Miracle-dz/UniFAR-FTUs huggingface dataset:
Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization

The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence. ABSTRACT While neutralizing antibodies that target the HIV-1 fusion peptide have been elicited in mice by vaccination, antibodies reported thus far have been from only a single antibody class that could neutralize ~30% of HIV-1 strains. To explore the ability of the murine immune system to generate cross-clade neutralizing antibodies and to investigate how higher breadth and potency might be achieved, we tested 17 prime-boost regimens that utilized diverse fusion peptide-carrier conjugates and HIV-1 envelope trimers with different fusion peptides. We observed priming in mice with fusion peptide-carrier conjugates of variable peptide length to elicit higher neutralizing responses, a result we confirmed in guinea pigs. From vaccinated mice, we isolated 21 antibodies, belonging to 4 distinct classes of fusion peptide-directed antibodies capable of cross-clade neutralization. Top antibodies from each class collectively neutralized over 50% of a 208-strain panel. Structural analyses – both X-ray and cryo-EM – revealed each antibody class to recognize a distinct conformation of fusion peptide and to have a binding pocket capable of accommodating diverse fusion peptides. Murine vaccinations can thus elicit diverse neutralizing antibodies, and altering peptide length during prime can improve the elicitation of cross-clade responses targeting the fusion peptide site of HIV-1 vulnerability. IMPORTANCE The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence. We found that variation in peptide length during prime elicits enhanced neutralizing responses in mice and guinea pigs. We identified vaccine-elicited murine monoclonal antibodies from distinct classes capable of cross-clade neutralization and of diverse fusion peptide recognition. Our findings lend insight into improved immunogens and regimens for HIV-1 vaccine development.
Object Recognition Using Mechanical Impact, Viscoelasticity, and Surface Friction During Interaction

Current robotic haptic object recognition relies on statistical measures derived from movement dependent interaction signals such as force, vibration or position. Mechanical properties, which can be estimated from these signals, are intrinsic object properties that may yield a more robust object representation. Therefore, this paper proposes an object recognition framework using multiple representative mechanical properties: stiffness, viscosity and friction coefficient as well as the coefficient of restitution, which has been rarely used to recognise objects. These properties are estimated in real-time using a dual Kalman filter (without tangential force measurements) and then are used for object classification and clustering. The proposed framework was tested on a robot identifying 20 objects through haptic exploration. The results demonstrate the technique's effectiveness and efficiency, and that all four mechanical properties are required for the best recognition rate of 98.18 $\pm$ 0.424%. For object clustering, the use of these mechanical properties also results in superior performance when compared to methods based on statistical parameters.
The DNA Damage Sensor MRE11 Regulates Efficient Replication of the Autonomous Parvovirus Minute Virus of Mice

The cellular DNA damage response (DDR) machinery protects the host genome from the deleterious consequences of DNA breaks and recognizes invading viral pathogens. DNA viruses that replicate in the nucleus have evolved distinct strategies to evade or usurp these DDR proteins. ABSTRACT Parvoviruses are single-stranded DNA viruses that utilize host proteins to vigorously replicate in the nuclei of host cells, leading to cell cycle arrest. The autonomous parvovirus, minute virus of mice (MVM), forms viral replication centers in the nucleus which are adjacent to cellular DNA damage response (DDR) sites, many of which are fragile genomic regions prone to undergoing DDR during the S phase. Since the cellular DDR machinery has evolved to transcriptionally suppress the host epigenome to maintain genomic fidelity, the successful expression and replication of MVM genomes at these cellular sites suggest that MVM interacts with DDR machinery distinctly. Here, we show that efficient replication of MVM requires binding of the host DNA repair protein MRE11 in a manner that is independent of the MRE11-RAD50-NBS1 (MRN) complex. MRE11 binds to the replicating MVM genome at the P4 promoter, remaining distinct from RAD50 and NBS1, which associate with cellular DNA break sites to generate DDR signals in the host genome. Ectopic expression of wild-type MRE11 in CRISPR knockout cells rescues virus replication, revealing a dependence on MRE11 for efficient MVM replication. Our findings suggest a new model utilized by autonomous parvoviruses to usurp local DDR proteins that are crucial for viral pathogenesis and distinct from those of dependoparvoviruses, like adeno-associated virus (AAV), which require a coinfected helper virus to inactivate the local host DDR. IMPORTANCE The cellular DNA damage response (DDR) machinery protects the host genome from the deleterious consequences of DNA breaks and recognizes invading viral pathogens. DNA viruses that replicate in the nucleus have evolved distinct strategies to evade or usurp these DDR proteins. We have discovered that the autonomous parvovirus, MVM, which is used to target cancer cells as an oncolytic agent, depends on the initial DDR sensor protein MRE11 to express and replicate efficiently in host cells. Our studies reveal that the host DDR interacts with replicating MVM molecules in ways that are distinct from viral genomes being recognized as simple broken DNA molecules. These findings suggest that autonomous parvoviruses have evolved distinct mechanisms to usurp DDR proteins, which can be used to design potent DDR-dependent oncolytic agents.
Molecular Characterization and Phylogenetic Analysis of Dengue Fever Viruses in Three Outbreaks in Tanzania Between 2017 and 2019

Background Dengue is a disease of public health interest, and Tanzania experienced major outbreaks in 2014 and 2019. Here, we report our findings on the molecular characterization of dengue viruses (DENV) that circulated during two smaller outbreaks (2017 and 2018) and one major epidemic (2019) in Tanzania. Methodology/Principal findings We tested archived serum samples from 1,381 suspected dengue fever patients, with a median age of 29 (IQR:22–40) years, referred to the National Public Health Laboratory for confirmation of DENV infection. DENV serotypes were identified by reverse transcription polymerase chain reaction (RT-PCR), and specific genotypes were identified by sequencing the envelope glycoprotein gene and phylogenetic inference methods. DENV was confirmed in 823 (59.6%) cases. More than half (54.7%) of patients with dengue fever infection were males, and nearly three-quarters (73%) of the infected individuals were living in Kinondoni district, Dar es Salaam. DENV-3 Genotype III caused the two smaller outbreaks in 2017 and 2018, while DENV-1 Genotype V caused the 2019 epidemic. DENV-1 Genotype I was also detected in one patient in 2019. Conclusion/Significance This study has demonstrated the molecular diversity of dengue viruses circulating in Tanzania. We found that contemporary circulating serotypes did not cause the major epidemic of 2019 but rather due to a serotype shift from DENV-3 (2017/2018) to DENV-1 in 2019. Such a change increases the risk for patients previously infected with a particular serotype to develop severe symptoms upon potential re-infection with a heterologous serotype due to antibody-dependent enhancement of infection. Therefore, the circulation of serotypes emphasizes the need to strengthen the country’s dengue surveillance system for better management of patients, early detection of outbreaks, and vaccine development.
B.Y.O. Bees: Managing wild bee biodiversity in urban greenspaces

As cities become more populated and the density of urban development increases, local biodiversity is threatened. Urban greenspaces have the capacity to preserve pollinator biodiversity, but the quality of support they provide depends on greenspace landscape attributes, including the availability of pollinator habitat and foraging resources. Wild native bees provide important pollination services to urban ecosystems, yet relatively little is known about how urban landscape management influences pollinator community composition and diversity. Our study explores how wild bee communities are affected by greenspace and landscape-level features like pollinator management practices, in urban greenspaces in and around Appleton Wisconsin: a mid-sized urban community spanning more than 100 sq. km. We sampled and identified native bees periodically between late-May 2017 and mid-September of 2018 using standardized arrays of pan traps at 15 sites around the city. We classified greenspaces based on their level of development (urban or suburban) and whether they were managed or unmanaged for increasing wild pollinator diversity. We quantified floral species diversity, floral color diversity, tree species diversity, and proximity of sites to open water for each site and used remotely sensed satellite data from both the USGS National Land Cover Database (NLCD) and the Normalized Difference Vegetation Index (NDVI). All variables were tested as potential correlates of wild bee abundance and species richness. Active pollinator management sites supported higher levels of bee abundance and richness. Notably, active greenspace management (e.g. planting native wildflowers) was a stronger correlate of bee abundance and richness than greenspace size and other landscape-level attributes. Within-greenspace attributes such as floral diversity, tree diversity, and proximity to open water contributed positively to both bee abundance and richness. Based on these findings, we suggest that urban greenspaces may be managed more efficiently and cost-effectively by focusing resources on active management by planting wildflowers, removing invasive species, creating nesting habitat, and providing water resources, rather than simply expanding in area.
Draft Genome Sequence of Bacillus thuringiensis SS2, from Dibenzofuran-Contaminated Soil, Reveals Putative Aromatic Compound Degradation Genes

The draft genome sequence of strain Bacillus thuringiensis SS2 consists of 426 contigs assembled at the scaffold level, totaling 5,030,306 bp, and contains 5,288 putative PATRIC protein-coding genes, including genes responsible for total benzoate consumption, degradation of halogenated compounds, heavy metal tolerance/resistance, biosynthesis of secondary metabolites, and microcin C7 self-immunity protein. ABSTRACT The draft genome sequence of strain Bacillus thuringiensis SS2 consists of 426 contigs assembled at the scaffold level, totaling 5,030,306 bp, and contains 5,288 putative PATRIC protein-coding genes, including genes responsible for total benzoate consumption, degradation of halogenated compounds, heavy metal tolerance/resistance, biosynthesis of secondary metabolites, and microcin C7 self-immunity protein.
Orbit modeling related to cartwheel geometry

This paper suggests a way to calculate a "realistic" orbit model. A satellite is always subject to several perturbations caused by inhomogeneities in the Earth's gravitational field, atmospheric drag, solar pressure and further stochastic influences. For most of these perturbations, especially for gravitation and atmospheric drag there are models existing, whereas in this paper we will confine ourselves to the gravitational influence.
Tracing 2D Growth of Pancreatic Tumoroids Using the Combination of Image Processing Techniques and Mini-Opto Tomography Imaging System

Objectives: In this study, we aimed to trace the 2D growth development of tumoroids produced with MIA PaCa-2 pancreatic cancer cells at different time points. Methods We cultured 3 different tumoroids with 0.5%, 0.8%, and 1.5% agarose concentrations and calculated the growth rate of the tumoroids with their images acquired at 9 imaging time points by mini-Opto tomography imaging system applying image processing techniques. We used the metrics contrast-to-noise ratio (CNR), peak signal-to-noise ratio (PSNR), and mean squared error (MSE) to analyze the distinguishability of the tumoroid structure from its surroundings, quantitatively. Additionally, we calculated the increase of the radius, the perimeter, and the area of 3 tumoroids over a time period. Results In the quantitative assessment, the bilateral and Gaussian filters gave the highest CNR values (ie, Gaussian filter: at each of 9 imaging time points in range of 1.715 to 15.142 for image set-1). The median filter gave the highest values in PSNR in the range of 43.108 to 47.904 for image set-2 and gave the lowest values in MSE in the range of 0.604 to 2.599 for image set-3. The areas of tumoroids with 0.5%, 0.8%, and 1.5% agarose concentrations were 1.014 mm2, 1.047 mm2, and 0.530 mm2 in the imaging time point-1 and 33.535 mm2, 4.538 mm2, and 2.017 mm2 in the imaging time point-9. The tumoroids with 0.5%, 0.8%, and 1.5% agarose concentrations grew up to times of 33.07, 4.33, and 3.80 in area size over this period, respectively. Conclusions The growth rate and the widest borders of the different tumoroids in a time interval could be detected automatically and successfully. This study that combines the image processing techniques with mini-Opto tomography imaging system ensured significant results in observing the tumoroid's growth rate and enlarging border over time, which is very critical to provide an emerging methodology in vitro cancer studies.
Removal of Motion Artifacts in Capacitive Electrocardiogram Acquisition: A Review

Capacitive electrocardiogram (cECG) systems are increasingly used for the monitoring of cardiac activity. They can operate within the presence of a small layer of air, hair or cloth and do not require a qualified technician. They can be integrated into wearables, clothing or objects of daily life, such as beds or chairs. While they offer many advantages over conventional electrocardiogram systems (ECG) that rely on wet electrodes, they are more prone to be affected by motion artifacts (MAs). These effects, which are due to the relative movement of the electrode in relation to the skin, are several orders of magnitude higher than ECG signal amplitudes, they occur in frequencies that might overlap with the ECG signal, and they may saturate the electronics in the most severe cases. In this paper, we provide a detailed description of MA mechanisms that translate into capacitance variations due to electrode-skin geometric changes or into triboelectric effects due to electrostatic charge redistribution. A state-of-the-art overview of the different approaches based on materials and construction, analog circuits and digital signal processing is provided as well as the trade-offs to be made using these techniques, to mitigate MAs efficiently.
Resolving the nanostructure of plasma-enhanced chemical vapor deposited nanocrystalline SiOx layers for application in solar cells

Nanocrystalline silicon suboxides (nc-SiOx) have attracted attention during the past years for the use in thin-film silicon solar cells. We investigated the relationships between the nanostructure as well as the chemical, electrical, and optical properties of phosphorous, doped, nc-SiO0.8:H fabricated by plasma-enhanced chemical vapor deposition. The nanostructure was varied through the sample series by changing the deposition pressure from 533 to 1067 Pa. The samples were then characterized by X-ray photoelectron spectroscopy, spectroscopic ellipsometry, Raman spectroscopy, aberration-corrected high-resolution transmission electron microscopy, selected-area electron diffraction, and a specialized plasmon imaging method. We found that the material changed with increasing pressure from predominantly amorphous silicon monoxide to silicon dioxide containing nanocrystalline silicon. The nanostructure changed from amorphous silicon filaments to nanocrystalline silicon filaments, which were found to cause aniso.
A Unified Active Learning Framework for Annotating Graph Data with Application to Software Source Code Performance Prediction

Most machine learning and data analytics applications, including performance engineering in software systems, require a large number of annotations and labelled data, which might not be available in advance. Acquiring annotations often requires significant time, effort, and computational resources, making it challenging. We develop a unified active learning framework specializing in software performance prediction to address this task. We begin by parsing the source code to an Abstract Syntax Tree (AST) and augmenting it with data and control flow edges. Then, we convert the tree representation of the source code to a Flow Augmented-AST graph (FA-AST) representation. Based on the graph representation, we construct various graph embeddings (unsupervised and supervised) into a latent space. Given such an embedding, the framework becomes task agnostic since active learning can be performed using any regression method and query strategy suited for regression. Within this framework, we investigate the impact of using different levels of information for active and passive learning, e.g., partially available labels and unlabeled test data. Our approach aims to improve the investment in AI models for different software performance predictions (execution time) based on the structure of the source code. Our real-world experiments reveal that respectable performance can be achieved by querying labels for only a small subset of all the data.
Process Tracking and Analysis with Lx Exponential Smoothing from Noisy Measurements

Abstract Tracking process mean from noisy measurements is important in real time data-based analysis since outliers are frequently present in many process measurement systems. This paper discusses robust on-line process mean estimation using L 1 exponential smoothing (L 1 -ES). Robustness properties and mean squared error efficiency are investigated. The adaptability of the L l -ES estimator to processes subject to unknown mean changes is also analyzed and compared with traditional exponentially weighted moving average and median estimators.
On-skin biosensors for noninvasive monitoring of postoperative free flaps and replanted digits

Severe soft tissue defects and amputated digits are clinically common injuries. Primary treatments include surgical free flap transfer and digit replantation, but these can fail because of vascular compromise. Postoperative monitoring is therefore crucial for timely detection of vessel obstruction and survival of replanted digits and free flaps. However, current postoperative clinical monitoring methods are labor intensive and highly dependent on the experience of nurses and surgeons. Here, we developed on-skin biosensors for noninvasive and wireless postoperative monitoring based on pulse oximetry. The on-skin biosensor was made of polydimethylsiloxane with gradient cross-linking to create a self-adhesive and mechanically robust substrate that interfaces with skin. The substrate was shown to exhibit appropriate adhesion on one side for both high-fidelity measurements of the sensor and low risk of peeling injury to delicate tissues. The other side demonstrated mechanical integrity to facilitate flexible hybrid integration of the sensor. Validation studies using a model of vascular obstruction in rats demonstrated the effectiveness of the sensor in vivo. Clinical studies indicated that the on-skin biosensor was accurate and more responsive than current clinical monitoring methods in identifying microvascular conditions. Comparisons with existing monitoring techniques, including laser Doppler flowmetry and micro-lightguide spectrophotometry, further verified the sensor’s accuracy and ability to identify both arterial and venous insufficiency. These findings suggest that this on-skin biosensor may improve postoperative outcomes in free flap and replanted digit surgeries by providing sensitive and unbiased data directly from the surgical site that can be remotely monitored. Description On-skin biosensors were developed to noninvasively monitor blood flow after surgical repair of soft tissue defects in patients. Sensing when surgeries don’t go with the flow Current clinical methods for postoperative monitoring of soft tissue defect repair and digit replantation are often subjective or inaccurate, increasing the risk for surgical complications and failure. Here, Wu and colleagues designed an on-skin biosensor using a gradient crosslinked polymer. This system allowed for appropriate flexibility and sensitivity for adhesion to skin, accurate monitoring of blood flow, and sufficient rigidity for necessary electrical components. They demonstrated that these sensors could successfully detect vascular compromise in a variety of preclinical and clinical scenarios through pulse wave detection and analysis. These results suggest that on-skin biosensors may provide a simple, noninvasive, and unbiased method for the detection of vascular complications in postsurgical settings. —AW