University of Washington Seattle

Suction-based robotic grippers are common in industrial applications due to their simplicity and robustness but struggle with geometric complexity. Grippers that can handle varied surfaces as easily as traditional suction grippers would be more effective. Here we show how a fractal structure allows suction-based grippers to increase conformability and expand approach angle range. We develop a model for how the design parameters affect the range of curvatures and payloads a gripper can hold, and show when joint braking can increase payload capacity. We build a prototype gripper and develop a compact vacuum brake system for it. We then perform a series of experiments that demonstrate how the fractal structure enables corner grasping and expands the approach angle range from 5° to 45°. We also show that adding brakes improves performance by over 30% at moderate contact angles. This work demonstrates how fractal structures increase the utility of suction grippers through underactuation and locking.

This paper proposes a methodology combining Long-Short-Term-Memory (LSTM)-assisted kinematic motion prediction with a hybrid coding algorithm for compressing the trajectory data of Connected Autonomous Vehicles (CAVs). The vehicle locations after the first two time steps are predicted based on the vehicle positions at the first two time steps and the kinematic equation. The vehicle velocities and accelerations are predicted based on the vehicle locations and LSTM. The hybrid coding algorithm integrates differential coding, Binary Coded Decimal (BCD) coding and arithmetic coding. Differential coding converts the original data into the difference between the original data and the predicted data. Since the length of the original data is large but the difference between it and predicted data is small, the required space for storing the data can be greatly reduced. BCD coding converts subsequences of different lengths to the subsequences with the same length so that the original information can be correctly reproduced after decompression. Arithmetic coding expresses the information in small space by converting the character sequence into a decimal between 0 and 1. The proposed algorithm is evaluated on the Next Generation Simulation Trajectory dataset. The experiment results show that the compression ratio and compression rate obtained by the proposed algorithm are respectively higher and lower than those obtained by the baseline algorithms. Also, the sum of compression time, decompression time and transmission time associated with the proposed algorithm is less than that associated with most baseline algorithms and transmission without compression.

We demonstrate a MEMS-compatible detector with a single channel that employs chemical vapor-deposited graphene (G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CVD</sub> ) in a chamberless, non-dispersive infrared gas sensing configuration. The detector, designed to function as a thermistor bolometer, is intricately crafted by integrating serpentine-shaped G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CVD</sub> into flexible, epoxy-based SU-8 photopolymer, covering an area of 500 × 500 μm². Experimental evaluations of the detector were carried out at a distance of 30 mm away from the light source within a chamberless setup to assess its performance metrics. The results unveil a peak responsivity of approximately 0.65 V/W for the G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CVD</sub> -based detector. This outcome underscores the simplicity of the fabrication process, eliminating the necessity for implementing intricate structures like p-n junctions, surface plasmons, or microcavities. Moreover, the detector demonstrates rapid resistance switching, with an impressive response time of 1.2 s and a recovery time of 1.7 s observed during the electrical chopping of the light source.

We sought to identify which aspects of our professional development program, the Consortium for the Advancement of Undergraduate STEM Education (CAUSE), were most useful for the participants. CAUSE was designed to support STEM faculty as they implement evidence-based teaching practices. We interviewed six faculty participants (Fellows) to address two questions: (1) Which aspects of CAUSE were useful for participants? and (2) What factors influenced implementation of evidencebased teaching? We conducted a qualitative thematic analysis of the interviews by iteratively coding the transcripts and organizing final codes into themes. We found five themes. Two themes addressed the social and educational value CAUSE offered. Fellows valued curated references with empirical evidence of the impact of teaching practices on student learning and valued the strong social support from interacting with a consistent cohort of faculty over time. Three themes identified factors that influenced faculty to implement evidence-based teaching. Fellows explained that class context and their teaching experience or motivation influenced how they implemented teaching practices. A final theme showed Fellows’ strong concern and respect for students as partners in the learning process during their journey of change. Our qualitative analysis of faculty interviews found that change is a complex process that is as varied as the individuals engaging in change.

Background KCNE1 encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility. Methods In this study, we leveraged the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein-coding KCNE1 variants. Results We comprehensively assayed KCNE1 variant cell surface expression (2554/2709 possible single-amino-acid variants) and function (2534 variants). Our study identified 470 loss- or partial loss-of-surface expression and 574 loss- or partial loss-of-function variants. Of the 574 loss- or partial loss-of-function variants, 152 (26.5%) had reduced cell surface expression, indicating that most functionally deleterious variants affect channel gating. Nonsense variants at residues 56–104 generally had WT-like trafficking scores but decreased functional scores, indicating that the latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation (with > 70% loss-of-function variants) were in predicted close contact with binding partners KCNQ1 or calmodulin. Our functional assay data were consistent with gold standard electrophysiological data (ρ = − 0.64), population and patient cohorts (32/38 presumed benign or pathogenic variants with consistent scores), and computational predictors (ρ = − 0.62). Our data provide moderate-strength evidence for the American College of Medical Genetics/Association of Molecular Pathology functional criteria for benign and pathogenic variants. Conclusions Comprehensive variant effect maps of KCNE1 can both provide insight into IKs channel biology and help reclassify variants of uncertain significance.

Importance Outcomes from protocol-directed active surveillance for favorable-risk prostate cancers are needed to support decision-making. Objective To characterize the long-term oncological outcomes of patients receiving active surveillance in a multicenter, protocol-directed cohort. Design, Setting, and Participants The Canary Prostate Active Surveillance Study (PASS) is a prospective cohort study initiated in 2008. A cohort of 2155 men with favorable-risk prostate cancer and no prior treatment were enrolled at 10 North American centers through August 2022. Exposure Active surveillance for prostate cancer. Main Outcomes and Measures Cumulative incidence of biopsy grade reclassification, treatment, metastasis, prostate cancer mortality, overall mortality, and recurrence after treatment in patients treated after the first or subsequent surveillance biopsies. Results Among 2155 patients with localized prostate cancer, the median follow-up was 7.2 years, median age was 63 years, 83% were White, 7% were Black, 90% were diagnosed with grade group 1 cancer, and median prostate-specific antigen (PSA) was 5.2 ng/mL. Ten years after diagnosis, the incidence of biopsy grade reclassification and treatment were 43% (95% CI, 40%-45%) and 49% (95% CI, 47%-52%), respectively. There were 425 and 396 patients treated after confirmatory or subsequent surveillance biopsies (median of 1.5 and 4.6 years after diagnosis, respectively) and the 5-year rates of recurrence were 11% (95% CI, 7%-15%) and 8% (95% CI, 5%-11%), respectively. Progression to metastatic cancer occurred in 21 participants and there were 3 prostate cancer–related deaths. The estimated rates of metastasis or prostate cancer–specific mortality at 10 years after diagnosis were 1.4% (95% CI, 0.7%-2%) and 0.1% (95% CI, 0%-0.4%), respectively; overall mortality in the same time period was 5.1% (95% CI, 3.8%-6.4%). Conclusions and Relevance In this study, 10 years after diagnosis, 49% of men remained free of progression or treatment, less than 2% developed metastatic disease, and less than 1% died of their disease. Later progression and treatment during surveillance were not associated with worse outcomes. These results demonstrate active surveillance as an effective management strategy for patients diagnosed with favorable-risk prostate cancer.

Escape from cytotoxic T lymphocyte (CTL) responses toward HIV-1 Gag and Nef has been associated with reduced control of HIV-1 replication in adults. However, less is known about CTL-driven immune selection in infants as longitudinal studies of infants are limited. Here, 1,210 gag and 1,264 nef sequences longitudinally collected within 15 months after birth from 14 HIV-1 perinatally infected infants and their mothers were analyzed. The number of transmitted founder (T/F) viruses and associations between virus evolution, selection, CTL escape, and disease progression were determined. The analyses indicated that a paraphyletic-monophyletic relationship between the mother-infant sequences was common (80%), and that the HIV-1 infection was established by a single T/F virus in 10 of the 12 analyzed infants (83%). Furthermore, most HIV-1 CTL escape mutations among infants were transmitted from the mothers and did not revert during the first year of infection. Still, immune-driven selection was observed at approximately 3 months after HIV-1 infection in infants. Moreover, virus populations with CTL escape mutations in gag evolved faster than those without, independently of disease progression rate. These findings expand the current knowledge of HIV-1 transmission, evolution, and CTL escape in infant HIV-1 infection and are relevant for the development of immune-directed interventions in infants. IMPORTANCE Despite increased coverage in antiretroviral therapy for the prevention of perinatal transmission, paediatric HIV-1 infection remains a significant public health concern, especially in areas of high HIV-1 prevalence. Understanding HIV-1 transmission and the subsequent virus adaptation from the mother to the infant’s host environment, as well as the viral factors that affect disease outcome, is important for the development of early immune-directed interventions for infants. This study advances our understanding of vertical HIV-1 transmission, and how infant immune selection pressure is shaping the intra-host evolutionary dynamics of HIV-1.

With the growing attention on large-scale educational testing and assessment, the ability to process substantial volumes of response data becomes crucial. Current estimation methods within item response theory (IRT), despite their high precision, often pose considerable computational burdens with large-scale data, leading to reduced computational speed. This study introduces a novel “divide- and-conquer” parallel algorithm built on the Wasserstein posterior approximation concept, aiming to enhance computational speed while maintaining accurate parameter estimation. This algorithm enables drawing parameters from segmented data subsets in parallel, followed by an amalgamation of these parameters via Wasserstein posterior approximation. Theoretical support for the algorithm is established through asymptotic optimality under certain regularity assumptions. Practical validation is demonstrated using real-world data from the Programme for International Student Assessment. Ultimately, this research proposes a transformative approach to managing educational big data, offering a scalable, efficient, and precise alternative that promises to redefine traditional practices in educational assessments.

Plants and animals detect biomolecules termed microbe-associated molecular patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multicopy MAMPs on immune induction is unknown. Here, we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in both Arabidopsis and tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy, and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple cold shock proteins, and 46% carry a nonimmunogenic form. We uncovered a mechanism for immune evasion, intrabacterial antagonism, where a nonimmunogenic cold shock protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation.

The human infectious reservoir of Plasmodium falciparum is governed by transmission efficiency during vector-human contact and mosquito biting preferences. Understanding biting bias in a natural setting can help target interventions to interrupt transmission. In a 15-month cohort in western Kenya, we detected P. falciparum in indoor-resting Anopheles and human blood samples by qPCR and matched mosquito bloodmeals to cohort participants using short-tandem repeat genotyping. Using risk factor analyses and discrete choice models, we assessed mosquito biting behavior with respect to parasite transmission. Biting was highly unequal; 20% of people received 86% of bites. Biting rates were higher on males (biting rate ratio (BRR): 1.68; CI: 1.28–2.19), children 5–15 years (BRR: 1.49; CI: 1.13–1.98), and P. falciparum-infected individuals (BRR: 1.25; CI: 1.01–1.55). In aggregate, P. falciparum-infected school-age (5–15 years) boys accounted for 50% of bites potentially leading to onward transmission and had an entomological inoculation rate 6.4x higher than any other group. Additionally, infectious mosquitoes were nearly 3x more likely than non-infectious mosquitoes to bite P. falciparum-infected individuals (relative risk ratio 2.76, 95% CI 1.65–4.61). Thus, persistent P. falciparum transmission was characterized by disproportionate onward transmission from school-age boys and by the preference of infected mosquitoes to feed upon infected people.

In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9–14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.

We construct non-linear machine learning (ML) prediction models for systolic and diastolic blood pressure (SBP, DBP) using demographic and clinical variables and polygenic risk scores (PRSs). We developed a two-model ensemble, consisting of a baseline model, where prediction is based on demographic and clinical variables only, and a genetic model, where we also include PRSs. We evaluate the use of a linear versus a non-linear model at both the baseline and the genetic model levels and assess the improvement in performance when incorporating multiple PRSs. We report the ensemble model’s performance as percentage variance explained (PVE) on a held-out test dataset. A non-linear baseline model improved the PVEs from 28.1 to 30.1% (SBP) and 14.3% to 17.4% (DBP) compared with a linear baseline model. Including seven PRSs in the genetic model computed based on the largest available GWAS of SBP/DBP improved the genetic model PVE from 4.8 to 5.1% (SBP) and 4.7 to 5% (DBP) compared to using a single PRS. Adding additional 14 PRSs computed based on two independent GWASs further increased the genetic model PVE to 6.3% (SBP) and 5.7% (DBP). PVE differed across self-reported race/ethnicity groups, with primarily all non-White groups benefitting from the inclusion of additional PRSs. In summary, non-linear ML models improves BP prediction in models incorporating diverse populations.