Rapid Extraction of Respiratory Waveforms from Photoplethysmography: A Deep Encoder Approach

Much of the information of breathing is contained within the photoplethysmography (PPG) signal, through changes in venous blood flow, heart rate and stroke volume. We aim to leverage this fact, by employing a novel deep learning framework which is a based on a repurposed convolutional autoencoder. Our model aims to encode all of the relevant respiratory information contained within photoplethysmography waveform, and decode it into a waveform that is similar to a gold standard respiratory reference. The model is employed on two photoplethysmography data sets, namely Capnobase and BIDMC. We show that the model is capable of producing respiratory waveforms that approach the gold standard, while in turn producing state of the art respiratory rate estimates. We also show that when it comes to capturing more advanced respiratory waveform characteristics such as duty cycle, our model is for the most part unsuccessful. A suggested reason for this, in light of a previous study on in-ear PPG, is that the respiratory variations in finger-PPG are far weaker compared with other recording locations. Importantly, our model can perform these waveform estimates in a fraction of a millisecond, giving it the capacity to produce over 6 hours of respiratory waveforms in a single second. Moreover, we attempt to interpret the behaviour of the kernel weights within the model, showing that in part our model intuitively selects different breathing frequencies. The model proposed in this work could help to improve the usefulness of consumer PPG-based wearables for medical applications, where detailed respiratory information is required

Interactive effects of acute exercise and carbohydrate-energy replacement on insulin sensitivity in healthy adults

This study investigated whether carbohydrate-energy replacement immediately after prolonged endurance exercise attenuates insulin sensitivity the following morning, and whether exercise improves insulin sensitivity the following morning independent of an exercise-induced carbohydrate deficit. Oral glucose tolerance and whole-body insulin sensitivity were compared the morning after three evening conditions, involving: (1) treadmill exercise followed by carbohydrate replacement drink (200 or 150 g maltodextrin for males and females, respectively; CHO-replace); (2) treadmill exercise followed by a non-caloric, taste-matched placebo (CHO-deficit); or (3) seated rest with no drink provided (Rest). Treadmill exercise involved 90 minutes at ~80% age-predicted maximum heart rate. Seven males and two females (aged 23 1 years; body mass index 24.0 2.7 kgm-2) completed all conditions in a randomized order. Matsuda index improved by 22% (2.2 [0.3, 4.0] au, p = .03) and HOMA2-IR improved by 10% (-0.04 [-0.08, 0.00] au, p = .04) in CHO-deficit versus CHO-replace, without corresponding changes in postprandial glycemia. Outcomes were similar between Rest and other conditions. These data suggest that improvements to insulin sensitivity in healthy populations following acute moderate/vigorous intensity endurance exercise may be dependent on the presence of a carbohydrate-energy deficit. NOVELTY • Restoration of carbohydrate balance following acute endurance exercise attenuated whole-body insulin sensitivity • Exercise per se failed to enhance whole-body insulin sensitivity • Maximizing or prolonging the post-exercise carbohydrate deficit may enhance acute benefits to insulin sensitivityThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Structure and Kinetic Investigation of Streptococcus pyogenes Family GH38 α-Mannosidase

BACKGROUND: The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. These enzymes are found in different GH sequence-based families. Considerable research has probed the role of higher eukaryotic "GH38" alpha-mannosides that play a key role in the modification and diversification of hybrid N-glycans; processes with strong cellular links to cancer and autoimmune disease. The most extensively studied of these enzymes is the Drosophila GH38 alpha-mannosidase II, which has been shown to be a retaining alpha-mannosidase that targets both alpha-1,3 and alpha-1,6 mannosyl linkages, an activity that enables the enzyme to process GlcNAc(Man)(5)(GlcNAc)(2) hybrid N-glycans to GlcNAc(Man)(3)(GlcNAc)(2). Far less well understood is the observation that many bacterial species, predominantly but not exclusively pathogens and symbionts, also possess putative GH38 alpha-mannosidases whose activity and specificity is unknown. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that the Streptococcus pyogenes (M1 GAS SF370) GH38 enzyme (Spy1604; hereafter SpGH38) is an alpha-mannosidase with specificity for alpha-1,3 mannosidic linkages. The 3D X-ray structure of SpGH38, obtained in native form at 1.9 A resolution and in complex with the inhibitor swainsonine (K(i) 18 microM) at 2.6 A, reveals a canonical GH38 five-domain structure in which the catalytic "-1" subsite shows high similarity with the Drosophila enzyme, including the catalytic Zn(2+) ion. In contrast, the "leaving group" subsites of SpGH38 display considerable differences to the higher eukaryotic GH38s; features that contribute to their apparent specificity. CONCLUSIONS/SIGNIFICANCE: Although the in vivo function of this streptococcal GH38 alpha-mannosidase remains unknown, it is shown to be an alpha-mannosidase active on N-glycans. SpGH38 lies on an operon that also contains the GH84 hexosaminidase (Spy1600) and an additional putative glycosidase. The activity of SpGH38, together with its genomic context, strongly hints at a function in the degradation of host N- or possibly O-glycans. The absence of any classical signal peptide further suggests that SpGH38 may be intracellular, perhaps functioning in the subsequent degradation of extracellular host glycans following their initial digestion by secreted glycosidases

Photonic mid-infrared nulling for exoplanet detection on a planar chalcogenide platform

The future of exoplanet detection lies in the mid-infrared (MIR). The MIR region contains the blackbody peak of both hot and habitable zone exoplanets, making the contrast between starlight and planet light less extreme. It is also the region where prominent chemical signatures indicative of life exist, such as ozone at 9.7 microns. At a wavelength of 4 microns the difference in emission between an Earth-like planet and a star like our own is 80 dB. However a jovian planet, at the same separation exhibits 60 dB of contrast, or only 20 dB if it is hot due to its formation energy or being close to its host star. A two dimensional nulling interferometer, made with chalcogenide glass, has been measured to produce a null of 20 dB, limited by scattered light. Measures to increase the null depth to the theoretical limit of 60 dB are discussed.Comment: Was published in SPIE: Optical and Infrared Interferometry and Imaging VI, Mike Ireland presente

Scaling of the B and D meson spectrum in lattice QCD

We give results for the $B$ and the $D$ meson spectrum using NRQCD on the lattice in the quenched approximation. The masses of radially and orbitally excited states are calculated as well as $S$-wave hyperfine and $P$-wave fine structure. Radially excited $P$-states are observed for the first time. Radial and orbital excitation energies match well to experiment, as does the strange-non-strange $S$-wave splitting. We compare the light and heavy quark mass dependence of various splittings to experiment. Our $B$-results cover a range in lattice spacings of more than a factor of two. Our $D$-results are from a single lattice spacing and we compare them to numbers in the literature from finer lattices using other methods. We see no significant dependence of physical results on the lattice spacing. PACS: 11.15.Ha 12.38.Gc 14.40.Lb 14.40.NdComment: 78 pages, 29 tables, 30 figures Revised version. Minor corrections to spelling and wordin

A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus

Dietary fiber is an important food source for members of the human gut microbiome. Members of the dominant Bacteroidetes phylum capture diverse polysaccharides via the action of multiple cell surface proteins encoded within Polysaccharide Utilization Loci (PUL). The independent activities of PUL-encoded glycoside hydrolases (GH) and surface glycan-binding proteins (SGBPs) for the harvest of various glycans have been studied in detail, but how these proteins work together to coordinate uptake is poorly understood. Here, we combine genetic and biochemical approaches to discern the interplay between the BoGH9 endoglucanase and the xyloglucan-binding proteins SGBP-A and SGBP-B from the Bacteroides ovatus Xyloglucan Utilization Locus (XyGUL). The expression of BoGH9, a weakly active xyloglucanase in isolation, is required in a strain that expresses a non-binding version of SGBP-A (SGBP-A*). The crystal structure of the BoGH9 enzyme suggests the molecular basis for its robust activity on mixed-linkage β-glucan compared to xyloglucan. Yet, catalytically inactive site-directed mutants of BoGH9 fail to complement the deletion of the active BoGH9 in a SGBP-A* strain. We also find that SGBP-B is needed in an SGBP-A* background to support growth on xyloglucan, but that the non-binding SGBP-B* protein acts in a dominant negative manner to inhibit growth on xyloglucan. We postulate a model whereby the SGBP-A, SGBP-B and BoGH9 work together at the cell surface, likely within a discrete complex, and that xyloglucan binding by SGBP-B and BoGH9 may facilitate the orientation of the xyloglucan for transfer across the outer membrane

Author Correction: 150,000-year palaeoclimate record from northern Ethiopia supports early, multiple dispersals of modern humans from Africa

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper

A β-mannanase with a lysozyme-like fold and a novel molecular catalytic mechanism

The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β- Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β- mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4 ‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner