DiffTune: Auto-Tuning through Auto-Differentiation

The performance of robots in high-level tasks depends on the quality of their lower-level controller, which requires fine-tuning. However, the intrinsically nonlinear dynamics and controllers make tuning a challenging task when it is done by hand. In this paper, we present DiffTune, a novel, gradient-based automatic tuning framework. We formulate the controller tuning as a parameter optimization problem. Our method unrolls the dynamical system and controller as a computational graph and updates the controller parameters through gradient-based optimization. The gradient is obtained using sensitivity propagation, which is the only method for gradient computation when tuning for a physical system instead of its simulated counterpart. Furthermore, we use $\mathcal{L}_1$ adaptive control to compensate for the uncertainties (that unavoidably exist in a physical system) such that the gradient is not biased by the unmodelled uncertainties. We validate the DiffTune on a Dubin's car and a quadrotor in challenging simulation environments. In comparison with state-of-the-art auto-tuning methods, DiffTune achieves the best performance in a more efficient manner owing to its effective usage of the first-order information of the system. Experiments on tuning a nonlinear controller for quadrotor show promising results, where DiffTune achieves 3.5x tracking error reduction on an aggressive trajectory in only 10 trials over a 12-dimensional controller parameter space.Comment: Minkyung Kim and Lin Song contributed equally to this wor

Case Report Unclassified mixed germ cell-sex cord-stromal tumor with multiple malignant cellular elements in a young woman: a case report and review of the literature

Abstract: Unclassified mixed germ cell-sex cord-stromal tumor composed of germ cells and sex cord derivatives is a rare neoplasm. Approximately 10% of such tumors have malignant germ cell components. We report the case of a 28 year-old female with a right adnexal mass measuring 8 cm in greatest dimension, containing areas with both germ cell and sex cord components. The germ cell portion contained multiple growth patterns with a malignant appearance, while the sex cord element consisted mainly of annular tubules. Within the malignant germ cell elements was a dysgerminoma that accounted for approximately 75% of the tumor volume. Other malignant germ cell elements included yolk sac tumor, embryonal carcinoma, and choriocarcinoma, which comprised about 15% of the tumor volume. The annular tubule structures comprised about 10% of the total tumor volume. To our knowledge, this is the first case reported in the literature of an unclassified mixed germ cell-sex cord-stromal tumor associated with embryonal carcinoma components. The patient had a 46XX karyotype, regular menstrual periods, and no evidence of gross abnormalities in the contralateral ovary. The patient remained clinically well and disease-free 2 years after surgery. In addition to a thorough case description, the literature concerning this entity is reviewed and discussed

Transport of Pacific water into the Canada Basin and the formation of the Chukchi Slope Current

Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 7453-7471, doi:10.1029/2018JC013825.A high‐resolution regional ocean model together with moored hydrographic and velocity measurements is used to identify the pathways and mechanisms by which Pacific water, modified over the Chukchi shelf, crosses the shelf break into the Canada Basin. Most of the Pacific water flowing into the Arctic Ocean through Bering Strait enters the Canada Basin through Barrow Canyon. Strong advection allows the water to cross the shelf break and exit the shelf. Wind forcing plays little role in this process. Some of the outflowing water from Barrow Canyon flows to the east into the Beaufort Sea; however, approximately 0.4 to 0.5 Sv turns to the west forming the newly identified Chukchi Slope Current. This transport occurs at all times of year, channeling both summer and winter waters from the shelf to the Canada Basin. The model indicates that approximately 75% of this water was exposed to the mixed layer within the Chukchi Sea, while the remaining 25% was able to cross the shelf during the stratified summer before convection commences in late fall. We view the Ό(0.5) Sv of the Chukchi Slope Current as replacing Beaufort Gyre water that would have come from the east in the absence of the cross-topography flow in Barrow Canyon. The weak eastward flow on the Beaufort slope is also consistent with the local disruption of the Beaufort Gyre by the Barrow Canyon outflow.Bureau of Ocean and Energy Management Grant Number: M12AC00008; DOC | National Oceanic and Atmospheric Administration (NOAA) Grant Number: NA16OAR4310248; National Science Foundation (NSF) Grant Numbers: PLR-1415489, OCE-15331702019-04-2

Well-posedness in energy space for the periodic modified Benjamin-Ono equation

We prove that the periodic modified Benjamin-Ono equation is locally well-posed in the energy space $H^{1/2}$. This ensures the global well-posedness in the defocusing case. The proof is based on an $X^{s,b}$ analysis of the system after gauge transform.Comment: 26 pages, 0 figure. Title changed, introduction modifie

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The osmotic regulator OmpR in <it>Escherichia coli </it>regulates differentially the expression of major porin proteins OmpF and OmpC. In <it>Yersinia enterocolitica </it>and <it>Y. pseudotuberculosis</it>, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in <it>Y. pestis </it>are not yet fully understood.</p> <p>Results</p> <p><it>Y. pestis </it>OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The <it>ompR </it>mutation likely did not affect the virulence of <it>Y. pestis </it>strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the <it>ompR </it>mutation, indicating the global regulatory role of OmpR in <it>Y. pestis</it>. Real-time RT-PCR or <it>lacZ </it>fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner.</p> <p>Conclusion</p> <p>OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. <it>Y. pestis </it>OmpR regulates <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and × at high osmolarity in <it>Y. pestis</it>, in contrast to the reciprocal regulation of them in <it>E. coli</it>. The main difference is that <it>ompF </it>expression is not repressed at high osmolarity in <it>Y. pestis</it>, which is likely due to the absence of a promoter-distal OmpR-binding site for <it>ompF</it>.</p

Regulatory effects of cAMP receptor protein (CRP) on porin genes and its own gene in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The cAMP receptor protein (CRP) is a global bacterial regulator that controls many target genes. The CRP-cAMP complex regulates the <it>ompR-envZ </it>operon in <it>E. coli </it>directly, involving both positive and negative regulations of multiple target promoters; further, it controls the production of porins indirectly through its direct action on <it>ompR-envZ</it>. Auto-regulation of CRP has also been established in <it>E. coli</it>. However, the regulation of porin genes and its own gene by CRP remains unclear in <it>Y. pestis</it>.</p> <p>Results</p> <p><it>Y. pestis </it>employs a distinct mechanism indicating that CRP has no regulatory effect on the <it>ompR-envZ </it>operon; however, it stimulates <it>ompC </it>and <it>ompF </it>directly, while repressing <it>ompX</it>. No transcriptional regulatory association between CRP and its own gene can be detected in <it>Y. pestis</it>, which is also in contrast to the fact that CRP acts as both repressor and activator for its own gene in <it>E. coli</it>. It is likely that <it>Y. pestis </it>OmpR and CRP respectively sense different signals (medium osmolarity, and cellular cAMP levels) to regulate porin genes independently.</p> <p>Conclusion</p> <p>Although the CRP of <it>Y. pestis </it>shows a very high homology to that of <it>E. coli</it>, and the consensus DNA sequence recognized by CRP is shared by the two bacteria, the <it>Y. pestis </it>CRP can recognize the promoters of <it>ompC</it>, <it>F</it>, and <it>X </it>directly rather than that of its own gene, which is different from the relevant regulatory circuit of <it>E. coli</it>. Data presented here indicate a remarkable remodeling of the CRP-mediated regulation of porin genes and of its own one between these two bacteria.</p

High-performance and Scalable Software-based NVMe Virtualization Mechanism with I/O Queues Passthrough

NVMe(Non-Volatile Memory Express) is an industry standard for solid-state drives (SSDs) that has been widely adopted in data centers. NVMe virtualization is crucial in cloud computing as it allows for virtualized NVMe devices to be used by virtual machines (VMs), thereby improving the utilization of storage resources. However, traditional software-based solutions have flexibility benefits but often come at the cost of performance degradation or high CPU overhead. On the other hand, hardware-assisted solutions offer high performance and low CPU usage, but their adoption is often limited by the need for special hardware support or the requirement for new hardware development. In this paper, we propose LightIOV, a novel software-based NVMe virtualization mechanism that achieves high performance and scalability without consuming valuable CPU resources and without requiring special hardware support. LightIOV can support thousands of VMs on each server. The key idea behind LightIOV is NVMe hardware I/O queues passthrough, which enables VMs to directly access I/O queues of NVMe devices, thus eliminating virtualization overhead and providing near-native performance. Results from our experiments show that LightIOV can provide comparable performance to VFIO, with an IOPS of 97.6%-100.2% of VFIO. Furthermore, in high-density VMs environments, LightIOV achieves 31.4% lower latency than SPDK-Vhost when running 200 VMs, and an improvement of 27.1% in OPS performance in real-world applications

The ratio of systolic and diastolic pressure is associated with carotid and femoral atherosclerosis

BackgroundAlthough the impact of hypertension on carotid intima-media thickness (IMT) and plaques has been well established, its association with femoral IMT and plaques has not been extensively examined. In addition, the role of the ratio of systolic and diastolic pressure (SDR) in the subclinical atherosclerosis (AS) risk remains unknown. We assessed the relationship between SDR and carotid and femoral AS in a general population.MethodsA total of 7,263 participants aged 35–74 years enrolled from January 2019 to June 2021 in a southeast region of China were included in a cross-sectional study. Systolic and diastolic blood pressure (SBP and DBP) were used to define SDR. Ultrasonography was applied to assess the AS, including thickened IMT (TIMT) and plaque in the carotid and femoral arteries. Logistic regression and restricted cubic spline (RCS) models were the main approaches.ResultsThe prevalence of TIMT, plaque, and AS were 17.3%, 12.4%, and 22.7% in the carotid artery; 15.2%, 10.7%, and 19.5% in the femoral artery; and 23.8%, 17.9% and 30.0% in either the carotid or femoral artery, respectively. Multivariable logistic regression analysis found a significant positive association between high-tertile SDR and the higher risk of overall TIMT (OR = 1.28, 95% CI = 1.10–1.49), plaques (OR = 1.36, 95%CI = 1.16–1.61), or AS (OR = 1.36, 95% CI = 1.17–1.57), especially in the carotid artery. RCS analysis further revealed the observed positive associations were linear. Further analyses showed that as compared to the low-tertile SDR and non-hypertension group, high-tertile SDR was associated with increased risks of overall and carotid TIMT, plaques, or AS in both groups with or without hypertension.ConclusionsSDR is related to a higher risk of subclinical AS, regardless of hypertension or not, suggesting that as a readily obtainable index, SDR can contribute to providing additional predictive value for AS

Seasonal climatic effects and feedbacks of anthropogenic heat release due to global energy consumption with CAM5

Anthropogenic heat release (AHR) is the heat generated in global energy consumption, which has not been considered in global climate models generally. The global high-resolution AHR from 1992 to 2013, which is estimated by using the Defense Meteorological Satellite Program (DMSP)/Operational Linescan System (OLS) satellite data, is implemented into the Community Atmosphere Model version 5 (CAM5). The seasonal climatic effects and possible feedbacks of AHR are examined in this study. The modeling results show that AHR increases the global annual mean surface temperature and land surface temperature by 0.02 ± 0.01 K (1σ uncertainty) and 0.05 ± 0.02 K (1σ uncertainty), respectively. The global climatic effect of AHR varies with season: with a stronger climatic effect in the boreal winter leading to global mean land surface temperature increases by 0.10 ± 0.01 K (1σ uncertainty). In the selected regions (40°N–60°N, 0°E–45°E) of Central and Western Europe the average surface temperature increases by 0.46 K in the boreal summer, and in the selected regions (45°N–75°N, 30°E–140°E) of northern Eurasia the average surface temperature increases by 0.83 K in the boreal winter. AHR changes the height and thermodynamic structure of the global planetary boundary layer, as well as the stability of the lower troposphere, which affects the global atmospheric circulation and low cloud fraction. In addition, at the surface both the shortwave radiation flux in the boreal summer and the down-welling longwave flux in the boreal winter change signifi- cantly, as a result of the change in low clouds caused by the effect of AHR. This study suggests a possible new mechanism of AHR effect on global climate through changing the global low-cloud fraction, which is crucial for global energy balance, by modifying the thermodynamic structure and stability of the lower troposphere. Thus this study improves our understanding of the global climate change caused by human activities

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data