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At least 469 records · Page 26

A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope

Glypican 2 (GPC2) is a MYCN-regulated, differentially expressed cell-surface oncoprotein and target for immune-based therapies in neuroblastoma. Here, we build on GPC2’s immunotherapeutic attributes by finding that it is also a highly expressed, MYCN-driven oncoprotein on small-cell lung cancers (SCLCs), with significantly enriched expression in both the SCLC and neuroblastoma stem cell compartment.By solving the crystal structure of the D3-GPC2-Fab/GPC2 complex at 3.3 Å resolution, we further illustrate that the GPC2-directed antibody-drug conjugate (ADC; D3-GPC2-PBD), that links a human GPC2 antibody (D3) to DNA-damaging pyrrolobenzodiazepine (PBD) dimers, binds a tumor-specific, conformation-dependent epitope of the core GPC2 extracellular domain. We then show that this ADC induces durable neuroblastoma and SCLC tumor regression via induction of DNA damage, apoptosis, and bystander cell killing, notably with no signs of ADC-induced in vivo toxicity. Furthermore, these studies provide preclinical data to support the clinical translation of ADCs targeting GPC2.

60 APPLIED LIFE SCIENCES↗

An atypical BRCT–BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex

The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.

59 BASIC BIOLOGICAL SCIENCES↗

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.

60 APPLIED LIFE SCIENCES↗

Broad betacoronavirus neutralization by a stem helix–specific human antibody

Targeting a range of betacoranaviruses In the past 20 years, three highly pathogenic β-coronaviruses have crossed from animals to humans, including the most recent: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A spike protein that decorates these viruses has an S1 domain that binds host cell receptors and an S2 domain that fuses the viral and cell membranes to allow cell entry. The S1 domain is the target of many neutralizing antibodies but is more genetically variable than S2, and antibodies can exert selective pressure, leading to resistant variants. Pinto et al . identified five monoclonal antibodies that interact with a helix in the S2 domain. The most broadly neutralizing antibody inhibited all β-coronavirus subgenera and reduced viral burden in hamsters infected with SARS-CoV-2. —VV

59 BASIC BIOLOGICAL SCIENCES↗

Unified Language Frontend for Physic-Informed AI/ML

Artificial intelligence and machine learning (AI/ML) are becoming important tools for scientific modeling and simulation as in several other fields such as image analysis and natural language processing. ML techniques can leverage the computing power available in modern systems and reduce the human effort needed to configure experiments, interpret and visualize results, draw conclusions from huge quantities of raw data, and build surrogates for physics based models. Domain scientists in fields like fluid dynamics, microelectronics and chemistry can automate many of their most difficult and repetitive tasks or improve the design times by use of the faster ML-surrogates. However, modern ML and traditional scientific highperformance computing (HPC) tend to use completely different software ecosystems. While ML frameworks like PyTorch and TensorFlow provide Python APIs, most HPC applications and libraries are written in C++. Direct interoperability between the two languages is possible but is tedious and error-prone. In this work, we show that a compiler-based approach can bridge the gap between ML frameworks and scientific software with less developer effort and better efficiency. We use the MLIR (multi-level intermediate representation) ecosystem to compile a pre-trained convolutional neural network (CNN) in PyTorch to freestanding C++ source code in the Kokkos programming model. Kokkos is a programming model widely used in HPC to write portable, shared-memory parallel code that can natively target a variety of CPU and GPU architectures. Our compiler-generated source code can be directly integrated into any Kokkosbased application with no dependencies on Python or cross-language interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Enhanced/Synthetic Vision Systems for Advanced Flight Decks

One of the most challenging arenas for enhanced and synthetic vision systems is the flight deck. Here, pilots must perform active and supervisory control behaviors based on imagery generated in real time or transduced from imaging sensors. Although enhanced and synthetic vision technologies have been used in military vehicles for more than two decades, they have only recently been considered for civilian transport aircraft. In this paper we discuss the human performance issues still to be resolved for these systems, and consider the special constraints that must be considered for their use in the transport domain.

Kaiser, Mary K.↗

Software Innovation in a Mission Critical Environment

Operating in mission-critical environments requires trusted solutions, and the preference for "tried and true" approaches presents a potential barrier to infusing innovation into mission-critical systems. This presentation explores opportunities to overcome this barrier in the software domain. It outlines specific areas of innovation in software development achieved by the Johnson Space Center (JSC) Engineering Directorate in support of NASA's major human spaceflight programs, including International Space Station, Multi-Purpose Crew Vehicle (Orion), and Commercial Crew Programs. Software engineering teams at JSC work with hardware developers, mission planners, and system operators to integrate flight vehicles, habitats, robotics, and other spacecraft elements for genuinely mission critical applications. The innovations described, including the use of NASA Core Flight Software and its associated software tool chain, can lead to software that is more affordable, more reliable, better modelled, more flexible, more easily maintained, better tested, and enabling of automation.

Fredrickson, Steven↗

Towards a flexible framework for community-wide ensemble forecasting tailored for major space environment impacts

To build continuously improving space weather predictive capabilities based on science and enable assessments and rapid implementations of advances in research into source-to-impact modelling systems we need: to assemble parts of the puzzle by solving problems focused on specific physical domains; to identify essential space environment quantities (ESEQs) passed between domains and linked to impacts; evaluate modeling capabilities for each ESEQ; connect all validated solutions from space weather origins on the sun to impacts on humans and critical infrastructure; to design displays for ensemble predictions tailored for major space weather user groups; to build a collaborative environment for efficient sharing of information and capabilities (models/data/expertise) and collaborative development. The presentation will overview existing community-wide space weather forecasting frameworks and research-to-operations pipelines and discuss opportunities to build a collaborative plug-and-play platform for interconnecting predictive capabilities developed under different space weather programs.

space weather↗

Towards A Flexible Framework for Community-Wide Ensemble Forecasting Tailored for Major Space Environment Impacts

To build continuously improving space weather predictive capabilities based on science and enable assessments and rapid implementations of advances in research into source-to-impact modelling systems we need: to assemble parts of the puzzle by solving problems focused on specific physical domains; to identify essential space environment quantities (ESEQs) passed between domains and linked to impacts; evaluate modeling capabilities for each ESEQ; connect all validated solutions from space weather origins on the sun to impacts on humans and critical infrastructure; to design displays for ensemble predictions tailored for major space weather user groups; to build a collaborative environment for efficient sharing of information and capabilities (models/data/expertise) and collaborative development. The presentation will overview existing community-wide space weather forecasting frameworks and research-to-operations pipelines and discuss opportunities to build a collaborative plug-and-play platform for interconnecting predictive capabilities developed under different space weather programs.

space weather↗

Activation of polycystin-1 signaling by binding of stalk-derived peptide agonists

Polycystin-1 (PC1) is the protein product of thePKD1gene whose mutation causes autosomal dominant Polycystic Kidney Disease (ADPKD). PC1 is an atypical G protein-coupled receptor (GPCR) with an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal and membrane-embedded C-terminal (CTF) fragments. Recently, activation of PC1 CTF signaling was shown to be regulated by a stalk tethered agonist (TA), resembling the mechanism observed for adhesion GPCRs. Here, synthetic peptides of the first 9- (p9), 17- (p17), and 21-residues (p21) of the PC1 stalk TA were shown to re-activate signaling by a stalkless CTF mutant in human cell culture assays. Novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) simulations elucidated binding conformations of p9, p17, and p21 and revealed multiple specific binding regions to the stalkless CTF. Peptide agonists binding to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of stalk TA-mediated PC1 CTF activation. Additional sequence coevolution analyses showed the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. These insights into the structural dynamic mechanism of PC1 activation by TA peptide agonists provide an in-depth understanding that will facilitate the development of therapeutics targeting PC1 for ADPKD treatment.

Life Sciences & Biomedicine - Other Topics↗

Defining Collaborative Control Interactions Using Systems Theory

Human teams collaborate by establishing roles, changing functional authorities, maintaining team cognition, coordinating, and mutually helping one another close control loops. These complex inter-actions are inspiring novel concepts to improve human-machine and multi-machine collaboration. However, these new systems face engineering gaps in modeling, analysis, design, and assurance. As such, few have been fielded in safety-critical domains like aerospace. To analyze safety, this paper introduces a system-theoretic framework to describe interactions that are—or are planned to be—used in multi-controller systems. It outlines a taxonomy of seven structural dimensions that influence controller interactions and nine dynamics observed in collaborative control that are defined using Systems Theory. An analyzed set of 101 controller interactions in aerospace systems demonstrates how to apply the framework and that designers are trying to create more sophisticated systems. This framework provides the foundation to extend system-theoretic hazard analysis techniques to systematically find collabora-tive-control causal factors.

Human machine teaming↗

Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.

60 APPLIED LIFE SCIENCES↗

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease

Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI–EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV.

60 APPLIED LIFE SCIENCES↗

Two VHH Antibodies Neutralize Botulinum Neurotoxin E1 by Blocking Its Membrane Translocation in Host Cells

Botulinum neurotoxin serotype E (BoNT/E) is one of the major causes of human botulism, which is a life-threatening disease caused by flaccid paralysis of muscles. After receptor-mediated toxin internalization into motor neurons, the translocation domain (HN) of BoNT/E transforms into a protein channel upon vesicle acidification in endosomes and delivers its protease domain (LC) across membrane to enter the neuronal cytosol. It is believed that the rapid onset of BoNT/E intoxication compared to other BoNT serotypes is related to its swift internalization and translocation. We recently identified two neutralizing single-domain camelid antibodies (VHHs) against BoNT/E1 termed JLE-E5 and JLE-E9. Here, we report the crystal structures of these two VHHs bound to the LCHN domain of BoNT/E1. The structures reveal that these VHHs recognize two distinct epitopes that are partially overlapping with the putative transmembrane regions on HN, and therefore could physically block membrane association of BoNT/E1. This is confirmed by our in vitro studies, which show that these VHHs inhibit the structural change of BoNT/E1 at acidic pH and interfere with BoNT/E1 association with lipid vesicles. Therefore, these two VHHs neutralize BoNT/E1 by preventing the transmembrane delivery of LC. Furthermore, structure-based sequence analyses show that the 3-dimensional epitopes of these two VHHs are largely conserved across many BoNT/E subtypes, suggesting a broad-spectrum protection against the BoNT/E family. In summary, this work improves our understanding of the membrane translocation mechanism of BoNT/E and paves the way for developing VHHs as diagnostics or therapeutics for the treatment of BoNT/E intoxication.

60 APPLIED LIFE SCIENCES↗

Discovery of Activities via Statistical Clustering of Fixation Patterns

Human behavior often consists of a series of distinct activities, each characterized by a unique signature of visual behavior. This is true even in a restricted domain, such as piloting an aircraft, where patterns of visual signatures might represent activities like communicating, navigating, and monitoring. We propose a novel analysis method for gaze-tracking data, to perform blind discovery of these activities based on their behavioral signatures. The method is in some respects similar to recurrence analysis, but here we compare not individual fixations, but groups of fixations aggregated over a fixed time interval. The duration of this interval is a parameter that we will refer to as τ. We assume that the environment has been divided into a set of N different areas-of-interest (AOIs). For a given interval of time of duration τ, we compute the proportion of time spent fixating each AOI, resulting in an N-dimensional vector. These proportions can be converted to counts by multiplying by τ divided by the average fixation duration (another parameter that we fix at 280 milliseconds). We compare different intervals by computing the chi-square statistic. The p-value associated with the statistic is the likelihood of observing the data under the hypothesis that the data in the two intervals were generated by a single process with a single set of probabilities governing the fixation of each AOI. We have investigated the method using a set of 10 synthetic "activities," that sample 4 AOIs. Four of these activities visit 3 of the 4 AOIs, with equal probability; as there are four different ways to leave-one- out, there are four such activities. Similarly, there are six different activities that leave-two-out. Sequences of simulated behavior were generated by running each activity for 40 seconds, in sequence, for a total of 6.7 minutes. The figure to the right shows the matrix of chi-square statistics, using a value of 2.8 seconds for τ, corresponding to 10 fixations. Low values (dark) indicate poor evidence for activity differences, while high values (bright) indicate strong evidence. The dark squares along the main diagonal each correspond to the forty second intervals in which the activity was held constant; the 4x4 block at the lower left corresponds to the four leave-one-out activities, while the 6x6 block in the upper right corresponds to the leave-two-out activities. (The anti-diagonal pattern of white squares indicates those activity pairs that share no AOIs.) The chi-square values can be binarized by choosing a particular significance level; we are interested in grouping bins that represent the same activity, effectively accepting the null hypothesis. Therefore, we may adopt a relatively lax criterion; for example, choosing a p-value of 0.2 means that two behaviors that have only a 1-in-5 chance of being produced by a single activity might nevertheless be clustered together. We have explored several methods to perform clustering on the data and solving for the activity probabilities. Greedy methods begin by selecting the time bin that is similar to the most (or least) other bins, and then forming a cluster from it and all other non-discriminable bins. These methods show mediocre performance, as they do not take into account temporal contiguity. Preliminary results indicate that methods that "grow" clusters in time from seed points perform better.

activity analysis↗

How Autonomous Intelligent Systems Can Facilitate Earth-independent Medical Care: Going Beyond Telepresence

During the last decade, teleoperated robotic systems have extended humans’ sensorimotor competence to digitally fly beyond the physical barrier of distance and scale and thus transmit sensorimotor skills of the human through direct communication. Telepresence capabilities have enabled tele-physical remote access at small scales thanks to telerobotic mediums. Although the concept was initially motivated by space applications, such technologies quickly have expanded into the medical domain and resulted in teleoperated medical robots, including telerobotic surgical systems (such as the da Vinci surgical system). Effective telepresence fundamentally depends on an agile, reliable, and secure communication medium that can transmit real-time information between the operator and a remote device. However, direct telepresence may not be achievable for long-duration exploration spaceflight missions. Thus, autonomous systems and local intelligence represent potential solutions to the aforementioned issues. One example solution employs demonstration systems which enable learning from the pre-captured inputs of a skilled human operator. These will be computationally modeled and later probabilistically replicated toward the completion of remote physical tasks when direct telepresence is not viable - such as under communication blackout conditions. In other words, trained autonomous systems (e.g., robots) can perform remote operations that mimic the physical performance of experts during remote operations/training. Beyond learning the physics of the task, autonomous agents can also be used to conduct algorithmic decision-making that mimics the higher-level cognition of the expert. Thus, using an autonomous system, pre-trained cognitive and manipulation-based skills can be leveraged (acquired during pre-mission events) to produce digital twins of an intelligent operator. Such systems can be used for the real-time conduction of intricate tasks in complex and unstructured environments. Such systems will operationalize “cognitive digital twins” and can expand the reach of human cognition and manipulation through the power of data-driven learning from demonstration algorithms. This system category will be discussed as a fully autonomous operation in this talk. In addition to the above, we will also propose and discuss the possibility of partial-automation using remote intelligence and remote sensing. In contrast to full automation, partial automation can close the loop through a local operator equipped with augmented sensory awareness through wearable systems. Such technologies will allow the local operator to conduct delicate tasks while being guided using sensory augmentation and being monitored to gauge her/his level of cognitive focus and performance. The difference with the previous category is that a remote human will conduct the task. Further, rather than making a digital twin of human cognition, we will augment the control inputs of the local human to match those of the skilled expert operator who is not accessible in real-time. Going beyond classic telepresence and thus approaching intelligent telepresence, our vision is that autonomous agents will eventually enable the safe, consistent and efficient delivery of complex, remote and smart medical care during space exploration across operators in an Earth-independent fashion. We will discuss our collective vision from NASA and MERIIT@NYU lab in this talk.

Telepresence↗

Discovery of Activities via Statistical Clustering of Fixation Patterns

Human behavior often consists of a series of distinct activities, each characterized by a unique pattern of interaction with the visual environment. This is true even in a restricted domain, such as a piloting an aircraft, where activities with distinct visual signatures might be things like communicating, navigating, and monitoring. We propose a novel analysis method for gaze-tracking data, to perform blind discovery of these hypothetical activities. The method is in some respects similar to recurrence analysis, but here we compare not individual fixations, but groups of fixations aggregated over a fixed time interval. The duration of this interval is a parameter that we will refer to as delta. We assume that the environment has been divided into a set of N different areas-of-interest (AOIs). For a given interval of time of duration delta, we compute the proportion of time spent fixating each AOI, resulting in an N-dimensional vector. These proportions can be converted to integer counts by multiplying by delta divided by the average fixation duration (another parameter that we fix at 280 milliseconds). We compare different intervals by computing the chi-square statistic. The p-value associated with the statistic is the likelihood of observing the data under the hypothesis that the data in the two intervals were generated by a single process with a single set of probabilities governing the fixation of each AOI. The method has been applied to approximately 100 hours of eye movement data collected from pilots in a high-fidelity B747 flight simulator, and the results have been compared to synthetic data in which the each activity is represented as first-order Markov process with random probabilities assigned to the AOIs. Randomly-generated synthetic activities can require thousands of fixations to be discriminated with statistical significance, while the human data can be clustered using averaging windows of some 10's of seconds, suggesting that the actual activities are much more narrowly focused than random Markov models.

activity analysis↗