Robust Single-view Cone-beam X-ray Pose Estimation with Neural Tuned Tomography (NeTT) and Masked Neural Radiance Fields (mNeRF)

Many tasks performed in image-guided, mini-invasive, medical procedures can be cast as pose estimation problems, where an X-ray projection is utilized to reach a target in 3D space. Expanding on recent advances in the differentiable rendering of optically reflective materials, we introduce new methods for pose estimation of radiolucent objects using X-ray projections, and we demonstrate the critical role of optimal view synthesis in performing this task. We first develop an algorithm (DiffDRR) that efficiently computes Digitally Reconstructed Radiographs (DRRs) and leverages automatic differentiation within TensorFlow. Pose estimation is performed by iterative gradient descent using a loss function that quantifies the similarity of the DRR synthesized from a randomly initialized pose and the true fluoroscopic image at the target pose. We propose two novel methods for high-fidelity view synthesis, Neural Tuned Tomography (NeTT) and masked Neural Radiance Fields (mNeRF). Both methods rely on classic Cone-Beam Computerized Tomography (CBCT); NeTT directly optimizes the CBCT densities, while the non-zero values of mNeRF are constrained by a 3D mask of the anatomic region segmented from CBCT. We demonstrate that both NeTT and mNeRF distinctly improve pose estimation within our framework. By defining a successful pose estimate to be a 3D angle error of less than 3 deg, we find that NeTT and mNeRF can achieve similar results, both with overall success rates more than 93%. However, the computational cost of NeTT is significantly lower than mNeRF in both training and pose estimation. Furthermore, we show that a NeTT trained for a single subject can generalize to synthesize high-fidelity DRRs and ensure robust pose estimations for all other subjects. Therefore, we suggest that NeTT is an attractive option for robust pose estimation using fluoroscopic projections

REFORMS: Reporting Standards for Machine Learning Based Science

Machine learning (ML) methods are proliferating in scientific research. However, the adoption of these methods has been accompanied by failures of validity, reproducibility, and generalizability. These failures can hinder scientific progress, lead to false consensus around invalid claims, and undermine the credibility of ML-based science. ML methods are often applied and fail in similar ways across disciplines. Motivated by this observation, our goal is to provide clear reporting standards for ML-based science. Drawing from an extensive review of past literature, we present the REFORMS checklist ($\textbf{Re}$porting Standards $\textbf{For}$ $\textbf{M}$achine Learning Based $\textbf{S}$cience). It consists of 32 questions and a paired set of guidelines. REFORMS was developed based on a consensus of 19 researchers across computer science, data science, mathematics, social sciences, and biomedical sciences. REFORMS can serve as a resource for researchers when designing and implementing a study, for referees when reviewing papers, and for journals when enforcing standards for transparency and reproducibility

Agricultural Research Service Weed Science Research: Past, Present, and Future

The U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) has been a leader in weed science research covering topics ranging from the development and use of integrated weed management (IWM) tactics to basic mechanistic studies, including biotic resistance of desirable plant communities and herbicide resistance. ARS weed scientists have worked in agricultural and natural ecosystems, including agronomic and horticultural crops, pastures, forests, wild lands, aquatic habitats, wetlands, and riparian areas. Through strong partnerships with academia, state agencies, private industry, and numerous federal programs, ARS weed scientists have made contributions to discoveries in the newest fields of robotics and genetics, as well as the traditional and fundamental subjects of weed-crop competition and physiology and integration of weed control tactics and practices. Weed science at ARS is often overshadowed by other research topics; thus, few are aware of the long history of ARS weed science and its important contributions. This review is the result of a symposium held at the Weed Science Society of America\u27s 62nd Annual Meeting in 2022 that included 10 separate presentations in a virtual Weed Science Webinar Series. The overarching themes of management tactics (IWM, biological control, and automation), basic mechanisms (competition, invasive plant genetics, and herbicide resistance), and ecosystem impacts (invasive plant spread, climate change, conservation, and restoration) represent core ARS weed science research that is dynamic and efficacious and has been a significant component of the agency\u27s national and international efforts. This review highlights current studies and future directions that exemplify the science and collaborative relationships both within and outside ARS. Given the constraints of weeds and invasive plants on all aspects of food, feed, and fiber systems, there is an acknowledged need to face new challenges, including agriculture and natural resources sustainability, economic resilience and reliability, and societal health and well-being

The Intrinsic Antiviral Defense to Incoming HSV-1 Genomes Includes Specific DNA Repair Proteins and Is Counteracted by the Viral Protein ICP0

Cellular restriction factors responding to herpesvirus infection include the ND10 components PML, Sp100 and hDaxx. During the initial stages of HSV-1 infection, novel sub-nuclear structures containing these ND10 proteins form in association with incoming viral genomes. We report that several cellular DNA damage response proteins also relocate to sites associated with incoming viral genomes where they contribute to the cellular front line defense. We show that recruitment of DNA repair proteins to these sites is independent of ND10 components, and instead is coordinated by the cellular ubiquitin ligases RNF8 and RNF168. The viral protein ICP0 targets RNF8 and RNF168 for degradation, thereby preventing the deposition of repressive ubiquitin marks and counteracting this repair protein recruitment. This study highlights important parallels between recognition of cellular DNA damage and recognition of viral genomes, and adds RNF8 and RNF168 to the list of factors contributing to the intrinsic antiviral defense against herpesvirus infection

Enhancements to angioplasty for peripheral arterial occlusive disease: systematic review, cost-effectiveness assessment and expected value of information analysis

BACKGROUND: There have been rapid technological developments aimed at improving short- and long-term results of percutaneous transluminal balloon angioplasty (PTA) in peripheral arterial occlusive disease (PAD). OBJECTIVES: To assess current clinical effectiveness and cost-effectiveness evidence of additional techniques to standard PTA for PAD, develop a health economic model to assess cost-effectiveness and to identify where further research is needed. DATA SOURCES: Relevant electronic databases, including MEDLINE, EMBASE and The Cochrane Library were searched from inception to 2011, between May and October 2011. METHODS: Systematic reviews were conducted of clinical effectiveness and cost-effectiveness. The population was participants with symptomatic PAD undergoing endovascular treatment for disease distal to the inguinal ligament. Interventions were modifications of and adjuncts to PTA in the peripheral circulation, compared with conventional PTA. Outcomes included measures of clinical effectiveness and costs. Data were extracted from randomised controlled trials (RCTs), which were quality assessed using standard criteria. Where appropriate, meta-analyses using fixed- and random-effects methods produced relative risks (RRs). A discrete-event simulation model was developed to assess the relative cost-effectiveness of the interventions from a NHS perspective over a lifetime. The patient populations of intermittent claudication (IC) and critical limb ischaemia (CLI) were modelled separately. Univariate and probabilistic sensitivity analyses were undertaken. RESULTS: In total, 40 RCTs were included, many of which had small sample sizes. Significantly reduced restenosis rates were shown in meta-analyses of self-expanding stents (SES) {RR 0.67 [95% confidence interval (CI) 0.52 to 0.87]}, endovascular brachytherapy (EVBT) [RR 0.63 (95% CI 0.48 to 0.83)] at 12 months and drug-coated balloons (DCBs) at 6 months [RR 0.40 (95% CI 0.23 to 0.69)], and single studies of stent-graft or drug-eluting stent (DES), compared with PTA; a single study showed improvements with DES versus bare-metal stents (BMSs). Compared with PTA, walking capacity was not significantly affected by cutting balloon, balloon-expandable stents or EVBT; in SES, there was evidence of improvement in walking capacity after up to 12 months. The use of DCBs dominated both the assumed standard practice of PTA with bailout BMS and all other interventions because it lowered lifetime costs and improved quality of life (QoL). These results were seen for both patient populations (IC and CLI). Sensitivity analyses showed that the results were robust to different assumptions about the clinical benefits attributable to the interventions, suggesting that the use of DCBs is cost-saving. LIMITATIONS: Differing definitions of restenosis made direct comparison across trials difficult. There were few data available for walking capacity and QoL. CONCLUSIONS: The evidence showed a significant benefit to reducing restenosis rates for self-expanding and DESs, stent-graft, EVBT and DCBs. If it is assumed that patency translates into beneficial long-term clinical outcomes, then DCB and bail-out DES are most likely to be the cost-effective enhancements to PTA. A RCT comparing current recommended practice (PTA with bail-out BMS) with DCB and bail-out DES could assess long-term follow-up and cost-effectiveness. Data relating patency status to the need for reintervention and to the probability of symptoms returning should be collected, as should health-related QoL measures [European Quality of Life-5 Dimensions (EQ-5D) and maximum walking distance]. STUDY REGISTRATION: This study is registered as PROSPERO CRD42012002014. FUNDING: The National Institute for Health Research Health Technology Assessment programme

ILK mediates the effects of strain on intestinal epithelial wound closure

The intestinal epithelium is subjected to repetitive deformation during normal gut function by peristalsis and villous motility. Such repetitive strain promotes intestinal epithelial migration across fibronectin in vitro, but signaling mediators for this are poorly understood. We hypothesized that integrin-linked kinase (ILK) mediates strain-stimulated migration in intestinal epithelial cells cultured on fibronectin. ILK kinase activity increased rapidly 5 min after strain induction in both Caco-2 and intestinal epithelial cell-6 (IEC-6) cells. Wound closure in response to strain was reduced in ILK small interfering RNA (siRNA)-transfected Caco-2 cell monolayers when compared with control siRNA-transfected Caco-2 cells. Pharmacological blockade of phosphatidylinositol-3 kinase (PI3K) or Src or reducing Src by siRNA prevented strain activation of ILK. ILK coimmunoprecipitated with focal adhesion kinase (FAK), and this association was decreased by mutation of FAK Tyr925 but not FAK Tyr397. Strain induction of FAK Tyr925 phosphorylation but not FAK Tyr397 or FAK Tyr576 phosphorylation was blocked in ILK siRNA-transfected cells. ILK-Src association was stimulated by strain and was blocked by the Src inhibitor PP2. Finally, ILK reduction by siRNA inhibited strain-induced phosphorylation of myosin light chain and Akt. These results suggest a strain-dependent signaling pathway in which ILK association with FAK and Src mediates the subsequent downstream strain-induced motogenic response and suggest that ILK induction by repetitive deformation may contribute to recovery from mucosal injury and restoration of the mucosal barrier in patients with prolonged ileus. ILK may therefore be an important target for intervention to maintain the mucosa in such patients