Complementary Windows Research Articles

Harnessing Evolution’s Gift of Borderless Wonder to Open New Economic Frontiers for Global Sustainability

Evolution transcends the natural world, oblivious to political borders. It is at the transnational scale of Earth’s evolutionary heritage where transformative scientific discoveries await. These discoveries’ potential to bolster environmental health and resilience by unmasking the most consequential evolutionary trajectories is increasingly coming to light. However, overlooked is a borderless mega-reserve of wonder unearthed along these trajectories and begging to be recognized and harnessed as an unmatched resource for charting a global pathway into a sustainable future. The article backs this assertion with a business model designed to engender a new-generation world travel industry that opens transnational frontiers for the confluence of science-, art-, and faith-based appreciation and guardianship of nature. This model reinforces with economic energy the inspiration it has drawn from Francisco J. Ayala’s engagement of art to bridge evolution, creativity, and the future of humanity, and from his treatment of science and religion as complementary windows into human understanding of the world.

Dispersion, Procreation and Mission: the Emergence of Protestantism in Early Modern West Africa

Abstract This article explores the emergence of Protestantism in West Africa in the 17th century, using both primary and secondary sources. Its central argument is that the history of Protestantism in early modern Africa has mainly been examined within the paradigm of mission history, thus reducing the history of Protestantism to a history of Protestant missionary endeavors. By intersecting three complementary windows, – a Roman Catholic window, a chartered company window and a Euro-African window –, the article traces the wider history of Protestantism in early modern West Africa. It maps the impact of Protestantism on Roman Catholics in West Africa, sketches the significance of Protestantism for certain Euro-Africans, and shows that through a combination of dispersion, procreation and mission Protestantism became a reality in West Africa as early as the 17th century.

SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data.

A protein’s structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600–1700 cm−1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.

Dinosaur bonebed amber from an original swamp forest soil.

Dinosaur bonebeds with amber content, yet scarce, offer a superior wealth and quality of data on ancient terrestrial ecosystems. However, the preserved palaeodiversity and/or taphonomic characteristics of these exceptional localities had hitherto limited their palaeobiological potential. Here, we describe the amber from the Lower Cretaceous dinosaur bonebed of Ariño (Teruel, Spain) using a multidisciplinary approach. Amber is found in both a root layer with amber strictly in situ and a litter layer mainly composed of aerial pieces unusually rich in bioinclusions, encompassing 11 insect orders, arachnids, and a few plant and vertebrate remains, including a feather. Additional palaeontological data-charophytes, palynomorphs, ostracods- are provided. Ariño arguably represents the most prolific and palaeobiologically diverse locality in which fossiliferous amber and a dinosaur bonebed have been found in association, and the only one known where the vast majority of the palaeontological assemblage suffered no or low-grade pre-burial transport. This has unlocked unprecedentedly complete and reliable palaeoecological data out of two complementary windows of preservation-the bonebed and the amber-from the same site.

Gravitational Waves and Proton Decay: Complementary Windows into Grand Unified Theories.

Proton decay is a smoking gun signature of grand unified theories (GUTs). Searches by Super-Kamiokande have resulted in stringent limits on the GUT symmetry-breaking scale. The large-scale multipurpose neutrino experiments DUNE, Hyper-Kamiokande, and JUNO will either discover proton decay or further push the symmetry-breaking scale above 10^{16} GeV. Another possible observational consequence of GUTs is the formation of a cosmic string network produced during the breaking of the GUT to the standard model gauge group. The evolution of such a string network in the expanding Universe produces a stochastic background of gravitational waves which will be tested by a number of gravitational wave detectors over a wide frequency range. We demonstrate the nontrivial complementarity between the observation of proton decay and gravitational waves produced from cosmic strings in determining SO(10) GUT-breaking chains. We show that such observations could exclude SO(10) breaking via flipped SU(5)×U(1) or standard SU(5), while breaking via a Pati-Salam intermediate symmetry, or standard SU(5)×U(1), may be favored if a large separation of energy scales associated with proton decay and cosmic strings is indicated. We note that recent results by the NANOGrav experiment have been interpreted as evidence for cosmic strings at a scale of ∼10^{14} GeV. This would strongly point toward the existence of GUTs, with SO(10) being the prime candidate. We show that the combination with already available constraints from proton decay allows us to identify preferred symmetry-breaking routes to the standard model.

PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation.

The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency of peptide precursors. In Orbitrap-based mass spectrometers, separation efficiency of peptide precursors is limited by the relatively slow scanning rate compared to time of flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS. This is achieved by equally dividing the conventional DIA analysis covering the entire mass range into multiple injections for DIA analyses with complementary windows. Using mouse liver digests, the PulseDIA method identified up to 50% more peptides and 29% more protein groups than that by conventional DIA with the same length of effective gradient time. Compared to conventional multi-injection GPF, PusleDIA exhibited higher flexibility and identified up to 18% more peptides and 8% more protein groups using two injections. The gain of peptides per effective time unit was the highest in PulseDIA compared to conventional DIA and GPF. We further applied the PulseDIA method to profile the proteome of 18 human tissue samples (benign and malignant) from nine cholangiocarcinoma (CCA) patients. PulseDIA identified 7796 protein groups in these CCA samples, with a 14% increase of protein group identification compared to the conventional DIA method. The missing value for protein matrix dropped by 7% using PulseDIA compared to DIA. A total of 681 significantly altered proteins were detected in CCA samples using PulseDIA, including several dysregulated proteins, which were absent in the conventional DIA analysis. Taken together, we present PulseDIA as an enhanced DIA-MS method with improved sensitivity and reproducibility.

Complementary realities: Public domain Internet measurements in the development of Canada’s universal access policies

As access to the Internet has become increasingly essential for social and economic participation, public domain Internet measurements have become indispensable for users to validate quality of service their network operator delivers and for policymakers to identify and address gaps in broadband infrastructure. This article evaluates public domain Internet performance measurements available for assessing the state of connectivity and developing universal access service quality standards in Canada. The analysis suggests that different approaches to Internet measurement represent complementary windows into a complex and fast evolving reality of broadband connectivity. Despite their potential shortcomings, large-scale crowdsourced open data network testing platforms have a central role to play in enabling broadband infrastructure policy coordination across different levels of government, empowerment of consumers, and achievement of universal service objectives for quality of service users experience when accessing the open Internet.

Multimodal Parcellations and Extensive Behavioral Profiling Tackling the Hippocampus Gradient.

The hippocampus displays a complex organization and function that is perturbed in many neuropathologies. Histological work revealed a complex arrangement of subfields along the medial-lateral and the ventral-dorsal dimension, which contrasts with the anterior-posterior functional differentiation. The variety of maps has raised the need for an integrative multimodal view. We applied connectivity-based parcellation to 1) intrinsic connectivity 2) task-based connectivity, and 3) structural covariance, as complementary windows into structural and functional differentiation of the hippocampus. Strikingly, while functional properties (i.e., intrinsic and task-based) revealed similar partitions dominated by an anterior-posterior organization, structural covariance exhibited a hybrid pattern reflecting both functional and cytoarchitectonic subdivision. Capitalizing on the consistency of functional parcellations, we defined robust functional maps at different levels of partitions, which are openly available for the scientific community. Our functional maps demonstrated a head-body and tail partition, subdivided along the anterior-posterior and medial-lateral axis. Behavioral profiling of these fine partitions based on activation data indicated an emotion-cognition gradient along the anterior-posterior axis and additionally suggested a self-world-centric gradient supporting the role of the hippocampus in the construction of abstract representations for spatial navigation and episodic memory.

Active galactic nuclei: what’s in a name?

Active Galactic Nuclei (AGN) are energetic astrophysical sources powered by accretion onto supermassive black holes in galaxies, and present unique observational signatures that cover the full electromagnetic spectrum over more than twenty orders of magnitude in frequency. The rich phenomenology of AGN has resulted in a large number of different "flavours" in the literature that now comprise a complex and confusing AGN "zoo". It is increasingly clear that these classifications are only partially related to intrinsic differences between AGN, and primarily reflect variations in a relatively small number of astrophysical parameters as well the method by which each class of AGN is selected. Taken together, observations in different electromagnetic bands as well as variations over time provide complementary windows on the physics of different sub-structures in the AGN. In this review, we present an overview of AGN multi-wavelength properties with the aim of painting their "big picture" through observations in each electromagnetic band from radio to gamma-rays as well as AGN variability. We address what we can learn from each observational method, the impact of selection effects, the physics behind the emission at each wavelength, and the potential for future studies. To conclude we use these observations to piece together the basic architecture of AGN, discuss our current understanding of unification models, and highlight some open questions that present opportunities for future observational and theoretical progress.

Complementary Realities: Public Domain Internet Measurements in the Development of Canadaas Universal Access Policies

This paper evaluates public domain Internet performance measurements available for characterizing the state of connectivity and developing universal access service quality standards in Canada. As access to the Internet has become more essential to social and economic participation, public domain Internet measurements have become an indispensable tool for users to validate quality of service their network operator delivers and for policymakers to identify and address gaps in broadband infrastructure. Unfortunately, most data about Internet performance remains in the private domain. Furthermore, due to their distinctive methodologies, different sources of broadband speed measurements can generate inconsistent results both in terms of absolute performance metrics and in relative terms. This creates a significant problem for validating service level agreements by users and minimum standards of universal service policymakers are increasingly adopting around the world. In contrast to previous debates about which testing approach is more or less “realistic”, we argue that distinctive approaches to Internet measurement should be viewed as complementary windows into a complex and fast evolving reality of broadband connectivity. We explore how “big data” and “small data” approaches to measurement can complement each other in universal access standard setting. Despite their potential shortcomings, large scale crowdsourced open data network testing platforms have a central role to play in enabling broadband infrastructure policy coordination across different levels of government, empowering consumers, and validating speed and universal service quality standards.

Benefits of multi-modal fusion analysis on a large-scale dataset: Life-span patterns of inter-subject variability in cortical morphometry and white matter microstructure

Neuroimaging studies have become increasingly multimodal in recent years, with researchers typically acquiring several different types of MRI data and processing them along separate pipelines that provide a set of complementary windows into each subject's brain. However, few attempts have been made to integrate the various modalities in the same analysis. Linked ICA is a robust data fusion model that takes multi-modal data and characterizes inter-subject variability in terms of a set of multi-modal components. This paper examines the types of components found when running Linked ICA on a large magnetic resonance imaging (MRI) morphometric and diffusion tensor imaging (DTI) data set comprising 484 healthy subjects ranging from 8 to 85 years of age. We find several strong global features related to age, sex, and intracranial volume; in particular, one component predicts age to a high accuracy (r=0.95). Most of the remaining components describe spatially localized modes of variability in white or gray matter, with many components including both tissue types. The multimodal components tend to be located in anatomically-related brain areas, suggesting a morphological and possibly functional relationship. The local components show relationships between surface-based cortical thickness and arealization, voxel-based morphometry (VBM), and between three different DTI measures. Further, we report components related to artifacts (e.g. scanner software upgrades) which would be expected in a dataset of this size. Most of the 100 extracted components showed interpretable spatial patterns and were found to be reliable using split-half validation. This work provides novel information about normal inter-subject variability in brain structure, and demonstrates the potential of Linked ICA as a feature-extracting data fusion approach across modalities. This exploratory approach automatically generates models to explain structure in the data, and may prove especially powerful for large-scale studies, where the population variability can be explored in increased detail.

A Comparison of Gene Expression Responses in Rat Whole Embryo Culture and In Vivo: Time-Dependent Retinoic Acid-Induced Teratogenic Response

The whole embryo culture (WEC) model serves as a potential alternative for classical in vivo developmental toxicity testing. In the WEC, cultured rat embryos are exposed during neurulation and early organogenesis and evaluated for morphological effects. Toxicogenomic-based approaches may improve the predictive ability of WEC by providing molecular-based markers associated with chemical exposure, which can be compared across multiple parameters (e.g., exposure duration, developmental time, experimental model). Additionally, comparisons between in vitro and in vivo models may identify objective relevant molecular responses linked with developmental toxicity endpoints in vivo. In this study, using a transcriptomic approach, we compared all-trans retinoic acid (RA)-exposed and nonexposed Wistar rat embryos derived using WEC (RA, 0.5 μg/ml) or in vivo (RA, 50 mg/kg, oral gavage) to identify overlapping and nonoverlapping effects of RA on RNA expression in parallel with morphological changes. Across six time points (gestational day 10 + 2-48 h), we observed strong similarities in RA response at the gene (directionality, significance) and functional (e.g., embryonic development, cell differentiation) level which associated with RA-induced adverse morphological effects, including growth reduction as well as alterations in neural tube, limb, branchial, and mandible development. We observed differences between models in the timing of RA-induced effects on genes related to embryonic development and RA metabolism. These observations on the gene expression level were associated with specific differential morphological outcomes. This study supports the use of WEC to examine compound-induced molecular responses relative to in vivo and, furthermore, assists in defining the applicability domain of the WEC in determining complementary windows of sensitivity for developmental toxicological investigations.

The Properties of High Redshift Galaxies

In recent years, a variety of techniques at optical, near-infrared, sub-mm, and radio wavelengths have opened complementary windows on the high-redshift Universe. Here we review the current understanding of the general properties of the z>~2 galaxies detected in the optical (Lyman-break galaxies) and in the sub-mm (SCUBA sources). We list some of the key questions that need to be answered in order to understand the nature and evolution of the high-redshift galaxies. Wherever possible, we present tentative answers given so far to those questions, in particular on the low-redshift couterparts of the high-redshift galaxies, on the impact of dust obscuration on the observed quantities, and on physical characteristics of the high-z systems as inferred from observations.

Combination of muon spin relaxation and neutron scattering studies on magnetism

We combine the results from muon spin relaxation (μSR) and neutron scattering measurements performed on the same specimen (or system) of magnetic materials. The example on a spin glassCuMn (5%) shows that the two techniques have complementary time windows for studying dynamic spin fluctuations. In combining the results, one should note that muons and neutrons probe dynamic phenomena with different wavevectors. The results on antiferromagnetic La2CuO4−y illustrate the difference in the spatial range of static spin correlations reflected in the μSR precession frequency and the neutron Bragg peak intensity. With the examples of CeCu2.1Si2, YBa2Cu3Ox and Bi2Sr2YCu2O8+y, we point out that μSR is a superb tool for discovering static magnetic order while neutron scattering is the unique method to determine the spin structure. We emphasize that it is very fruitful to perform μSR and neutron experiments on the same specimen and to compare and combine the results for the better understanding of magnetism of various system.