Unveiling success determinants for AMB-assisted phase expansion of fusion proteins in ARP/wARP.

Fusion proteins (FPs) are frequently utilized as a biotechnological tool in the determination of macromolecular structures using X-ray methods. Here, we explore the use of different protein tags in various FP, to obtain initial phases by using them in a partial molecular replacement (MR) and constructing the remaining FP structure with ARP/wARP. Usually, the tag is removed prior to crystallization, however leaving the tag on may facilitate crystal formation, and structural determination by expanding phases from known to unknown segments of the complex. In this study, the Protein Data Bank was mined for an up-to-date list of FPs with the most used protein tags, Maltose Binding Protein (MBP), Green Fluorescent Protein (GFP), Thioredoxin (TRX), Glutathione transferase (GST) and the Small Ubiquitin-like Modifier Protein (SUMO). Partial MR using the protein tag, followed by automatic model building, was tested on a subset of 116 FP. The efficiency of this method was analyzed and factors that influence the coordinate construction of a substantial portions of the fused protein were identified. Using MBP, GFP, and SUMO as phase generators it was possible to build at least 75 % of the protein of interest in 36 of the 116 cases tested. Our results reveal that tag selection has a significant impact; tags with greater structural stability, such as GFP, increase the success rate. Further statistical analysis identifies that resolution, Wilson B factor, solvent percentage, completeness, multiplicity, protein tag percentage in the FP (considering amino acids), and the linker length play pivotal roles using our approach. In cases where a structural homologous is absent, this method merits inclusion in the toolkit of protein crystallographers.

Development of a Novel Energy Saving and Environmentally Friendly Starch via a Graft Copolymerization Strategy for Efficient Warp Sizing and Easy Removal.

Warp sizing is a key process in textile production. However, before the yarn/fabric finishing, such as dyeing, the paste adhering to the warp must be eliminated to ensure optimal dyeing properties and the flexibility of the fabric. Therefore, the sizing will often consume a lot of energy and produce a lot of industrial wastewater, which will cause serious harm to the environment. In this study, we have developed an energy saving and environmentally friendly starch-based slurry by modifying natural starch with acrylamide. The paste has excellent viscosity stability and fiber adhesion, and exhibits excellent performance during warp sizing. In addition, the slurry has good water solubility at 60-70 °C, so it is easy to desize at low temperatures. Because of this, the sizing of the warp can be deslimed directly from the yarn during subsequent washing processes. This work can not only reduce some costs for the textile industry, but also achieve the purpose of energy conservation and emission reduction.

Dynamic time warp analysis of individual symptom trajectories in individuals with bipolar disorder.

BACKGROUND: Manic and depressive mood states in bipolar disorder (BD) may emerge from the non-linear relations between constantly changing mood symptoms exhibited as a complex dynamic system. Dynamic Time Warp (DTW) is an algorithm that may capture symptom interactions from panel data with sparse observations over time. METHODS: The Young Mania Rating Scale and Quick Inventory of Depressive Symptomatology were repeatedly assessed in 141 individuals with BD, with on average 5.5 assessments per subject every 3-6 months. Dynamic Time Warp calculated the distance between each of the 27 × 27 pairs of standardized symptom scores. The changing profile of standardized symptom scores of BD participants was analyzed in individual subjects, yielding symptom dimensions in aggregated group-level analyses. Using an asymmetric time-window, symptom changes that preceded other symptom changes (i.e., Granger causality) yielded a directed network. RESULTS: The mean age of the BD participants was 40.1 (SD 13.5) years old, and 60% were female participants. Idiographic symptom networks were highly variable between subjects. Yet, nomothetic analyses showed five symptom dimensions: core (hypo)mania (6 items), dysphoric mania (5 items), lethargy (7 items), somatic/suicidality (6 items), and sleep (3 items). Symptoms of the "Lethargy" dimension showed the highest out-strength, and its changes preceded those of "somatic/suicidality," while changes in "core (hypo)mania" preceded those of "dysphoric mania." CONCLUSION: Dynamic Time Warp may help to capture meaningful BD symptom interactions from panel data with sparse observations. It may increase insight into the temporal dynamics of symptoms, as those with high out-strength (rather than high in-strength) could be promising targets for intervention.

Muscle forces acting on the greater trochanter lead to a dorsal warping of the apophyseal growth plate.

The apophyseal growth plate of the greater trochanter, unlike most other growth plates of the human body, exhibits a curved morphology that results in a divergent pattern resembling an open crocodile mouth on plain antero-posterior radiographs. To quantify the angular alignment of the growth plate and to draw conclusions about the function of the muscles surrounding it, we analyzed 57 MRI images of 51 children and adolescents aged 3-17 years and of six adults aged 18-52 years. We measured the angulation of the plate relative to the horizontal plane (AY angle) and the trajectories of the muscles attaching to the greater trochanter of the proximal femur. From anterior to posterior, the AY angle shows a decrease of 33.44°. In the anterior third, the cartilage is angled at a mean of 51.64°, and in the posterior third, the mean angulation is 18.6°. This indicates that the cartilage in the anterior region of the greater trochanteric apophysis is subject to more vertically oriented force vectors compared to the posterior region, as the growth plates align perpendicular to the force vectors acting on them. Combining the measured muscle trajectories with the physiological cross-sectional areas (PCSA) available from the literature revealed that, in addition to the known internal and external lateral traction ligament systems, a third, dorsally located traction ligament system exists that may be responsible for the dorsal deformation of the AY angle.

Breaking the cycle: Identifying key symptom pathways of eating disorders and the influence of childhood maltreatment.

BACKGROUND: Most network analyses on central symptoms in eating disorders (EDs) have been cross-sectional. Longitudinal within-person analyses of therapy processes are scarce. Our aim was to investigate central change processes in therapy in a transdiagnostic sample, considering the influence of childhood maltreatment. METHOD: We employed dynamic time warping analyses to identify clusters of symptoms that tended to change similarly across therapy on a within-person level. Symptoms were measured by a 28-item Eating Disorder Examination Questionnaire (EDE-Q). Furthermore, we examined the temporal direction of symptom change to identify symptoms that tended to precede and predict other symptoms. Finally, we estimated two directed, temporal networks in patients with and without a history of childhood maltreatment. RESULTS: Our analysis included 122 ED patients (mean age = 30.9, SD = 9.7; illness duration = 14.2 years, SD = 8.9; prior treatment = 5.6 years, SD = 5.1). The initial network revealed three robust clusters of symptoms over time: (1) ED behavior, (2) inhibition, and (3) cognitions and feelings about body and weight. Overvaluation of shape had the highest out-strength preceding and predicting other symptoms. Dissatisfaction with weight preceded and predicted other symptoms in the maltreatment network. The non-maltreatment network showed a similar structure to the transdiagnostic network. CONCLUSION: Targeting and monitoring feelings and cognitions related to shape may be crucial for achieving lasting symptom improvement in a transdiagnostic sample. Furthermore, our findings highlight the need for further investigation into the different processes driving EDs based on maltreatment status. PUBLIC SIGNIFICANCE: There is limited understanding of the processes that occur for patients with eating disorders between admission and discharge in therapy, especially for patients with a history of childhood maltreatment. Our analyses suggest that changes in cognitions regarding shape precede and predict changes in cognitions about weight. Different processes may be driving the eating disorder according to maltreatment status, which might further illuminate the riddle of dropout and relapse in therapy for patients with a history of childhood maltreatment. These findings suggest the need for further investigation into the specific dynamics occurring during therapy for individuals with a history of childhood maltreatment.

Performance and Quality Comparison of Movie Alignment Software for Cryogenic Electron Microscopy.

Cryogenic electron microscopy (Cryo-EM) has been established as one of the key players in structural biology. It can reconstruct a 3D model of a sample at a near-atomic resolution. With the increasing number of facilities, faster microscopes, and new imaging techniques, there is a growing demand for algorithms and programs able to process the so-called movie data produced by the microscopes in real time while preserving a high resolution and maximal information. In this article, we conduct a comparative analysis of the quality and performance of the most commonly used software for movie alignment. More precisely, we compare the most recent versions of FlexAlign (Xmipp v3.23.03), MotionCor2 (v1.6.4), Relion MotionCor (v4.0-beta), Warp (v1.0.9), and CryoSPARC (v4.0.3). We tested the quality of the alignment using generated phantom data, as well as real datasets, comparing the alignment precision, power spectra density, and performance scaling of each program.

3D Textiles Based on Warp Knitted Fabrics: A Review.

Fibre-reinforced composites (FRCs) are already well established in several industrial sectors such as aerospace, automotive, plant engineering, shipbuilding and construction. The technical advantages of FRCs over metallic materials are well researched and proven. The key factors for an even wider industrial application of FRCs are the maximisation of resource and cost efficiency in the production and processing of the textile reinforcement materials. Due to its technology, warp knitting is the most productive and therefore cost-effective textile manufacturing process. In order to produce resource-efficient textile structures with these technologies, a high degree of prefabrication is required. This reduces costs by reducing the number of ply stacks, and by reducing the number of extra operations through final path and geometric yarn orientation of the preforms. It also reduces waste in post-processing. Furthermore, a high degree of prefabrication through functionalisation offers the potential to extend the application range of textile structures as purely mechanical reinforcements by integrating additional functions. So far, there is a gap in terms of an overview of the current state-of-the-art of relevant textile processes and products, which this work aims to fill. The focus of this work is therefore to provide an overview of warp knitted 3D structures.

Exact distributed kinetic Monte Carlo simulations for on-lattice chemical kinetics: lessons learnt from medium- and large-scale benchmarks.

Kinetic Monte Carlo (KMC) simulations have been instrumental in multiscale catalysis studies, enabling the elucidation of the complex dynamics of heterogeneous catalysts and the prediction of macroscopic performance metrics, such as activity and selectivity. However, the accessible length- and time-scales have been a limiting factor in such simulations. For instance, handling lattices containing millions of sites with 'traditional' sequential KMC implementations is prohibitive owing to large memory requirements and long simulation times. We have recently established an approach for exact, distributed, lattice-based simulations of catalytic kinetics which couples the Time-Warp algorithm with the Graph-Theoretical KMC framework, enabling the handling of complex adsorbate lateral interactions and reaction events within large lattices. In this work, we develop a lattice-based variant of the Brusselator system, a prototype chemical oscillator pioneered by Prigogine and Lefever in the late 60s, to benchmark and demonstrate our approach. This system can form spiral wave patterns, which would be computationally intractable with sequential KMC, while our distributed KMC approach can simulate such patterns 15 and 36 times faster with 625 and 1600 processors, respectively. The medium- and large-scale benchmarks thus conducted, demonstrate the robustness of the approach, and reveal computational bottlenecks that could be targeted in further development efforts. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

A research of the respiratory status detection method measured by abdominal rise and fall.

Respiratory activity is the most important basic life activity of human body, respiratory state detection is of great practical significance. Based on the characteristic of high correlation between the change of tidal volume and the change of abdominal displacement, a method of detecting respiratory status through abdominal displacement data is proposed. The method uses a gas pressure sensor to collect the tidal volume in the steady state of the subject once, which is used as the baseline data. The abdominal displacement data of the subject in the three breathing states of slow breathing, steady breathing and rapid breathing were collected with an acceleration sensor. The warp path distance between the lung and abdominal data in the three different states was calculated, this warp path distance together with the period extracted from the abdominal data is used as a two-dimensional feature and input to the support vector machine classifier. The experiments show that the accuracy of the classification results reaches 90.23%. The method only needs to measure the lung data once in smooth breathing state, and the subsequent continuous detection is achieved by measuring the displacement of the abdomen only. This method has the advantages of stable and reliable acquisition results, low implementation cost and simplified wearing method, and has high practicality.

Comparative Analysis of Facial Coloration between Introduced and Source Populations of the Red Wood Ant Formica paralugubris.

The variation in the typical black-reddish color of red wood ants (Formica rufa group) has been recently suggested as a good indicator of habitat quality, being dependent on environmental conditions. However, the relative contribution of external factors and heritability in shaping this trait is poorly investigated. In this study, we compared the facial coloration of workers from four introduced populations of Formica paralugubris with those of the two Alpine populations from which they had been taken. We used a Relative Warp Analysis to describe the variations in the shape of this trait. We expected each introduced population to be more similar to its population of origin if the color pattern was predominantly genetically determined. On the contrary, due to the considerable differences in habitat type and climate between the Alps and the Apennines, we expected to observe differences between the introduced population and their origin population if the coloration was mostly environmentally determined. With one exception that we discuss, the results showed that ants from the two source populations had different phenotypes, and that the introduced populations had a shape similar to the population of origin, suggesting a stable genetic background. Surprisingly, the habitat type seems to have a less clear effect, even if within-population differences suggest the influence of very localized environmental factors. Finally, we found that the facial coloration shape is affected by the ant's size, a result in line with previous studies.

Eating disorder psychopathology dimensions based on individual co-occurrence patterns of symptoms over time: a dynamic time warp analysis in a large naturalistic patient cohort.

PURPOSE: Most of the network approaches in eating disorders found the highest degree of centrality for symptoms related to weight and shape concerns. However, longitudinal analyses are scarce and may increase our insight of the complex characteristics and dynamics over time. In the current study, an alternative non-linear method to perform longitudinal network analyses, the dynamic time warp approach, was used to examine whether robust dimensions of eating disorder psychopathology symptoms could be found based on the individual dynamic interplay of eating disorder symptoms co-occurrence patterns in time. METHODS: The study sample included a naturalistic cohort of patients (N = 255) with all eating disorder subtypes who were assessed with the eating disorder examination questionnaire (EDE-Q) at a minimum of four times during treatment. Dynamic time warp analyses yielded distance matrices within each individual patient, which were subsequently aggregated into symptom networks and dimensions at the group level. RESULTS: Aggregation of the individual distance matrices at the group level yielded four robust symptom dimensions: 1. restraint/rules, 2. secret eating/fasting, 3. worries/preoccupation, and 4. weight and shape concern. The items 'fear of weight gain' and 'guilt' were bridge symptoms between the dimensions 1, 3 and 4. CONCLUSION: Dynamic time warp could capture the within-person dynamics of eating disorder symptoms. Sumscores of the four dimensions could be used to follow patients over time. This approach could be applied in the future to visualize eating disorder symptom dynamics and signal the central symptoms within an individual and groups of patients. LEVEL OF EVIDENCE: Level III: evidence obtained from well-designed cohort or case-control analytic studies. .

Study on Flexural Behaviour of Ferrocement Composites Reinforced with Polypropylene Warp Knitted Fabric.

Ferrocement is a cost-effective construction material used in the low-cost constructions. It is produced with the combination of cement mortar with closely spaced wire mesh known as chicken wire mesh. Ferrocement process eliminates coarse aggregates when compared to reinforced concrete thus makes the process simple. This paper deals with the influence of various characteristics of warp knitted fabric on the flexural properties of ferrocement composites. Ferrocement composites have a wide range of applications in the construction industry and it has some limitations due to the durability issues. Among the various durability issues, corrosion is one of the main issues to be addressed to enhance the long-term service life of the ferrocement composites. The idea of using non-metallic mesh to eliminate the corrosion problem is discussed in this paper. In this experiment, warp knitted fabric reinforced ferrocement composites were produced using polypropylene warp knitted fabrics. This paper deals with the flexural properties of ferrocement composites made of warp knitted fabric coated with expoxy. This paper deals with the flexural properties of ferrocement composites made of warp knitted fabric coated with expoxy. These composites were analyzed for their flexural strength, energy absorption and ductile property. The variables in the experiment are filament thickness, warp knitted structure and number of layers in the composites. Experimental results proved that the replacement of chicken mesh wire by warp knitted fabrics has an impact in the flexural properties of the composites and the effect of variables in the experiment set up has been analyzed. There is an imporvement of 200% is observed in the first crack load and 120% improvement in the ultimate load of the warp knit fabric reinforced composite compared to control sample. Experimental results proved that there is an increase in flexural strength of ferrocement composites made up with warp knitted fabrics. Microstructure studies like SEM and EDX on ferrocement laminates confirmed good bonding between the mortar mix and warp knitted fabrics.

Network structure of time-varying depressive symptoms through dynamic time warp analysis in late-life depression.

OBJECTIVES: Late-life major depressive disorder (MDD) can be conceptualized as a complex dynamic system. However, it is not straightforward how to analyze the covarying depressive symptoms over time in case of sparse panel data. Dynamic time warping (DTW) analysis may yield symptom networks and dimensions both at the patient and group level. METHODS: In the Netherlands Study of Depression in Older People (NESDO) depressive symptoms were assessed every 6 months using the 30-item Inventory of Depressive Symptomatology (IDS) with up to 13 assessments per participant. Our sample consisted of 182 persons, aged ≥ 60 years, with an IDS total score of 26 or higher at baseline. Symptom networks dimensions, and centrality metrics were analyzed using DTW and Distatis analyses. RESULTS: The mean age was 69.8 years (SD 7.1), with 69.0% females, and a mean IDS score of 38.0 (SD = 8.7). DTW enabled visualization of an idiographic symptom network in a single NESDO participant. In the group-level nomothetic approach, four depressive symptom dimensions were identified: "core symptoms", "lethargy/somatic", "sleep", and "appetite/atypical". Items of the "internalizing symptoms" dimension had the highest centrality, whose symptom changes over time were most similar to those changes of other symptoms. CONCLUSIONS: DTW revealed symptom networks and dimensions based on the within-person symptom changes in older MDD patients. Its centrality metrics signal the most influential symptoms, which may aid personalized care.

Mechanical Behavior and Energy Dissipation of Woven and Warp-Knitted Pvc Membrane Materials under Multistage Cyclic Loading.

In order to study the mechanical behavior and energy dissipation of architectural membrane materials under multistage cyclic loading, the deformation behavior, energy dissipation, and damage characteristics of four kinds of warp-knitted and woven polyvinyl chloride (PVC) membrane materials were analyzed using multistage cyclic loading experiments. The results show that, compared with the uniaxial tensile strength, the peak values of the cyclic loading and unloading of the four material samples are lower in the warp direction but higher in the fill (weft) direction. Under multistage cyclic loading, the loading and unloading moduli of the warp knitting membrane increase with the increase in fabric density. At the same fabric density, the loading modulus and the unloading modulus are smaller than those of the warp knitting material. The total absorbed strain energy, elastic strain energy, and dissipation energy of the fill samples are higher than those of the warp samples at a low load level but lower than those at a high load level. PVC membrane materials' use strength should be controlled below a 15% stress level under long-term external force loading. In the cyclic loading process, the four PVC membrane materials are viscoelastic-plastic, so it is reasonable to define the damage variable based on the accumulation of plastic deformation.

PatchWarp: Corrections of non-uniform image distortions in two-photon calcium imaging data by patchwork affine transformations.

Complex distortions on calcium imaging often impair image registration accuracy. Here, we developed a registration algorithm, PatchWarp, to robustly correct slow image distortion for calcium imaging data. PatchWarp is a two-step algorithm with rigid and non-rigid image registrations. To correct non-uniform image distortions, it splits the imaging field and estimates the best affine transformation matrix for each of the subfields. The distortion-corrected subfields are stitched together like a patchwork to reconstruct the distortion-corrected imaging field. We show that PatchWarp robustly corrects image distortions of calcium imaging data collected from various cortical areas through glass window or gradient-index (GRIN) lens with a higher accuracy than existing non-rigid algorithms. Furthermore, it provides a fully automated method of registering images from different imaging sessions for longitudinal neural activity analyses. PatchWarp improves the quality of neural activity analyses and is useful as a general approach to correct image distortions in a wide range of disciplines.

Preparation of carboxymethyl cellulose nanofibers and their application in warp size of textile.

How to develop the warp sizing process with energy saving and emission reduction have been a problem for the textile sizing industry. In this work, a series of carboxymethyl cellulose nanofibers (CCNFs) with different degree of substitution (DS) were prepared from bleached eucalyptus kraft pulp, and their applications in warp size of textile were investigated in detail. AFM and TEM analyses confirmed that the prepared CCNFs were of nanoscale fibers. Zeta potential analysis showed that CCNFs aqueous dispersion had good stability. Response surface methodology was applied to optimize the high-count cotton warp sizing formula containing a small amount of CCNFs. It could be found that the optimized sizing formula still had much better sizing performance than that of the original sizing formula even if the sizing percentage and temperature were reduced. The results exhibited that CCNFs with DS of 0.38 had a potential industry application prospect as sizing auxiliary in pure cotton warp sizing, and the new developed sizing formula had the advantages of excellent sizing performance, environmental friendliness, energy saving and emission reduction.

Influence of head orientation and implantation site of a novel transcutaneous bone conduction implant on MRI metal artifact reduction sequence.

PURPOSE: The use of magnetic resonance imaging (MRI) is often limited in patients with auditory implants because of the presence of metallic components and magnets. The aim of this study was to evaluate the clinical usefulness of a customized MRI sequence for metal artifact suppression in patients with BONEBRIDGETM BCI 602 implants (MED-EL, Innsbruck, Austria), the successor of the BCI 601 model. METHODS: Using our in-house developed and customized metal artifact reduction sequence (SEMAC-VAT WARP), MRI artifacts were evaluated qualitatively and quantitatively. MRI sequences were performed with and without artifact reduction on two whole head specimens with and without the BCI 602 implant. In addition, the influence of two different implantation sites (mastoid versus retrosigmoid) and head orientation on artifact presence was investigated. RESULTS: Artifact volume was reduced by more than the 50%. Results were comparable with those obtained with the BCI 601, showing no significant differences in the dimensions of artifacts caused by the implant. CONCLUSION: SEMAC-VAT WARP was once more proved to be efficient at reducing metal artifacts on MR images. The dimensions of artifacts associated with the BCI 602 are not smaller than those caused by the BCI 601.

New classes of tests for the Weibull distribution using Stein's method in the presence of random right censoring.

We develop two new classes of tests for the Weibull distribution based on Stein's method. The proposed tests are applied in the full sample case as well as in the presence of random right censoring. We investigate the finite sample performance of the new tests using a comprehensive Monte Carlo study. In both the absence and presence of censoring, it is found that the newly proposed classes of tests outperform competing tests against the majority of the distributions considered. In the cases where censoring is present we consider various censoring distributions. Some remarks on the asymptotic properties of the proposed tests are included. We present another result of independent interest; a test initially proposed for use with full samples is amended to allow for testing for the Weibull distribution in the presence of censoring. The techniques developed in the paper are illustrated using two practical examples.

Rapid growth in the COVID-19 era.

ABSTRACT: From Operation Warp Speed to the lipid mRNA vaccine, the COVID-19 pandemic has been a watershed moment for technological development, production, and implementation. The scale and pace of innovation and global collaboration has likely not been experienced since World War II. This article highlights some of the engineering accomplishments that occurred during the pandemic. We provide a broad overview of the technological achievements in vaccine design, antibody engineering, drug repurposing, and rapid diagnostic testing. We also discuss what the future of these technologies and the future of large-scale collaborations might look like moving forward.