Reliability of ultrasound speckle tracking with singular value decomposition for quantifying displacement in the carpal tunnel

Inhibited movement patterns of carpal tunnel structures have been found in carpal tunnel syndrome (CTS) patients. Motion analysis on ultrasound images allows us to non-invasively study the (relative) movement of carpal tunnel structures and recently a speckle tracking method using singular value decomposition (SVD) has been proposed to optimize this tracking. This study aims to assess the reliability of longitudinal speckle tracking with SVD in both healthy volunteers and patients with CTS.Images from sixteen healthy volunteers and twenty-two CTS patients were used. Ultrasound clips of the third superficial flexor tendon and surrounding subsynovial connective tissue (SSCT) were acquired during finger flexion-extension. A custom made tracking algorithm was used for the analysis. Intra-class correlation coefficients (ICCs) were calculated using a single measure, two-way random model with absolute agreement and Bland-Altman plots were added for graphical representation.ICC values varied between 0.73 and 0.95 in the control group and 0.66–0.98 in the CTS patients, with the majority of the results classified as good to excellent. Tendon tracking showed higher reliability values compared to the SSCT, but values between the control and CTS groups were comparable.Speckle tracking with SVD can reliably be used to analyze longitudinal movement of anatomical structures with different sizes and compositions within the context of the carpal tunnel in both a healthy as well as a pathological state. Based on these results, this technique also holds relevant potential for areas where ultrasound based dynamic imaging requires quantification of motion.     

Development of a novel MATLAB-based framework for implementing mechanical joint stability constraints within OpenSim musculoskeletal models

The Static Optimization (SO) solver in OpenSim estimates muscle activations and forces that only equilibrate applied moments. In this study, SO was enhanced through an open-access MATLAB interface, where calculated muscle activations can additionally satisfy crucial mechanical stability requirements. This Stability-Constrained SO (SCSO) is applicable to many OpenSim models and can potentially produce more biofidelic results than SO alone, especially when antagonistic muscle co-contraction is required to stabilize body joints. This hypothesis was tested using existing models and experimental data in the literature. Muscle activations were calculated by SO and SCSO for a spine model during two series of static trials (i.e. simulation 1 and 2), and also for a lower limb model (supplementary material 2). In simulation 1, symmetric and asymmetric flexion postures were compared, while in simulation 2, various external load heights were compared, where increases in load height did not change the external lumbar flexion moment, but necessitated higher EMG activations. During the tasks in simulation 1, the predicted muscle activations by SCSO demonstrated less average deviation from the EMG data (6.8% −7.5%) compared to those from SO (10.2%). In simulation 2, SO predicts constant muscle activations and forces, while SCSO predicts increases in the average activations of back and abdominal muscles that better match experimental data. Although the SCSO results are sensitive to some parameters (e.g. musculotendon stiffness), when considering the strategy of the central nervous system in distributing muscle forces and in activating antagonistic muscles, the assigned activations by SCSO are more biofidelic than SO.     

Identification of assembly precursors to photosystems emitting fluorescence at 683 nm and 687 nm by cryogenic fluorescence microspectroscopy

Photosystem I (PSI) and photosystem II (PSII) play key roles in photoinduced electron-transfer reaction in oxygenic photosynthesis. Assemblies of these PSs can be initiated by illumination of the etiolated seedlings (greening). The study aimed to identify specific fluorescence spectral components relevant to PSI and PSII assembly intermediates emerging in greening seedlings of Zea mays, a typical C4 plant. The different PSII contents between the bundle sheath (BS) and mesophyll (M) cells were utilized to spectrally isolate the precursors to PSI and PSII. The greening Zea mays leaf thin sections were observed with the cryogenic microscope combined with a spectrometer. With the aid of the singular-value decomposition analysis, we could identify four independent fluorescent species, SAS677, SAS685, SAS683, and SAS687, named after their fluorescence peak wavelengths. SAS677 and SAS685 are the dominant components after the 30-minute greening, and the distributions of these components showed no clear differences between M and BS cells, indicating immature cell differentiation in this developing stage. On the other hand, the 1-hour greening resulted in reduced distributions of SAS683 in BS cells leading us to assign this species to PSII precursors. The 2-hour greening induced the enrichment of SAS687 in BS cells suggesting its PSI relevance. Similarity in the peak wavelengths of SAS683 and the reported reaction center of PSII implied their connection. SAS687 showed an intense sub-band at around 740 nm, which can be assigned to the emission from the red chlorophylls specific to the mature PSI.     

Molecular Modelling reveals the inhibition mechanism and structure–activity relationship of curcumin and its analogues to Staphylococcal aureus Sortase A

Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182 and ILE-199 are key residues in Sortase A-inhibitor complexes. Furthermore, interactions between the methoxyl group on the benzene ring in the conjugated molecule (curcumin, demethoxycurcumin, bisdemethoxycurcumin) and VAL-168, LEU-169 and GLN-172 induce the inhibitory activity based on the energy decomposition and distance analyses between the whole residues and inhibitors. However, because of its coiled structure, the non-conjugated molecule, tetrahydrocurcumin, with key residues in the binding sites of Sortase A, interacted weakly with SrtA, leading to the loss of inhibitory activity. Based on these results, the methoxyl group on the benzene ring in the conjugated molecule largely influenced the inhibitory activity of the Sortase A inhibitors.     

Study on the Decomposition of Pistia stratiotes L. (Araceae) in Cisne Reservoir,Uruguay

A study on the decomposition process of Pistia stratiotes L. was carried out in Cisne Reservoir, Uruguay. For this purpose, leaves and roots were considered separately, and the process was studied in the littoral and the pelagic zone. The litter bag technique was used to estimate dry weight losses at different times. Leaves decomposed faster than roots in both zones. Pistia decomposed faster in the pelagic zone due to better oxygen conditions and a more intensive water movement that removes material from within the bags. Phosphorus, potassium, sodium and magnesium were leached rapidly during the first week. Nitrogen content in the leaves initially increased, reaching its maximum in the littoral zone that coincided with that of bacterial numbers colonizing the litter. The number of macroinvertebrates, dominated by Chironomidae, was low. A rough estimation of the phosphorus impact on the littoral zone associated to the decomposition process shows that after 24 h between 13.9 and 16.8 μg-at.1⁻¹ have been released to the water.     

Functional differences in scavenger communities and the speed of carcass decomposition

Carcass decomposition largely depends on vertebrate scavengers. However, how behavioral differences between vertebrate scavenger species, the dominance of certain species, and the diversity of the vertebrate scavenger community affect the speed of carcass decomposition is poorly understood. As scavenging is an overlooked trophic interaction, studying the different functional roles of vertebrate species in the scavenging process increases our understanding about the effect of the vertebrate scavenger community on carcass decomposition. We used motion‐triggered infrared camera trap footages to profile the behavior and activity of vertebrate scavengers visiting carcasses in Dutch nature areas. We grouped vertebrate scavengers with similar functional roles. We found a clear distinction between occasional scavengers and more specialized scavengers, and we found wild boar (Sus scrofa) to be the dominant scavenger species in our study system. We showed that these groups are functionally different within the scavenger community. We found that overall vertebrate scavenger diversity was positively correlated with carcass decomposition speed. With these findings, our study contributes to the understanding about the different functional roles scavengers can have in ecological communities.     

Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations

A subnanomolar inhibitor of human immunodeficiency virus type 1 (HIV-1) protease, designated QF34, potently inhibits the wild-type and drug-resistant enzyme. To explain its broad activity, the binding of QF34 to the wild-type HIV-1 protease is investigated by molecular dynamics simulations and compared to the binding of two inhibitors that are used clinically, saquinavir (SQV) and indinavir (IDV). Analysis of the flexibility of protease residues and inhibitor segments in the complex reveals that segments of QF34 were more mobile during the dynamics studies than the segments of SQV and IDV. The dynamics of hydrogen bonding show that QF34 forms a larger number of stable hydrogen bonds than the two inhibitors that are used clinically. Absolute binding free energies were calculated with molecular mechanics-generalized Born surface area (MM-GBSA) methodology using three protocols. The most consistent results were obtained using the single-trajectory approach, due to cancellation of errors and inadequate sampling in the separate-trajectory protocols. For all three inhibitors, energy components in favor of binding include van der Waals and electrostatic terms, whereas polar solvation and entropy terms oppose binding. Decomposition of binding energies reveals that more protease residues contribute significantly to the binding of QF34 than to the binding of SQV and IDV. Moreover, contributions from protease main chains and side chains are balanced in the case of QF34 (52:48 ratio, respectively), whereas side chain contributions prevail in both SQV and IDV (main-chain:side-chain ratios of 41:59 and 45:55, respectively). The presented results help explain the ability of QF34 to inhibit multiple resistant mutants and should be considered in the design of broad-specificity second-generation HIV-1 protease inhibitors.     

Extracting Wave Structure from Biological Data with Application to Responses in Turtle Visual Cortex

Waves have long been thought to be a fundamental mechanism for communicating information within a medium and are widely observed in biological systems. However, a quantitative analysis of biological waves is confounded by the variability and complexity of the response. This paper proposes a robust technique for extracting wave structure from experimental data by calculating "wave subspaces" from the KL decomposition of the data set. If a wave subspace contains a substantial portion of the data set energy during a particular time interval, one can deduce the structure of the wave and potentially isolate its information content. This paper uses the wave subspace technique to extract and compare wave structure in data from three different preparations of the turtle visual cortex. The paper demonstrates that wave subspace caricatures from the three cortical preparations have qualitative similarities. In the numerical model, where information about the underlying dynamics is available, wave subspace landmarks are related to activation and changes in behavior of other dynamic variables besides membrane potential.     

Test–Retest Reliability of Static EMG Scan Configural Profiling

Measurement techniques or instruments are typically evaluated along the dimensions of reliability and validity. The focus of this investigation was to assess the test–retest reliability of a static EMG scan profile (sESP) method using 64 chronic pain participants. The test–retest interval was 30–33 days. Reliability coefficients were expressed using the Profile Similarity Coefficient (r _p) in place of the more traditional Pearson Product Moment Correlation. sESP reliabilities were calculated for posture laterality for the head and neck, back, and overall profiles (head, neck, and back combined). The reliability coefficients ranged from .57 to .80. The back profile was the least reliable with a range of .55–.59 whereas the overall profiles were the most reliable, .78–.80. The analysis method was judged to be very conservative with its use of r _p, a protracted intertest interval period, and weighting the data by their variances. These results can be viewed as setting the lower reliability limit for sESP.     

Biobehavioral Intervention for Older Adults Coping with Essential Tremor

Four questions were addressed: (a) does biobehavioral intervention result in within-session reduction of tremor severity; (b) do relaxation and electromyographic (EMG) biofeedback training produce differential effects; (c) do within-session treatment effects generalize to daily performance; and (d) are reductions in tremor severity maintained at follow-up assessment? Three adults, ages 51, 77, and 83, each with a diagnosis of essential tremor (ET), and a long standing history of tremor of the hands uncontrolled by medication, took part. A repeated pre–post-training single-case experimental design embedded within a sequential A–B–C–D design was used; in addition, 1 participant received a return to the B phase. Outcome measures included within-session clinical and self-ratings of tremor severity, surface electromyography (sEMG) of forearm muscles, and daily self-ratings of tremor at home. Tremor was measured while participants engaged in eating or drinking tasks. The Behavioral Relaxation Scale (BRS) served as a process measure to assess relaxation proficiency. Clinical ratings of tremor and the BRS had high interobserver agreement. Visual inspection and statistical tests of single-case data were used to evaluate outcomes. Each participant showed significant within-session improvements on various measures of tremor and improvement during intervention as compared to baseline phases. There were no clear-cut differences between relaxation and biofeedback phases. Improvements declined somewhat at a 12-week follow-up. Relationships among measures of tremor are discussed. Biobehavioral interventions hold promise for older adults coping with ET. Further research is needed using an array of biobehavioral measures to assess intervention outcome.