Miracle-dz/UniFAR-FTUs huggingface dataset:
Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization

Black-box model-based optimization (MBO) problems, where the goal is to find a design input that maximizes an unknown objective function, are ubiquitous in a wide range of domains, such as the design of proteins, DNA sequences, aircraft, and robots. Solving model-based optimization problems typically requires actively querying the unknown objective function on design proposals, which means physically building the candidate molecule, aircraft, or robot, testing it, and storing the result. This process can be expensive and time consuming, and one might instead prefer to optimize for the best design using only the data one already has. This setting -- called offline MBO -- poses substantial and different algorithmic challenges than more commonly studied online techniques. A number of recent works have demonstrated success with offline MBO for high-dimensional optimization problems using high-capacity deep neural networks. However, the lack of standardized benchmarks in this emerging field is making progress difficult to track. To address this, we present Design-Bench, a benchmark for offline MBO with a unified evaluation protocol and reference implementations of recent methods. Our benchmark includes a suite of diverse and realistic tasks derived from real-world optimization problems in biology, materials science, and robotics that present distinct challenges for offline MBO. Our benchmark and reference implementations are released at github.com/rail-berkeley/design-bench and github.com/rail-berkeley/design-baselines.
Genes controlling the development and function of plant vacuoles

The formation of vacuolinos, small vacuoles coexisting with the central vacuole in petunia petal epidermal cells, was shown to be controlled by a set of conserved transcription factors, AN1-PH4-PH3. These proteins are part of the WMBW transcription complex, which is highly conserved among very different plant species. Based on RNAseq data, we have identified 750 genes which expression is significantly differential between wild type and an1 mutant petals, 692 genes differential in ph4 and 600 in ph3 . Among these genes, 31 genes were differential in all an1 , ph4 and ph3 mutants and therefore are potentially involved in the vacuolinos pathway. To date, based on trafficking of vacuolar proteins in RNA interference lines for CAC12.3 and PAT1 we identify these as genes required for different steps of the vacuolinos pathway. In addition, the comparison of the set of target genes of AN1-PH3-PH4 in petunia petals with those of the homologs in Arabidopsis leaves , resulted in the identification of a rather small group of overlapping targets. This suggests that the different functions of the WMBW complex in different developmental pathways like petals epidermal cells differentiation in petunia and trichome formation in Arabidopsis, are due to differences in the regulatory regions of their target genes, rather than in the regulatory proteins. This is consistent with the results of the analysis of the petunia MYBx gene. MYBx belongs to the R3 MYB family, like the Arabidopsis TRY and CPC factors, which are regulators of (non) hair differentiation in Arabidopsis . MYBx interacts withe AN1, participating in this way in the WMBW complex, probably as inhibitor. MYBx inhibits trichome formation and rescues root hair defects when expressed in Arabidopsis cpc mutants, while no trichome phenotype was detectable in transgenic plants expressing MYBx, which are instead affected in anthocyanin accumulation and vacuolar acidification in petals. Together, our findings provide novel insight into the function of the WMBW complexes in epidermal cells of different species and on the mechanisms by which these transcription factors acquired different functions during
Factors Affecting Entrainment Rate in Deep Convective Clouds and Parameterizations

The parameterization of cloud entrainment rate has been problematic for many years, hindering the accurate representation of convective processes in large‐scale models. Here, we extend our previous work on individual shallow convection to ensemble deep convection. Entrainment rate is estimated based on three‐dimensional convective clouds from August 19 to 20, 1999, during the Kwajalein Experiment, simulated using a high‐resolution cloud‐resolving model. They are found to be negatively correlated with both vertical velocity and buoyancy, and positively correlated with the vertical divergence of the vertical velocity and with the reciprocal of cloud radii. The physical mechanisms underlying these relationships are interpreted. It is found that the parameterizations with multiple properties perform better than those with a single property. Entrainment rate and relative humidity of entrained air are positively correlated at temperature higher than 0°C, but negatively correlated at temperature lower than 0°C. Relative humidity is also included in the parameterization of entrainment rate, which differs from our previous work on shallow cumulus clouds and other studies. Finally, two forms of parameterization for entrainment rate are recommended. The first treats the entrainment rate as a function of the vertical velocity and buoyancy for temperature higher than 0°C, but as a function of relative humidity and buoyancy for temperature lower than 0°C. The second involves an equation that relates entrainment rate to vertical velocity and buoyancy regardless of temperature.
Mathematical Analysis of Electromagnetic Plasmonic Metasurfaces | Multiscale Modeling & Simulation | Vol. 18, No. 2 | Society for Industrial and Applied Mathematics

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The Role of Antioxidants on Wound Healing: A Review of the Current Evidence

(1) Background: Reactive oxygen species (ROS) play a crucial role in the preparation of the normal wound healing response. Therefore, a correct balance between low or high levels of ROS is essential. Antioxidant dressings that regulate this balance are a target for new therapies. The purpose of this review is to identify the compounds with antioxidant properties that have been tested for wound healing and to summarize the available evidence on their effects. (2) Methods: A literature search was conducted and included any study that evaluated the effects or mechanisms of antioxidants in the healing process (in vitro, animal models or human studies). (3) Results: Seven compounds with antioxidant activity were identified (Curcumin, N-acetyl cysteine, Chitosan, Gallic Acid, Edaravone, Crocin, Safranal and Quercetin) and 46 studies reporting the effects on the healing process of these antioxidants compounds were included. (4) Conclusions: this review offers a map of the research on some of the antioxidant compounds with potential for use as wound therapies and basic research on redox balance and oxidative stress in the healing process. Curcumin, NAC, quercetin and chitosan are the antioxidant compounds that shown some initial evidence of efficacy, but more research in human is needed.
Streptococcuspyogenes infects human endometrium by limiting the innate immune response.

Group A Streptococcus (GAS), a Gram-positive human-specific pathogen yields 517,000 deaths annually worldwide, including 163,000 due to invasive infections and among them puerperal fever. Before efficient prophylactic measures were introduced, the mortality rate for mothers during childbirth was about 10%; puerperal fever still accounts for over 75,000 maternal deaths annually. Yet little is known regarding the factors and mechanisms of GAS invasion and establishment in postpartum infection. We characterized the early steps of infection in an ex vivo infection model of the human decidua, the puerperal fever portal of entry. Coordinate analysis of GAS behavior and the immune response led us to demonstrate that (i) GAS growth was stimulated by tissue products; (ii) GAS invaded tissue and killed ~50% of host cells within two hours; these processes required SpeB protease and Streptolysin O activities, respectively; (iii) GAS impaired the tissue immune response. Immune impairment occurred both at the RNA level, with only partial induction of the innate immune response, and protein level, in an SLO- and SpeB-dependent manner. Our study indicates that efficient GAS invasion of decidua and the restricted host immune response favored its propensity to develop rapid invasive infections in a gynecological-obstetrical context.
Occupational Therapy Students’ Test/Re-Test Reliability of the Readiness for Interprofessional Education Learning Scale and Interdisciplinary Education Perception Scale

The purpose of this study was to establish the test/re-test reliability of two interprofessional education (IPE) instruments, the Readiness for Interprofessional Learning Scale (RIPLS) and the Interdisciplinary Education Perception Scale (IEPS) among occupational therapy (OT) graduate students. The intent was to compare results based on previous IPE experience and year in the program. The RIPLS and IEPS were distributed to 111 OT students at one university. Both instruments were distributed a second time 10-14 days later. Cronbach’s alpha, weighted Kappas, intraclass correlation coefficients (ICC), standard error of measurement, and minimal detectable change were calculated for each instrument. Assessments occurred for all subjects, between students with and without previous IPE experience, and first and second-year students in the program. Overall and between group composite score reliability for the RIPLS and IEPS were fair to excellent (ICC≥0.72). RIPLS subscale ICC’s were variable per previous IPE experience and year in program, ranging from fair-excellent (ICC=0.45-0.93). IEPS subscale ICC’s were excellent for second-year students (ICC≥0.79), and fair-excellent for students with or without previous experience and first-year students (ICC=0.50-0.84). There were no differences for the RIPLS within or between sessions or groups. First-year students had significantly higher scores compared to second-year students within sessions for the IEPS composite score, Competency and Autonomy subscale, and Perception of Actual Cooperation subscale (p≤0.035). Both instruments have acceptable test-re-test reliability; however, previous IPE experience and year in program should be accounted for when distributing the instruments and interpreting the results.
Reaching Through Latent Space: From Joint Statistics to Path Planning in Manipulation

We present a novelapproach to path planning for robotic manipulators, in which paths are produced via iterative optimisation in the latent space of a generative model of robot poses. Constraints are incorporated through the use of constraint satisfaction classifiers operating on the same space. Optimisation leverages gradients through our learned models that provide a simple way to combine goal reaching objectives with constraint satisfaction, even in the presence of otherwise non-differentiable constraints. Our models are trained in a task-agnostic manner on randomly sampled robot poses. In baseline comparisons against a number of widely used planners, we achieve commensurate performance in terms of task success, planning time and path length, performing successful path planning with obstacle avoidance on a real 7-DoF robot arm.
Urban Driver: Learning to Drive from Real-world Demonstrations Using Policy Gradients

In this work we are the first to present an offline policy gradient method for learning imitative policies for complex urban driving from a large corpus of real-world demonstrations. This is achieved by building a differentiable data-driven simulator on top of perception outputs and high-fidelity HD maps of the area. It allows us to synthesize new driving experiences from existing demonstrations using mid-level representations. Using this simulator we then train a policy network in closed-loop employing policy gradients. We train our proposed method on 100 hours of expert demonstrations on urban roads and show that it learns complex driving policies that generalize well and can perform a variety of driving maneuvers. We demonstrate this in simulation as well as deploy our model to self-driving vehicles in the real-world. Our method outperforms previously demonstrated state-of-the-art for urban driving scenarios -- all this without the need for complex state perturbations or collecting additional on-policy data during training. We make code and data publicly available.
Bankruptcy Resolution: Misery or Strategy

Contrary to conventional wisdom, this study reports a positive relationship between large US firms' leverage levels and their likelihood of emerging from Chapter 11 bankruptcy. In anticipation of a favourable court outcome, which allows them to emerge from bankruptcy with reduced debt, firms tend to increase their leverage levels in the years preceding the bankruptcy filing year. This suggests strategic abuse of bankruptcy courts and creditors. Test results suggest that firms start acting strategically up to four years before filing for bankruptcy so that they can emerge with a reduced debt burden at the cost of creditors. Additionally, our study also contributes to the corporate bankruptcy literature by exploring a set of factors (related to the firm, judicial, case, geographic, and macroeconomic characteristics) explaining the likelihood of firms emerging from bankruptcy, and proposing a parsimonious multivariate model that best predicts the likelihood of surviving Chapter 11 bankruptcy.
Political Connections and Credit Allocations: Evidence from China’s State-owned Enterprises in Land Market

This study examines the underlying mechanisms that drive the price premiums State-owned Enterprises (SOEs) pay at land auctions using a comprehensive and representative dataset of 316,320 transactions of land use rights from 2000 to 2016 in approximately 2,300 counties of urban China. We find that the SOEs paid 9.65% more than their Private-owned Enterprises (POEs) counterparts for comparable land parcels at auctions, and the land quality can largely explain the price premiums SOEs pay. In addition, SOEs’ soft budget constraint enables them to overbid for the lands they desire, and SOEs even bid higher prices for land after the Economic Stimulas program. Lastly, we show that SOEs’ monetary wealth and political connections crowd out POEs in areas with quality land.
Local Labor Market Spillover of M&As

This paper examines the local labor spillover effect of mergers and acquisitions (M&As). By focusing on M&As in the manufacturing sector, I find that, in the metropolitan statistical areas (MSAs) where target firms reside, the negative effect of M&As on employment growth spills over from the manufacturing sector to the non-tradable sector through shrinking local consumer demand. Further tests with household-level data confirm this finding. The spillover effect is stronger when M&A transactions are horizontal and when an MSA relies more heavily on the manufacturing sector. Finally, lower minimum wage requirements may absorb the negative pressure from M&As on the non-tradable sector employment growth.
“Innocent” Hashtags? A Cautionary Tale: #IStandWithGreece as a Network of Intolerance on Twitter During a Land Border Crisis

This study explores the hashtag #IStandWithGreece as part of the meaning-making processes on Twitter around a border crisis at Europe’s periphery, the Greek–Turkish land border. Adopting a network perspective, we located the most influential Twitter accounts using #IStandWithGreece, the communities they formed in the microblog, and other hashtags used to communicate their views in relation to the unfolding events. This allowed the scanning of the broader ideological character of these influencers and their respective communities and, by extent, that of the debate around the hashtag. The study exposes the strategic use of a seemingly innocent hashtag by certain influential actors to disseminate antimigrant stances that cut across national contexts of the Global North.
Pathways to Federal Government: A Study of the Pathways Programs and Millennial Inclusion in Federal Government

This study seeks to better understand the federal government’s “Pathways Programs”, which are comprised of internships, recent graduate hiring priorities, and the Presidential Management Fellowship (PMF). The purpose of the Pathways Program is to increase younger generations’ access to federal employment. This study hopes to assess the relationship between participation in the Pathways Programs and the percentage of the millennials working within federal government, as a means of evaluating the success of the Pathways Programs. RUNNING HEAD: PATHWAYS TO FEDERAL GOVERNMENT 2
Invertible DenseNets

We introduce Invertible Dense Networks (i-DenseNets), a more parameter eﬃcient alternative to Residual Flows. The method relies on an analysis of the Lipschitz continuity of the concatenation in DenseNets, where we enforce the invertibility of the network by satisfying the Lipschitz constraint. Additionally, we extend this method by proposing a learnable concatenation, which not only improves the model performance but also indicates the importance of the concatenated representation. We demonstrate the performance of i-DenseNets and Residual Flows on toy, MNIST, and CIFAR10 data. Both i-DenseNets outperform Residual Flows evaluated in negative log-likelihood, on all considered datasets under an equal parameter budget.
Identification of a Diguanylate Cyclase That Facilitates Biofilm Formation on Electrodes by <named-content content-type='genus-species'>Shewanella oneidensis</named-content> MR-1

In many bacteria, cyclic diguanosine monophosphate (c-di-GMP), synthesized by diguanylate cyclase (DGC), serves as a second messenger involved in the regulation of biofilm formation. Although studies have suggested that c-di-GMP also regulates the formation of electrochemically active biofilms (EABFs) by Shewanella oneidensis MR-1, DGCs involved in this process remained to be identified. Here, we report that the SO_1646 gene, hereafter named dgcS, is upregulated under medium flow conditions in electrochemical flow cells (EFCs), and its product (DgcS) functions as a major DGC in MR-1. In vitro assays demonstrated that purified DgcS catalyzed the synthesis of c-di-GMP from GTP. Comparisons of intracellular c-di-GMP levels in the wild-type strain and a dgcS deletion mutant (DdgcS mutant) showed that production of c-di-GMP was markedly reduced in the DdgcS mutant when cells were grown in batch cultures and on electrodes in EFCs. Cultivation of the DdgcS mutant in EFCs also revealed that the loss of DgcS resulted in impaired biofilm formation and decreased current generation. These findings demonstrate that MR-1 uses DgcS to synthesize c-di-GMP under medium flow conditions, thereby activating biofilm formation on electrodes. IMPORTANCE Bioelectrochemical systems (BESs) have attracted wide attention owing to their utility in sustainable biotechnology processes, such as microbial fuel cells and electrofermentation systems. In BESs, electrochemically active bacteria (EAB) form biofilms on electrode surfaces, thereby serving as effective catalysts for the interconversion between chemical and electric energy. It is therefore important to understand mechanisms for the formation of biofilm by EAB grown on electrodes. Here, we show that a model EAB, S. oneidensis MR-1, expresses DgcS as a major DGC, thereby activating the formation of biofilms on electrodes via c-di-GMP-dependent signal transduction cascades. The findings presented herein provide the molecular basis for improving electrochemical interactions between EAB and electrodes in BESs. The results also offer molecular insights into how Shewanella regulates biofilm formation on solid surfaces in the natural environment.
Robustness Disparities in Commercial Face Detection

Facial detection and analysis systems have been deployed by large companies and 1 critiqued by scholars and activists for the past decade. Critiques that focus on 2 system performance analyze disparity of the system’s output, i.e., how frequently is 3 a face detected for different Fitzpatrick skin types or perceived genders. However, 4 we focus on the robustness of these system outputs under noisy natural perturba5 tions. We present the first of its kind detailed benchmark of the robustness of two 6 such systems: Amazon Rekognition and Microsoft Azure. We use both standard 7 and recently released academic facial datasets to quantitatively analyze trends in 8 robustness for each. Qualitatively across all the datasets and systems, we find that 9 photos of individuals who are older, masculine presenting, of darker skin type, or 10 have dim lighting are more susceptible to errors than their counterparts in other 11 identities. 12
CONVERGENCE RATE FOR THE HOMOGENIZATION OF DIFFUSIONS IN DILUTELY PERFORATED DOMAINS WITH REFLECTING BOUNDARIES

We revisit the homogenization problem for the Poisson equation in periodically perforated domains with zero Neumann data at the boundary of the holes and prescribed Dirichlet data at the outer boundary. It is known that, if the periodicity of the holes goes to zero but their volume fraction remains fixed and positive, the limit problem is a Dirichlet boundary value problem posed in the domain without the holes, and the effective diffusion coefficients are non-trivially modified; if that volume fraction goes to zero instead, i.e. the holes are dilute, the effective operator remains the Laplacian (that is, unmodified). Our main results contain the study of a “continuity” in those effective models with respect to the volume fraction of the holes and some new convergence rates for homogenization in the dilute setting. Our method explores the classical two-scale expansion ansatz and relies on asymptotic analysis of the rescaled cell problems using layer potential theory.
Model of Lithium Intercalation into Graphite by Potentiometric Analysis with Equilibrium and Entropy Change Curves of Graphite Electrode

One of the interests in studying the intercalation phenomenon of Li-ion is to explain the hystereses which are observed on the open circuit voltage curve of the graphite electrode during the charge and discharge. We investigated a potentiometric method to obtain the equilibrium curve and entropy change curve of the graphite electrode in charge and discharge. These curves lead to the analysis of the intercalation compounds in the graphite electrode. The results show a high hysteresis between the lithiation and delithiation in region II on the entropy curve. We do not observe the formation of LiC18 compound which would be observed at filling fraction x = 0.33 and there is no clear evidence of the LiC27 at x = 0.22. Based on our observations, we propose an intercalation model of Li into graphite in an attempt to explain the hysteresis phenomenon which was observed during charge and discharge in region II due to the possible presence of the compound LiC24. We have also observed a possible compound for the LiC24 by XRD post-mortem analysis. © The Author(s) 2018. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 License (CC BY, http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse of the work in any medium, provided the original work is properly cited. [DOI: 10.1149/2.1251802jes]