectra are measured at eight laboratory angles, ranging from 20 degrees to 160 degrees in steps of 20 degrees. Procedures for data taking and data reduction are presented. Deduced energy-differential, angle-differential and production cross sections are reported. Experimental cross sections are compared to theoretical reaction model calculations and experimental data in the literature.Comment: 23 pages, 10 figures, added wrap-around correction (see section 4.3) leading to changed cross-sections and figures, accepted Phys. Rev.

The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription

The ability to interpret daily and seasonal alterations in light and temperature signals is essential for plant survival. This is particularly important during seedling establishment when the phytochrome photoreceptors activate photosynthetic pigment production for photoautotrophic growth. Phytochromes accomplish this partly through the suppression of phytochrome interacting factors (PIFs), negative regulators of chlorophyll and carotenoid biosynthesis. While the bZIP transcription factor long hypocotyl 5 (HY5), a potent PIF antagonist, promotes photosynthetic pigment accumulation in response to light. Here we demonstrate that by directly targeting a common promoter cis-element (G-box), HY5 and PIFs form a dynamic activation-suppression transcriptional module responsive to light and temperature cues. This antagonistic regulatory module provides a simple, direct mechanism through which environmental change can redirect transcriptional control of genes required for photosynthesis and photoprotection. In the regulation of photopigment biosynthesis genes, HY5 and PIFs do not operate alone, but with the circadian clock. However, sudden changes in light or temperature conditions can trigger changes in HY5 and PIFs abundance that adjust the expression of common target genes to optimise photosynthetic performance and growth

Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

<div><p>Genome-scale metabolic networks provide a comprehensive structural framework for modeling genotype-phenotype relationships through flux simulations. The solution space for the metabolic flux state of the cell is typically very large and optimization-based approaches are often necessary for predicting the active metabolic state under specific environmental conditions. The objective function to be used in such optimization algorithms is directly linked with the biological hypothesis underlying the model and therefore it is one of the most relevant parameters for successful modeling. Although linear combination of selected fluxes is widely used for formulating metabolic objective functions, we show that the resulting optimization problem is sensitive towards stoichiometry representation of the metabolic network. This undesirable sensitivity leads to different simulation results when using numerically different but biochemically equivalent stoichiometry representations and thereby makes biological interpretation intrinsically subjective and ambiguous. We hereby propose a new method, Minimization of Metabolites Balance (MiMBl), which decouples the artifacts of stoichiometry representation from the formulation of the desired objective functions, by casting objective functions using metabolite turnovers rather than fluxes. By simulating perturbed metabolic networks, we demonstrate that the use of stoichiometry representation independent algorithms is fundamental for unambiguously linking modeling results with biological interpretation. For example, MiMBl allowed us to expand the scope of metabolic modeling in elucidating the mechanistic basis of several genetic interactions in <em>Saccharomyces cerevisiae</em>.</p> </div

Allosteric Regulation of Fibronectin/α5β1 Interaction by Fibronectin-Binding MSCRAMMs

Citation: Liang, X. W., Garcia, B. L., Visai, L., Prabhakaran, S., Meenan, N. A. G., Potts, J. R., . . . Hook, M. (2016). Allosteric Regulation of Fibronectin/alpha(5)beta(1) Interaction by Fibronectin-Binding MSCRAMMs. Plos One, 11(7), 17. doi:10.1371/journal.pone.0159118Adherence ofmicrobes to host tissues is a hallmark of infectious disease and is often mediated by a class of adhesins termed MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Numerous pathogens express MSCRAMMs that specifically bind the heterodimeric human glycoprotein fibronectin (Fn). In addition to roles in adhesion, Fn-binding MSCRAMMs exploit physiological Fn functions. For example, several pathogens can invade host cells by a mechanism whereby MSCRAMM-bound Fn bridges interaction with alpha(5)beta(1) integrin. Here, we investigate two Fn-binding MSCRAMMs, FnBPA (Staphylococcus aureus) and BBK32 (Borrelia burgdorferi) to probe structure-activity relationships of MSCRAMM-induced Fn/alpha(5)beta(1) integrin activation. Circular dichroism, fluorescence resonance energy transfer, and dynamic light scattering techniques uncover a conformational rearrangement of Fn involving domains distant from the MSCRAMM binding site. Surface plasmon resonance experiments demonstrate a significant enhancement of Fn/alpha(5)beta(1) integrin affinity in the presence of FnBPA or BBK32. Detailed kinetic analysis of these interactions reveal that this change in affinity can be attributed solely to an increase in the initial Fn/alpha(5)beta(1) on-rate and that this rate-enhancement is dependent on high-affinity Fn-binding by MSCRAMMs. These data implicate MSCRAMM-induced perturbation of specific intramolecular contacts within the Fn heterodimer resulting in activation by exposing previously cryptic alpha(5)beta(1) interaction motifs. By correlating structural changes in Fn to a direct measurement of increased Fn/alpha(5)beta(1) affinity, this work significantly advances our understanding of the structural basis for the modulation of integrin function by Fn-binding MSCRAMMs

95 MeV neutron scattering on hydrogen, deuterium, carbon, and oxygen

Three neutron-deuteron scattering experiments at 95 MeV have been performed recently at The Svedberg Laboratory in Uppsala. Subsets of the results of these experiments have been reported in two short articles, showing clear evidence for three-nucleon force effects. In this paper, we present a more detailed description of the experimental methods as well as further discussion of the results. In addition to neutron-deuteron scattering data, neutron-proton and 12 C(n, n) elastic scattering data have been measured for normalization purposes, and 16 O (n, n) data have been obtained for the first time at this energy. It was possible to extract 12 C(n, n )and 16 O (n, n ) inelastic scattering cross sections to excited states below 12 MeV excitation energy. The inelastic scattering data (for both carbon and oxygen) are shown to have a significant impact on the determination ofnuclear recoil kerma coefficients

Anti-angiogenic therapy for cancer: Current progress, unresolved questions and future directions

Tumours require a vascular supply to grow and can achieve this via the expression of pro-angiogenic growth factors, including members of the vascular endothelial growth factor (VEGF) family of ligands. Since one or more of the VEGF ligand family is overexpressed in most solid cancers, there was great optimism that inhibition of the VEGF pathway would represent an effective anti-angiogenic therapy for most tumour types. Encouragingly, VEGF pathway targeted drugs such as bevacizumab, sunitinib and aflibercept have shown activity in certain settings. However, inhibition of VEGF signalling is not effective in all cancers, prompting the need to further understand how the vasculature can be effectively targeted in tumours. Here we present a succinct review of the progress with VEGF-targeted therapy and the unresolved questions that exist in the field: including its use in different disease stages (metastatic, adjuvant, neoadjuvant), interactions with chemotherapy, duration and scheduling of therapy, potential predictive biomarkers and proposed mechanisms of resistance, including paradoxical effects such as enhanced tumour aggressiveness. In terms of future directions, we discuss the need to delineate further the complexities of tumour vascularisation if we are to develop more effective and personalised anti-angiogenic therapies. © 2014 The Author(s)

Prognostic value of baseline functional status measures and geriatric screening in vulnerable older patients with metastatic colorectal cancer receiving palliative chemotherapy – The randomized NORDIC9-study

Introduction Appropriate patient selection based on functional status is crucial when considering older adults for palliative chemotherapy. This pre-planned analysis of the randomized NORDIC9-study explored the prognostic value of four functional status measures regarding progression-free survival (PFS) and overall survival (OS) in vulnerable older patients with metastatic colorectal cancer (mCRC) receiving first-line palliative chemotherapy. Materials and methods Patients ≥70 years of age with mCRC not candidates for standard full-dose combination chemotherapy were randomized to receive full-dose S1 or reduced-dose S1 + oxaliplatin. At baseline, functional status was assessed using ECOG performance status (ECOG PS), frailty phenotype, Geriatric 8 (G8), and Vulnerable Elderly Survey-13 (VES-13). Multivariable regression models were applied and C-statistics were estimated. Results In total, 160 patients with a median age of 78 years (IQR: 76–81) were included. While in univariate analyses, ECOG PS, frailty phenotype, and VES-13 were statistically significantly associated with differences in OS between subgroups, G8 was not (HR = 1.55, 95%CI: 0.99–2.41, p = 0.050). In multivariable analyses adjusted for age, sex, body mass index, and treatment allocation, we found significant differences between subgroups for all applied tools and with C-statistics in the moderate range for ECOG PS and VES-13. Concerning PFS, statistically significant differences were observed between subgroups of ECOG PS, G8, and VES-13 both in uni- and multivariable analyses, but not for frailty phenotype. Discussion In this Nordic cohort of vulnerable older patients with mCRC, baseline ECOG PS, frailty phenotype, G8, and VES-13 showed prognostic value regarding overall survival, and moderate predictive value of models based on ECOG PS and VES-13 was demonstrated.publishedVersio