Secondary structure specific simpler prediction models for protein backbone angles.

MOTIVATION: Protein backbone angle prediction has achieved significant accuracy improvement with the development of deep learning methods. Usually the same deep learning model is used in making prediction for all residues regardless of the categories of secondary structures they belong to. In this paper, we propose to train separate deep learning models for each category of secondary structures. Machine learning methods strive to achieve generality over the training examples and consequently loose accuracy. In this work, we explicitly exploit classification knowledge to restrict generalisation within the specific class of training examples. This is to compensate the loss of generalisation by exploiting specialisation knowledge in an informed way. RESULTS: The new method named SAP4SS obtains mean absolute error (MAE) values of 15.59, 18.87, 6.03, and 21.71 respectively for four types of backbone angles [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]. Consequently, SAP4SS significantly outperforms existing state-of-the-art methods SAP, OPUS-TASS, and SPOT-1D: the differences in MAE for all four types of angles are from 1.5 to 4.1% compared to the best known results. AVAILABILITY: SAP4SS along with its data is available from https://gitlab.com/mahnewton/sap4ss .

Dephasing Dynamics across Different Local Vibrational Modes and Crystalline Environments.

The perturbed free induction decay (PFID) observed in ultrafast infrared spectroscopy was used to unveil the rates at which different vibrational modes of the same atomic-scale defect can interact with their environment. The N_{3}VH^{0} defect in diamond provided a model system, allowing a comparison of stretch and bend vibrational modes within different crystal lattice environments. The observed bend mode (first overtone) exhibited dephasing times T_{2}=2.8(1) ps, while the fundamental stretch mode had surprisingly faster dynamics T_{2}<1.7 ps driven by its more direct perturbation of the crystal lattice, with increased phonon coupling. Further, at high defect concentrations the stretch mode's dephasing rate was enhanced. The ability to reliably measure T_{2} via PFID provides vital insights into how vibrational systems interact with their local environment.

Erratum: Anharmonicity and Universal Response of Linear Carbon Chain Mechanical Properties under Hydrostatic Pressure [Phys. Rev. Lett. 125, 105501 (2020)].

This corrects the article DOI: 10.1103/PhysRevLett.125.105501.

Erratum: Anharmonicity and Universal Response of Linear Carbon Chain Mechanical Properties under Hydrostatic Pressure [Phys. Rev. Lett. 125, 105501 (2020)].

This corrects the article DOI: 10.1103/PhysRevLett.125.105501.

Thermodynamics of Linear Carbon Chains.

Linear carbon chains (LCCs) are one-dimensional materials with unique properties, including high Debye temperatures and restricted selection rules for phonon interactions. Consequently, their Raman C-band frequency's temperature dependence is a probe to their thermal properties, which are well described within the Debye formalism even at room temperatures. Therefore, with the basis on a semiempirical approach we show how to use the C band to evaluate the LCCs' internal energy, heat capacity, coefficient of thermal expansion, thermal strain, and Grüneisen parameter, providing universal relations for these quantities in terms of the number of carbons atoms and the temperature.

A single-crystal diamond X-ray pixel detector with embedded graphitic electrodes.

The first experimental results from a new transmissive diagnostic instrument for synchrotron X-ray beamlines are presented. The instrument utilizes a single-crystal chemical-vapour-deposition diamond plate as the detector material, with graphitic wires embedded within the bulk diamond acting as electrodes. The resulting instrument is an all-carbon transmissive X-ray imaging detector. Within the instrument's transmissive aperture there is no surface metallization that could absorb X-rays, and no surface structures that could be damaged by exposure to synchrotron X-ray beams. The graphitic electrodes are fabricated in situ within the bulk diamond using a laser-writing technique. Two separate arrays of parallel graphitic wires are fabricated, running parallel to the diamond surface and perpendicular to each other, at two different depths within the diamond. One array of wires has a modulated bias voltage applied; the perpendicular array is a series of readout electrodes. X-rays passing through the detector generate charge carriers within the bulk diamond through photoionization, and these charge carriers travel to the nearest readout electrode under the influence of the modulated electrical bias. Each of the crossing points between perpendicular wires acts as an individual pixel. The simultaneous read-out of all pixels is achieved using a lock-in technique. The parallel wires within each array are separated by 50 µm, determining the pixel pitch. Readout is obtained at 100 Hz, and the resolution of the X-ray beam position measurement is 600 nm for a 180 µm size beam.

Anharmonicity and Universal Response of Linear Carbon Chain Mechanical Properties under Hydrostatic Pressure.

Isolated linear carbon chains (LCCs) encapsulated by multiwalled carbon nanotubes are studied under hydrostatic pressure (P) via resonance Raman scattering. The LCCs' spectroscopic signature C band around 1850 cm^{-1} softens linearly with increasing P. A simple anharmonic force-constant model not only describes such softening but also shows that the LCCs' Young's modulus (E), Grüneisen parameter (γ), and strain (ϵ) follow universal P^{-1} and P^{2} laws, respectively. In particular, γ also presents a unified behavior for all LCCs. To the best of our knowledge, these are the first results reported on such isolated systems and the first work to explore universal P-dependent responses for LCCs' E, ϵ, and γ.

The Nuclear RNA-binding Protein RBSR1 Interactome in Trypanosoma cruzi.

Trypanosoma cruzi, the etiological agent of Chagas disease, has been widely studied, reflecting both its medical importance and the particular features that make this pathogen an attractive model for basic biological studies. The repression of transcripts by messenger ribonucleoprotein (mRNP) complexes is an important pathway of post-transcriptional regulation in eukaryotes, including T. cruzi. RBSR1 is a serine-arginine (SR)-rich RNA-binding protein (RBP) in T. cruzi that contains one RNA-recognition motif (RRM); this protein has a primarily nuclear localization and is developmentally regulated, not being detected in metacyclic trypomastigotes. RBSR1 interacts with other RBPs, such as UBP1 and UBP2, and the nuclear SR-protein TRRM1. Phylogenetic analysis indicated that RBSR1 is orthologous to the human splicing factor SRSF7, what might indicate its possible involvement in pre-RNA processing. Accordingly, ribonomics data showed the enrichment of snoRNAs and snRNAs in the RBSR1 immunoprecipiatation complex, hence reinforcing the supposition that this protein might be involved in RNA processing in the nucleus.

Remarkable Electronic Effect on the meso-Tetra(thienyl)porphyrins.

Complexes derived from meso-tetra(thienyl)porphyrins (TThP) and meso-tetra(pyridyl)porphyrin (TPyP) containing peripheral ruthenium complexes with general formulas {TPyP[RuCl(dppb)(5,5'-Mebipy)]4}(PF6)4, {TThP[RuCl(dppb)(5,5'-Mebipy)]4}(PF6)4, and {TThP-me-[RuCl(dppb)(5,5'-Mebipy)]4}(PF6)4 [5,5'-Mebipy = 5,5'-dimethyl-2,2'-bipyridine and dppb = 1,4-bis(diphenylphosphino)butane] were synthesized and characterized by spectroscopy techniques (1H- and 31P{1H}-NMR, IR, UV/vis, fluorescence, and electron paramagnetic resonance (EPR)), cyclic voltammetry, coulometry, molar conductivity, and elemental analysis. Voltammetry and UV/vis studies demonstrated differentiated electronic properties for ruthenium appended with TThP and TThP-me when compared to ruthenium appended with TPyP. The UV/vis analysis for the ruthenium complex derived from TThP and TThP-me, as well as the Soret and Q bands, characteristics of porphyrins, showed a band at 700 nm referring to the Ru → S electronic transition, and porphyrin TThP-me showed another band at 475 nm from the Ru-N transition. The attribution of these bands was confirmed by spectroelectrochemical analysis. Cyclic voltammetry analysis for the ruthenium complex derived from TPyP exhibited only an electrochemical process with E1/2 = 0.47 V assigned to the Ru(II)/Ru(III) redox pair (Fc/Fc+). On the other hand, two processes were observed for the ruthenium complexes derived from TThP and TThP-me, with E1/2 around 0.17 and 0.47 V, which were attributed to the formation of a mixed valence tetranuclear species containing Ru(II) and Ru(III) ions, showing that the peripheral groups are not oxidized at the same potential. Fluorescence spectroscopic experiments show the existence of a mixed state of emission in the supramolecular porphyrin moieties. The results suggest the formation of Ru(II)-Ru(III) mixed valence complexes when oxidation potential was applied around 0.17 V in the {TThP[RuCl(dppb)(5,5'-Mebipy)]4}(PF6)4 and {TThP-me-[RuCl(dppb)(5,5'-Mebipy)]4}(PF6)4 species.

The influence of aquaculture unit proximity on the pattern of Lepeophtheirus salmonis infection of anadromous Salmo trutta populations on the isle of Skye, Scotland.

A total of 230 anadromous Salmo trutta (brown trout) were sampled in five sheltered coastal fjords (or sea lochs) on the Isle of Skye, Scotland, U.K., in 2016 at varying distances from active Atlantic salmon Salmo salar farms. Statistical models were developed to investigate potential correlations between salmon lice Lepeophtheirus salmonis burdens on S. trutta hosts and their proximity to S. salar farm cages. Significant correlations were found between lice burdens and fish fork length and proximity to the nearest S. salar farm. The probability of the presence of L. salmonis on fish hosts increased with fish host size and with distance from the nearest S. salar farm, but total lice burdens were highest in fish sampled near S. salar farms and decreased with distance. The proportion of different life-cycle stages of L. salmonis were also dependent on S. salar farm proximity, with higher juvenile lice numbers recorded at sites near S. salar farm cages. These results highlight the complexity of the relationship between S. trutta and L. salmonis infections on wild fish and emphasize the requirement of further research to quantify these effects to better inform conservation and management strategies, particularly in areas of active S. salar farm facilities.

Acute mobilization and migration of bone marrow-derived stem cells following anterior cruciate ligament rupture.

OBJECTIVE: Little is known regarding acute local and systemic processes following anterior cruciate ligament (ACL) rupture. No study has elucidated whether bone marrow-derived mesenchymal stem cells (MSCs) are mobilized into circulation and recruited to the injured joint. METHODS: In Part 1, Lewis rats were randomized to noninvasive ACL rupture (Rupture) or non-injured (Control) (n = 6/group). After 72 h, whole blood MSC concentration was assessed using flow cytometry. Synovial fluid and serum were assayed for stromal cell-derived factor (SDF)-1α and cartilage degeneration biomarkers, respectively. In Part 2, 12 additional rats were randomized and intravenously-injected with fluorescently-labeled allogenic MSCs. Cell tracking was performed using longitudinal, in vivo and ex vivo near-infrared (NIR) imaging and histology. Synovium SDF-1α and interleukin (IL)-17A immunostaining was performed. Serum was assayed for SDF-1α and 29 other cytokines. RESULTS: In Part 1, there was a significant increase in MSC concentration and synovial fluid SDF-1α in Rupture. No differences in cartilage biomarkers were observed. In Part 2, Rupture had significantly higher NIR signal at 24, 48, and 72 h, indicating active recruitment of MSCs to the injured joint. Ex vivo cell tracking demonstrated MSC localization in the synovium and myotendinous junction (MTJ) of the quadriceps. Injured synovia exhibited increased synovitis grade and higher degree of IL-17A and SDF-1α immunostaining. CONCLUSION: ACL rupture induced peripheral blood mobilization of MSCs and migration of intravenously-injected allogenic MSCs to the injured joint, where they localized in the synovium and quadriceps MTJ.

Neutral Silicon-Vacancy Center in Diamond: Spin Polarization and Lifetimes.

We demonstrate optical spin polarization of the neutrally charged silicon-vacancy defect in diamond (SiV^{0}), an S=1 defect which emits with a zero-phonon line at 946 nm. The spin polarization is found to be most efficient under resonant excitation, but nonzero at below-resonant energies. We measure an ensemble spin coherence time T_{2}>100 µs at low-temperature, and a spin relaxation limit of T_{1}>25 s. Optical spin-state initialization around 946 nm allows independent initialization of SiV^{0} and NV^{-} within the same optically addressed volume, and SiV^{0} emits within the telecoms down-conversion band to 1550 nm: when combined with its high Debye-Waller factor, our initial results suggest that SiV^{0} is a promising candidate for a long-range quantum communication technology.

The effect of foraging and ontogeny on the prevalence and intensity of the invasive parasite Anguillicola crassus in the European eel Anguilla anguilla.

Infection patterns of the invasive Anguillicola crassus nematode were investigated in a population of the European eel Anguilla anguilla where parasite invasion is very recent, Loch Lomond, Scotland. Intensity levels of the parasite were associated with differences in fish ontogeny and trophic ecology. Although eels foraged on both fish and invertebrates, individuals which were smaller and fed on invertebrates (>70% contribution to diet) were found to contain a greater number of swim bladder parasites compared to larger eel with a predominance of fish (>60% contribution) in their diet. Within affected fish, a significant negative relationship was found between fish length and parasite intensity, with smaller individuals having higher parasite intensity than larger individuals. This study indicates that food intake and infection risk are linked in this recently infected host-parasite system. From a management perspective increasing our understanding of how infection intensity and repeated exposure is linked to resource use in an ecosystem is important for the future management of this endangered species in Europe.

Surface roughness and thickness analysis of contrast-enhanced articular cartilage using mesh parameterization.

OBJECTIVE: Articular cartilage (AC) morphology is an important metric for characterizing degeneration. We propose a novel morphologic analysis using mesh parameterization, enabling the use of surface roughness and thickness metrics to characterize degeneration in a rodent model of post-traumatic osteoarthritis. METHODS: Six rats underwent anterior cruciate ligament transection (ACL-T) and six were controls (Control). At 4-weeks, femora and tibiae were harvested and imaged using contrast-enhanced micro-computed tomography (µCT). Cartilage surfaces were manually outlined, and 2-dimensional thickness maps were generated using mesh parameterization and analyzed by thickness and surface roughness (Sa). The parameterization technique was validated against the direct distance transform (DDT) and histologic AC thickness from sagittal Safranin-O/Fast-Green sections. Parameterization and DDT measurements were also validated using known, virtual shapes with zero, one, and two planes of curvature. RESULTS: Parameterization had 0.00-6.26% error and DDT had 5.06-12.02% error in determining thicknesses of known shapes. Parameterization thickness correlated highly to DDT thickness (femur: r = 0.978, P < 0.001; tibia: r = 0.992, P < 0.001) and histologic thickness (femur: r = 0.952, P < 0.001; tibia: r = 0.959, P < 0.001). Thickness maps enabled visualization and quantification of AC degeneration. ACL-T samples displayed general thickening of cartilage, with adjacent regions of thickening and thinning on the medial femoral condyle. Compared to Control, ACL-T thickness was higher in the whole femur, whole tibia, and all compartments and sub-compartments. Sa was higher in the whole femur and medial and lateral condyle, and the whole tibia and medial and lateral plateau. The largest increases in Sa were observed on the medial femoral condyle. CONCLUSIONS: Cartilage analysis using parameterization effectively characterized early degeneration in AC, including sub-compartmental thickening/thinning, and is a powerful tool for assessing degeneration in preclinical osteoarthritis.

Articular cartilage degeneration following anterior cruciate ligament injury: a comparison of surgical transection and noninvasive rupture as preclinical models of post-traumatic osteoarthritis.

OBJECTIVE: Post-traumatic osteoarthritis (PTOA) is commonly studied using animal models. Surgical ACL transection is an established model, but noninvasive models may mimic human injury more closely. The purpose of this study was to quantify and compare changes in 3D articular cartilage (AC) morphology following noninvasive ACL rupture and surgical ACL transection. METHODS: Thirty-six rats were randomized to uninjured control, noninvasive ACL rupture (Rupture), and surgical ACL transection (Transection), and 4 and 10 week time points (n = 6 per group). Contrast-enhanced micro-computed tomography (CE-µCT) was employed for AC imaging. Femoral and tibial AC were segmented and converted into thickness maps. Compartmental and sub-compartmental AC thickness and surface roughness (Sa) were computed. OARSI histologic scoring was performed. RESULTS: In both injury groups, zones of adjacent thickening and thinning were evident on the medial femoral condyle, along with general thickening and roughening of femoral and tibial AC. The posterior tibia exhibited drastic thickening and surface degeneration, and this was worse in Transection. Both injury groups had increased AC thickness and Sa compared to Control at both time points, and Transection exhibited significantly higher Sa in every tibial compartment compared to Rupture. Histologic score was elevated in both groups, and the medial femur exhibited the most severe histologic degeneration. CONCLUSIONS: This is the first 3D quantification of preclinical AC remodeling after ACL injury. Both injury models induced similar changes in AC morphology, but Transection exhibited higher tibial Sa and a greater degree of posterior tibial degeneration. We conclude that AC degeneration is a time-, compartment-, and injury-dependent cascade.

Subchondral and epiphyseal bone remodeling following surgical transection and noninvasive rupture of the anterior cruciate ligament as models of post-traumatic osteoarthritis.

OBJECTIVE: Animal models are frequently used to study post-traumatic osteoarthritis (PTOA). A common anterior cruciate ligament (ACL) injury model is surgical transection, which may introduce confounding factors from surgery. Noninvasive models could model human injury more closely. The purpose of this study was to compare subchondral and epiphyseal trabecular bone remodeling after surgical transection and noninvasive rupture of the ACL. METHODS: Thirty-six rats were randomized to an uninjured control, surgical transection (Transection), or noninvasive rupture (Rupture). Animals were randomized to 4 or 10 week time points (n = 6 per group). Micro computed tomography (µCT) imaging was performed with an isotropic voxel size of 12 µm. Subchondral and epiphyseal bone was segmented semi-automatically, and morphometric analysis was performed. RESULTS: Transection caused a greater decrease in subchondral bone volume fraction (BV/TV) than Rupture in the femur and tibia. Rupture had greater subchondral bone tissue mineral density (TMD) at 4 and 10 weeks in the femur and tibia. Subchondral bone thickness (SCB.Th) was decreased in the femur in Transection only. Epiphyseal BV/TV was decreased in Transection only, and Rupture exhibited increased femoral epiphyseal TMD compared to both Control and Transection. Rupture exhibited greater femoral epiphyseal trabecular thickness (Tb.Th.) compared to Control and Transection at 4 weeks, and both Rupture and Transection had increased femoral epiphyseal Tb.Th. at 10 weeks. Epiphyseal trabecular number (Tb.N) was decreased in both injury groups at both time points. Femoral and tibial epiphyseal structure model index (SMI) increased in both groups. CONCLUSIONS: The two injury models cause differences in post-injury bone morphometry, and surgical transection may be introducing confounding factors that affect downstream bony remodeling.

Strain Discontinuity, Avalanche, and Memory in Carbon Nanotube Serpentine Systems.

This work addresses the problem of how a nano-object adheres to a supporting media. The case of study are the serpentine-like structures of single-wall carbon nanotubes (SWNTs) grown on vicinal crystalline quartz. We develop in situ nanomanipulation and confocal Raman spectroscopy in such systems, and to explain the results, we propose a dynamical equation in which static friction is treated phenomenologically and implemented as cutoff for velocities, via Heaviside step function and an adhesion force tensor. We demonstrate that the strain profiles observed along the SWNTs are due to anisotropic adhesion, adhesion discontinuities, strain avalanches, and memory effects. The equation is general enough to make predictions for various one- and two-dimensional nanosystems adhered to a supporting media.

Does size matter? A test of size-specific mortality in Atlantic salmon Salmo salar smolts tagged with acoustic transmitters.

Mortality rates of wild Atlantic salmon Salmo salar smolts implanted with acoustic transmitters were assessed to determine if mortality was size dependent. The routinely accepted, but widely debated, '2% transmitter mass: body mass' rule in biotelemetry was tested by extending the transmitter burden up to 12·7% of body mass in small [mean fork length (LF ) 138·3 mm, range 115-168 mm] downstream migrating S. salar smolts. Over the short timescale of emigration (range 11·9-44·5 days) through the lower river and estuary, mortality was not related to S. salar size, nor was a relationship found between mortality probability and transmitter mass: body mass or transmitter length: LF ratios. This study provides further evidence that smolt migration studies can deviate from the '2% rule' of thumb, to more appropriate study-specific measures, which enables the use of fishes representative of the body size in natural populations without undue effects.

Freshwater and coastal migration patterns in the silver-stage eel Anguilla anguilla.

The unimpeded downstream movement patterns and migration success of small female and male Anguilla anguilla through a catchment in north-west Europe were studied using an acoustic hydrophone array along the River Finn and into the Foyle Estuary in Ireland. Twenty silver-stage A. anguilla (total length, LT , range: 332-520 mm) were trapped 152 km upstream from a coastal marine sea-lough outlet and internally tagged with acoustic transmitters of which 19 initiated downstream migration. Migration speed was highly influenced by river flow within the freshwater (FW) compartment. Anguilla anguilla activity patterns were correlated with environmental influences; light, tidal direction and lunar phase all influenced the initiation of migration of tagged individuals. Migration speed varied significantly between upstream and lower river compartments. Individuals migrated at a slower speed in transitional water and sea-lough compartments compared with the FW compartment. While 88·5% survival was recorded during migration through the upper 121 km of the river and estuary, only 26% of A. anguilla which initiated downstream migration were detected at the outermost end of the acoustic array. Telemetry equipment functioned efficiently, including in the sea-lough, so this suggests high levels of mortality during sea-lough migration, or less likely, long-term sea-lough residence by silver A. anguilla emigrants. This has important implications for eel management plans.