Miracle-dz/UniFAR-FTUs huggingface dataset:
Improper Coordination of BamA and BamD Results in Bam Complex Jamming by a Lipoprotein Substrate

The β-barrel assembly machinery, the Bam complex, consists of five components, BamA to -E, among which BamA and BamD are highly conserved and essential. The nonessential components are believed to play redundant roles simply by improving the rate of β-barrel folding. Here we show that BamE contributes a specific and nonoverlapping function to the Bam complex. BamE coordinates BamA and BamD to form a complex between the lipoprotein RcsF and its partner outer membrane β-barrel protein, allowing RcsF to reach the cell surface. In the absence of BamE, RcsF accumulates on BamA, thus blocking the activity of the Bam complex. As the Bam complex is a major antibiotic target in Gram-negative bacteria, the discovery that a lipoprotein can act as a jamming substrate may open the door for development of novel Bam complex inhibitors. ABSTRACT The β-barrel assembly machinery, the Bam complex, is central to the biogenesis of integral outer membrane proteins (OMPs) as well as OMP-dependent surface-exposed lipoproteins, such as regulator of capsule synthesis protein F (RcsF). Previous genetic analysis established the model that nonessential components BamE and BamB have overlapping, redundant functions to enhance the kinetics of the highly conserved BamA/BamD core. Here we report that BamE plays a specialized nonredundant role in the Bam complex required for surface exposure of RcsF. We show that the lack of bamE, but not bamB, completely abolishes assembly of RcsF/OMP complexes and establish that the inability to assemble RcsF/OMP complexes is a molecular reason underlying all synthetic lethal interactions of ΔbamE. Our genetic analysis and biochemical cross-linking suggest that RcsF accumulates on BamA when BamA cannot engage with BamD because of its limited availability or the incompatible conformation. The role of BamE is to promote proper coordination of RcsF-bound BamA with BamD to complete OMP assembly around RcsF. We show that in the absence of BamE, RcsF is stalled on BamA, thus blocking its function, and we identify the lipoprotein RcsF as a bona fide jamming substrate of the Bam complex. IMPORTANCE The β-barrel assembly machinery, the Bam complex, consists of five components, BamA to -E, among which BamA and BamD are highly conserved and essential. The nonessential components are believed to play redundant roles simply by improving the rate of β-barrel folding. Here we show that BamE contributes a specific and nonoverlapping function to the Bam complex. BamE coordinates BamA and BamD to form a complex between the lipoprotein RcsF and its partner outer membrane β-barrel protein, allowing RcsF to reach the cell surface. In the absence of BamE, RcsF accumulates on BamA, thus blocking the activity of the Bam complex. As the Bam complex is a major antibiotic target in Gram-negative bacteria, the discovery that a lipoprotein can act as a jamming substrate may open the door for development of novel Bam complex inhibitors.
Reproducibility and discriminant validity of two clinically feasible measurement methods to obtain coronal plane gait kinematics in participants with a lower extremity amputation

Introduction Measuring coronal plane gait kinematics of the pelvis and trunk during rehabilitation of participants with a lower extremity amputation is important to detect asymmetries in gait which are hypothesised as associated with secondary complaints. The aim of this study was to test the reproducibility and discriminant validity of a three-dimensional (3-D; inertial measurement units) and a two-dimensional (2-D; video-based) system. Methods We tested the test-retest and inter-rater reproducibility of both systems and the 2-D system, respectively, in participants with a lower extremity amputation (group 1) and healthy subjects (group 2). The discriminant validity was determined with a within-group comparison for the 3-D system and with a between-group comparison for both systems. Results Both system showed to be test-retest reliable, both in group 1 (2-D system: ICC3.1agreement 0.52–0.83; 3-D system: ICC3.1agreement 0.81–0.95) and in group 2 (3-D system: ICC3.1agreement 0.33–0.92; 2-D system: ICC3.1agreement 0.54–0.95). The 2-D system was also inter-rater reliable (group 1: ICC2.1agreement 0.80–0.92; group 2: ICC2.1agreement 0.39–0.90). The within-group comparison of the 3-D system revealed a statistically significant asymmetry of 0.4°-0.5° in group 1 and no statistically significant asymmetry in group 2. The between-group comparison revealed that the maximum amplitude towards the residual limb (MARL) in the low back (3-D system) and the (residual) limb—trunk angle (2-D system) were significantly larger with a mean difference of 1.2° and 6.4°, respectively, than the maximum amplitude of healthy subjects. However, these average differences were smaller than the smallest detectable change (SDC) of group 1 for both the MARL (SDCagreement: 1.5°) and the residual limb—trunk angle (SDCagreement: 6.7°-7.6°). Conclusion The 3-D and 2-D systems tested in this study were not sensitive enough to detect real differences within and between participants with a lower extremity amputation and healthy subjects although promising reproducibility parameters for some of the outcome measures.
Diagnosis‐to‐ablation time in atrial fibrillation: A modifiable factor relevant to clinical outcome

Recurrences after atrial fibrillation (AF) ablation are still common. Among the reported clinical and imaging predictors of recurrences, diagnosis‐to‐ablation time (DAT) has been defined as a predictor of ablation outcome in single‐center studies. We aimed to validate DAT in a multicenter real‐life cohort.
Fine-scale behavioural adjustments of prey on a continuum of risk

In the wild, prey species often live in the vicinity of predators, rendering the ability to assess risk on a moment-to-moment basis crucial to survival. Visual cues are important as they allow prey to assess predator species, size, proximity and behaviour. However, few studies have explicitly examined prey's ability to assess risk based on predator behaviour and orientation. Using mosquitofish, Gambusia holbrooki, and their predator, jade perch, Scortum barcoo, under controlled conditions, we provide some of the first fine-scale characterization of how prey adapt their behaviour according to their continuous assessment of risk based on both predator behaviour and angular distance to the predator's mouth. When these predators were inactive and posed less of an immediate threat, prey within the attack cone of the predator showed reductions in speed and acceleration characteristic of predator-inspection behaviour. However, when predators became active, prey swam faster with greater acceleration and were closer together within the attack cone of predators. Most importantly, this study provides evidence that prey do not adopt a uniform response to the presence of a predator. Instead, we demonstrate that prey are capable of rapidly and dynamically updating their assessment of risk and showing fine-scale adjustments to their behaviour.
Developing Mass Egg-Laying Medium for the Edible Ruspolia differens (Orthoptera: Tettigonidae)

Abstract The edible katydid, Ruspolia differens (Serville), is an economically and nutritionally important insect species that is common and widespread in Africa. Currently, there are aims to develop mass-rearing methods suitable for this species, but a critical first step would require a suitable oviposition medium to ensure economic and easy production of eggs with high hatchability. The objective of the present study was to determine the oviposition preference and egg hatchability in different oviposition media. Based on preliminary testing of a wide range of different materials, two oviposition media, namely, artificial (folded plastic cloth) and natural medium (leaf sheath of Pennisetum purpureum Schumach attached to a stem), were selected for a detailed experiment. A two-choice laboratory experiment was conducted in which R. differens females were able to select between the folded plastic cloth (one side covered with short fleece) and a leaf sheath of P. purpureum (wrapped in polyester fiber). The results show that R. differens laid almost three times more eggs on the plastic cloth (mean ± SE, 169.3 ± 18.0) than on the natural substrate, P. purpurem (69.0 ± 13.9). However, the hatchability (overall mean% ± SE, 56.5 ± 4.7) of eggs in the two media did not differ. Folded plastic cloth, therefore, provided a more effective medium for egg laying by R. differens, and is thus a promising oviposition medium for getting natural populations to start laying eggs in future mass rearing.
Carbon Dioxide Improves Phosphorus Nutrition by Facilitating the Remobilization of Phosphorus From the Shoot Cell Wall in Rice (Oryza sativa)

Phosphorus (P) starvation leads to increased reutilization of cell wall P in rice (Oryza sativa). Carbon dioxide (CO2) is involved not only in plant growth and development but also in the response to abiotic stresses. However, it remains unclear whether CO2 affects the reutilization of cell wall P in rice when subjected to P deficiency. In the present study, elevated CO2 (600 μl·L−1) significantly increased the soluble P content in shoots when compared with ambient CO2 (400 μl·L−1). This positive effect was accompanied by an increase of pectin content, as well as an increase of pectin methylesterase (PME) activity, which results in P release from the shoot cell wall, making it available for plant growth. P deficiency significantly induced the expression of phosphate transporter genes (OsPT2, OsPT6, and OsPT8) and decreased the P content in the xylem sap, but elevated CO2 had no further effect, indicating that the increased soluble P content observed in shoots under elevated CO2 is attributable to the reutilization of shoot cell wall P. Elevated CO2 further increased the P deficiency-induced ethylene production in the shoots, and the addition of the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid (ACC) mimicked this effect, while the addition of the ethylene inhibitor aminoethoxyvinylglycine (AVG) abolished this effect. These results further support the role of ethylene in the alleviation of P deficiency under elevated CO2. Taken together, our results indicate that the improvement of P nutrition in rice by elevated CO2 is mediated by increasing the shoot cell wall pectin content and PME activity, possibly via the ethylene signaling pathway.
Ultrasound image segmentation and tissue characterization

Abstract Ultrasound image segmentation deals with delineating the boundaries of structures, as a step towards semi-automated or fully automated measurement of dimensions or for characterizing tissue regions. Ultrasound tissue characterization (UTC) is driven by knowledge of the physics of ultrasound and its interactions with biological tissue, and has traditionally used signal modelling and analysis to characterize and differentiate between healthy and diseased tissue. Thus, both aim to enhance the capabilities of ultrasound as a quantitative tool in clinical medicine, and the two end goals can be the same, namely to characterize the health of tissue. This article reviews both research topics, and finds that the two fields are becoming more tightly coupled, even though there are key challenges to overcome in each area, influenced by factors such as more open software-based ultrasound system architectures, increased computational power, and advances in imaging transducer design.
Robust adaptive control: The qLPV paradigm

The study of LPV systems is motivated by the gain scheduling control design methodology. The classical approach to gain-scheduling involves the design of several LTI controllers for a parameterized family of linearized models of a system and the interpolation of the controller gains. LPV control theory has been proven useful to simplify the interpolation and realization problems associated with conventional gain-scheduling since it allows us to treat gain-scheduled controllers as a single entity, with the gain-scheduling achieved entirely by the parameter dependent controller. Using scaled small-gain theorem, a systematic gain scheduling control design technique has been developed. When the parameter dependency in both plant and controller is linear fractional, the existence of such a gain-scheduled controller is fully characterized in terms of linear matrix inequalities (LMIs). The underlying synthesis problem is therefore a convex problem for which efficient optimization techniques are available. This control structure is applicable whenever the value of parameter is measured in real-time. The resulting controller is time-varying and smoothly scheduled by the measurements of parameter. In a parallel approach a single, possible parameter-dependent, Lyapunov function has been used in the analysis and control design for parameter-dependent plants in robust control framework. Known bounds on the rate of parameter variation can be also incorporated into the analysis conditions. The solution to the LPV control synthesis problem was formulated as a parameter-dependent LMI optimization problem. For a general parameter dependence a brutal force griding method can be used to divide the parameter space and to render the semiinfinite optimization problem to be finite one; an alternative and very appealing solution can be applied for affine parameterizations.
Environmental Risk Assessment for the Galenical Formulation of Solid Medicinal Products at Roche Basle, Switzerland

Abstract An environmental risk assessment for losses to wastewater from galenical manufacturing of solid medicinal products at F. Hoffmann-La Roche in Basle, Switzerland, was performed based on an annual total materials balance. This balance resulted in a loss factor of 0.2% relative to the sum of all starting materials, which was later confirmed as valid by analysis for 1 specific active pharmaceutical ingredient (API). The initial risk assessment for all 25 different APIs formulated resulted in no evident risk for the wastewater treatment plant, based on biodegradation no-effect data. However, based on acute ecotoxicity data, potential risk to the local receiving water, the River Rhine, was identified from 1 single API, the antibiotic sulfamethoxazole (SMX). A refinement of the risk assessment for SMX, based on chronic ecotoxicity data, or the predicted no-effect concentration (PNEC), and documented sewage works degradability, or the predicted environmental concentration (PEC), led to a significant decrease of the initial PEC/PNEC ratio to well below 1. In view of this refinement, the final conclusion is that the galenical production investigated poses no significant risk to the environment.
Regulostat Inferelator: a novel network biology platform to uncover molecular devices that predetermine cellular response phenotypes

Abstract With the emergence of genome editing technologies and synthetic biology, it is now possible to engineer genetic circuits driving a cell's phenotypic response to a stressor. However, capturing a continuous response, rather than simply a binary ‘on’ or ‘off’ response, remains a bioengineering challenge. No tools currently exist to identify gene candidates responsible for predetermining and fine-tuning cell response phenotypes. To address this gap, we devised a novel Regulostat Inferelator (RSI) algorithm to decipher intrinsic molecular devices or networks that predetermine cellular phenotypic responses. The RSI algorithm is designed to extract gene expression patterns from basal transcriptomic data in order to identify ‘regulostat’ constituent gene pairs, which exhibit rheostat-like mode-of-cooperation capable of fine-tuning cellular response. Our proof-of-concept study provides computational evidence for the existence of regulostats and that these networks predetermine cellular response prior to exposure to a stressor or drug. In addition, our work, for the first time, provides evidence of context-specific, drug–regulostat interactions in predetermining drug response phenotypes in cancer cells. Given RSI-inferred regulostat networks offer insights for prioritizing gene candidates capable of rendering a resistant phenotype sensitive to a given drug, we envision that this tool will be of great value in bioengineering and medicine.
BEERE: a web server for biomedical entity expansion, ranking and explorations

Abstract BEERE (Biomedical Entity Expansion, Ranking and Explorations) is a new web-based data analysis tool to help biomedical researchers characterize any input list of genes/proteins, biomedical terms or their combinations, i.e. ‘biomedical entities’, in the context of existing literature. Specifically, BEERE first aims to help users examine the credibility of known entity-to-entity associative or semantic relationships supported by database or literature references from the user input of a gene/term list. Then, it will help users uncover the relative importance of each entity—a gene or a term—within the user input by computing the ranking scores of all entities. At last, it will help users hypothesize new gene functions or genotype–phenotype associations by an interactive visual interface of constructed global entity relationship network. The output from BEERE includes: a list of the original entities matched with known relationships in databases; any expanded entities that may be generated from the analysis; the ranks and ranking scores reported with statistical significance for each entity; and an interactive graphical display of the gene or term network within data provenance annotations that link to external data sources. The web server is free and open to all users with no login requirement and can be accessed at http://discovery.informatics. uab.edu/beere/.
Uptake of couples HIV testing and counselling among heterosexual couples in Sub-Saharan Africa: a systematic review and meta-analysis

ABSTRACT There is a need for further research to inform policy and practice on Couples HIV Testing and Counselling (CHTC) in Sub-Saharan Africa (SSA). The aim of this systematic review and meta-analysis was to estimate and characterise the uptake of CHTC in the SSA. A comprehensive search of published studies was carried out in six electronic databases. Of 30,273 citations, 14 studies with a total of 97,030 study participants were identified. The pooled CHTC uptake was 31.48% (95%CI: 23.55–40.00) with significant heterogeneity between studies (I2 = 99.98%, p < 0.001). However, the sensitivity analysis after omitting two studies showed the pooled estimate for CHTC uptake was 24.05% (95%CI: 16.65–32.34, I2 = 99.86%, p < 0.001). Sub-group analyses indicated that both the study and population characteristics were a source of heterogeneity. The pooled CHTC uptake was higher among pregnant women and their partners (OR = 1.66, 95%CI: 1.58–1.84), and when one person in the dyad first tested individually (OR = 3.16, 95%CI: 2.69–3.72) compared to their counterparts. These findings suggest that people may be cautious of testing together as a couple. Further studies are required to explore how couples intend to use HIV-testing services including CHTC and under what circumstances CHTC may be beneficial to individuals in a relationship.
Head Pose Estimation Based on Random Forests for Multiclass Classification

Head pose estimation remains a unique challenge for computer vision system due to identity variation, illumination changes, noise, etc. Previous statistical approaches like PCA, linear discriminative analysis (LDA) and machine learning methods, including SVM and Adaboost, cannot achieve both accuracy and robustness that well. In this paper, we propose to use Gabor feature based random forests as the classification technique since they naturally handle such multi-class classification problem and are accurate and fast. The two sources of randomness, random inputs and random features, make random forests robust and able to deal with large feature spaces. Besides, we implement LDA as the node test to improve the discriminative power of individual trees in the forest, with each node generating both constant and variant number of children nodes. Experiments are carried out on two public databases to show the proposed algorithm outperforms other approaches in both accuracy and computational efficiency.
Predicting Time Series with Space-Time Convolutional and Recurrent Neural Networks

Convolutional neural networks (CNNs) with their ability to learn useful spatial features have revolutionized computer vision. The network topology of CNNs exploits the spatial relationship among the pixels in an image and this is one of the reasons for their success. In other domains deep learning has been less successful because it is not clear how the structure of non-spatial data can constrain network topology. Here, we show how multivariate time series can be interpreted as space-time pictures, thus expanding the applicability of the tricks-of-the-trade for CNNs to this important domain. We demonstrate that our model beats more traditional state-of-the-art models at predicting price development on the European Power Exchange (EPEX). Furthermore, we ﬁnd that the features discovered by CNNs on raw data beat the features that were hand-designed by an expert.
Epigenetic Mechanisms of Peptide-Driven Regulation and Neuroprotective Protein FKBP 1 b

Cortexin is a clinically approved cerebral cortex polypeptide complex in calves. The mechanism of cortexin action is not understood well. Two cortexin derivatives, short peptides EDR and DS with neuroprotective activity, were synthesized. According to the data of molecular modeling, these peptides are able to bind to the histone H1.3 protein. This can affect the conformation of histone H1.3, which leads to a change in the chromatin structure in the loci of some genes, in particular Fkbp1b encoding the FK506-binding protein. Electrophysiological processes associated with the Ca2+ exchange are disturbed in the pyramidal neurons of the hippocampus during aging of the brain. The Fkbp1b gene encodes peptidyl-prolyl cis-trans isomerase, regulating the release of calcium ions from the sarcoplasmic and endoplasmic reticulum of neurons. The activation of the Fkbp1b gene transcription under treatment with short peptides can promote the synthesis of its protein product and the activation of the Ca2+ release from organelles of the sarcoplasmic and endoplasmic reticulum of neurons, which, in turn, can lead to an increase in the functional activity of neurons.