cssi/SciSciGPT-SciSciNet huggingface dataset:
Example-driven query intent discovery: abductive reasoning using semantic similarity

Traditional relational data interfaces require precise structured queries over potentially complex schemas. These rigid data retrieval mechanisms pose hurdles for non-expert users, who typically lack language expertise and are unfamiliar with the details of the schema. Query by Example (QBE) methods offer an alternative mechanism: users provide examples of their intended query output and the QBE system needs to infer the intended query. However, these approaches focus on the structural similarity of the examples and ignore the richer context present in the data. As a result, they typically produce queries that are too general, and fail to capture the user's intent effectively. In this paper, we present SQuID, a system that performs semantic similarity-aware query intent discovery. Our work makes the following contributions: (1) We design an end-to-end system that automatically formulates select-project-join queries in an open-world setting, with optional group-by aggregation and intersection operators; a much larger class than prior QBE techniques. (2) We express the problem of query intent discovery using a probabilistic abduction model, that infers a query as the most likely explanation of the provided examples. (3) We introduce the notion of an abduction-ready database, which precomputes semantic properties and related statistics, allowing SQuID to achieve real-time performance. (4) We present an extensive empirical evaluation on three real-world datasets, including user-intent case studies, demonstrating that SQuID is efficient and effective, and outperforms machine learning methods, as well as the state-of-the-art in the related query reverse engineering problem.
Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome

The emerging and increasing prevalence of bacterial antibiotic resistance is a significant public health challenge. To begin to tackle this problem, it will be critical to not only understand the origins of this resistance but also document environmental reservoirs of antibiotic resistance. In this study we investigated the possibility that both colony and field caught mosquitoes could harbor antibiotic resistant bacteria. Specifically, we characterized the antibiotic resistant bacterial populations from colony-reared Aedes aegypti larvae and adults and two field caught mosquito species Coquillettidia perturbans and Ochlerotatus canadensis. The cultured bacterial populations were dominated by isolates belonging to the class Gammaproteobacteria. Among the antibiotic resistant populations, we found bacteria resistant to carbenicillin, kanamycin, and tetracycline, including bacteria resistant to a cocktail of all three antibiotics in combination. The antibiotic resistant bacteria were numerically rare, at most 5% of total cell counts. Isolates were characterized by 16S rRNA gene sequencing, and clustering into Operational Taxonomic Units (OTUs; 99% sequence identity). 27 antibiotic resistant OTUs were identified, although members of an OTU did not always share the same resistance profile. This suggests the clustering was either not sensitive enough to distinguish different bacteria taxa or different antibiotic resistant sub-populations exist within an OTU. Finally, the antibiotic selection opened up a niche to culture mosquito-associated fungi, and 10 fungal OTUs (28S rRNA gene sequencing) were identified. Two fungal OTUs both classified to the class Microbotryomycetes were commonly identified in the field-caught mosquitoes. Thus, in this study we demonstrate that antibiotic resistant bacteria and certain fungi are common and conserved mosquito microbiome members. These observations highlight the potential of invertebrates to serve as vehicles for the spread of antibiotic resistance throughout the environment.
Low provider and staff self-care in a large safety-net HIV clinic in the Southern United States: Implications for the adoption of trauma-informed care:

Objective:This mixed-methods needs assessment study examined self-care practices among providers, staff, and administrators at an HIV clinic and identified barriers and facilitators to strengthenin...
Real-Time Middleware for Cyber-Physical Event Processing

Cyber-physical systems (CPS) involve tight integration of cyber (computation) and physical domains, and both the effectiveness and correctness of a cyber-physical system application may rely on successful enforcement of constraints such as bounded latency and temporal validity subject to physical conditions. For many such systems (e.g., edge computing in the Industrial Internet of Things), it is desirable to enforce such constraints within a common middleware service (e.g., during event processing). In this article, we introduce CPEP, a new real-time middleware for cyber-physical event processing, with (1) extensible support for complex event processing operations, (2) execution prioritization and sharing, (3) enforcement of time consistency with load shedding, and (4) efficient memory management and concurrent data processing. We present the design, implementation, and empirical evaluation of CPEP and show that it can (1) support complex operations needed by many applications, (2) schedule data processing according to consumers’ priority levels, (3) enforce temporal validity, and (4) reduce processing delay and improve throughput of time-consistent events.
Safeguarding cryptographic keys

Certain cryptographic keys, such as a number which makes it possible to compute the secret decoding exponent in an RSA public key cryptosystem, 1 , 5 or the system master key and certain other keys in a DES cryptosystem, 3 are so important that they present a dilemma. If too many copies are distributed one might go astray. If too few copies are made they might all be destroyed.
Biangular Gabor frames and Zauner's conjecture

Two decades ago, Zauner conjectured that for every dimension d, there exists an equiangular tight frame consisting of d2 vectors in Cd . Most progress to date explicitly constructs the promised frame in various dimensions, and it now appears that a constructive proof of Zauner’s conjecture may require progress on the Stark conjectures. In this paper, we propose an alternative approach involving biangular Gabor frames that may eventually lead to an unconditional non-constructive proof of Zauner’s conjecture.
MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation

When reading medical images such as a computed tomography (CT) scan, radiologists generally search across the image to find lesions, characterize and measure them, and then describe them in the radiological report. To automate this process, we propose a multitask universal lesion analysis network (MULAN) for joint detection, tagging, and segmentation of lesions in a variety of body parts, which greatly extends existing work of single-task lesion analysis on specific body parts. MULAN is based on an improved Mask R-CNN framework with three head branches and a 3D feature fusion strategy. It achieves the state-of-the-art accuracy in the detection and tagging tasks on the DeepLesion dataset, which contains 32K lesions in the whole body. We also analyze the relationship between the three tasks and show that tag predictions can improve detection accuracy via a score refinement layer.
A dynamic strategy coach for effective negotiation

Negotiation is a complex activity involving strategic reasoning, persuasion, and psychology. An average person is often far from an expert in negotiation. Our goal is to assist humans to become better negotiators through a machine-in-the-loop approach that combines machine’s advantage at data-driven decision-making and human’s language generation ability. We consider a bargaining scenario where a seller and a buyer negotiate the price of an item for sale through a text-based dialogue. Our negotiation coach monitors messages between them and recommends strategies in real time to the seller to get a better deal (e.g., “reject the proposal and propose a price”, “talk about your personal experience with the product”). The best strategy largely depends on the context (e.g., the current price, the buyer’s attitude). Therefore, we first identify a set of negotiation strategies, then learn to predict the best strategy in a given dialogue context from a set of human-human bargaining dialogues. Evaluation on human-human dialogues shows that our coach increases the profits of the seller by almost 60%.
FLEET: Butterfly Estimation from a Bipartite Graph Stream

We consider space-efficient single-pass estimation of the number of butterflies, a fundamental bipartite graph motif, from a massive bipartite graph stream where each edge represents a connection between entities in two different partitions. We present a space lower bound for any streaming algorithm that can estimate the number of butterflies accurately, as well as FLEET, a suite of algorithms for accurately estimating the number of butterflies in the graph stream. Estimates returned by the algorithms come with provable guarantees on the approximation error, and experiments show good tradeoffs between the space used and the accuracy of approximation. We also present space-efficient algorithms for estimating the number of butterflies within a sliding window of the most recent elements in the stream. While there is a significant body of work on counting subgraphs such as triangles in a unipartite graph stream, our work seems to be one of the few to tackle the case of bipartite graph streams.
Editorial: Which Wei Wang?

The APS journals receive manuscripts from scientists all over the world. For authors whose names cannot be expressed in Latin characters, their names in the byline must be transliterated, a process that is not necessarily bidirectionally unique. For example, the eight Chinese names all transliterate as Wei Wang. To remove some of the ambiguity arising from this unfortunate degeneracy of names, APS will allow some authors the option to include their names in their own language in parentheses after the transliterated name, such as Wei Wang. The option to present names in the article byline in this manner is an experiment initially offered to Chinese, Japanese, and Korean authors, whose names can be expressed in Unicode characters. An example of a Japanese name is Tadanori Minamisono and a Korean name is Chang Kee Jung. In the English text the given name precedes the family name, while the reverse is true for the characters. As we gain experience, we may be able to broaden this offer to other languages. Authors who wish to try this option will need to prepare their manuscripts by following the special instructions at http://authors.aps.org/names.html.
Long-term Risk of Recurrence in Surgically Treated Renal Cell Carcinoma: A Post Hoc Analysis of the Eastern Cooperative Oncology Group—American College of Radiology Imaging Network E2805 Trial Cohort

Abstract Currently, surveillance guidelines following surgical resection of clinically localized renal cell carcinoma (RCC) are clear within the first 5 yr; however, these lack the same degree of objectivity following this cutoff. We sought to investigate the long-term risk of recurrence in surgically treated RCC in order to determine the utility of long-term surveillance. A post hoc analysis of patients within the Eastern Cooperative Oncology Group—American College of Radiology Imaging Network (ECOG-ACRIN) E2805 trial cohort was performed. The 36-mo cumulative incidence of recurrence was assessed at set intervals following surgery, in order to dynamically assess recurrence through the use of a conditional survival model. Of the 1943 patients included in the original cohort, 730 developed recurrence. The 36-mo cumulative incidences of recurrence were found to be 31%, 26%, 19%, 16%, 19%, and 20% for patients at 0, 12, 24, 36, 48, and 60 mo from surgery, respectively. At 0 mo from surgery, age, pathological T3/4 stage (hazard ratio [HR] = 1.56), pathological N1/2 stage (HR = 2.38), and Fuhrman grades 3 and 4 (HR = 1.36 and HR = 2.41, respectively) were independent predictors of recurrence; however, this was not seen at 60 mo following surgery. These findings support that surveillance imaging should be performed beyond 5 yr following surgical resection of intermediate- to high-risk RCC. Patient summary : Follow-up for surgically resected localized renal cell carcinoma should be performed beyond 5 yr, for the rates of recurrence remain significant beyond this 5 yr endpoint.
Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels

The 2015 American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that “well-established” functional studies can be used as evidence in variant classification. These guidelines articulated key attributes of functional data, including that assays should reflect the biological environment and be analytically sound; however, details of how to evaluate these attributes were left to expert judgment. The Clinical Genome Resource (ClinGen) designates Variant Curation Expert Panels (VCEPs) in specific disease areas to make gene-centric specifications to the ACMG/AMP guidelines, including more specific definitions of appropriate functional assays. We set out to evaluate the existing VCEP guidelines for functional assays. We evaluated the functional criteria (PS3/BS3) of six VCEPs (CDH1, Hearing Loss, Inherited Cardiomyopathy-MYH7, PAH, PTEN, RASopathy). We then established criteria for evaluating functional studies based on disease mechanism, general class of assay, and the characteristics of specific assay instances described in the primary literature. Using these criteria, we extensively curated assay instances cited by each VCEP in their pilot variant classification to analyze VCEP recommendations and their use in the interpretation of functional studies. Unsurprisingly, our analysis highlighted the breadth of VCEP-approved assays, reflecting the diversity of disease mechanisms among VCEPs. We also noted substantial variability between VCEPs in the method used to select these assays and in the approach used to specify strength modifications, as well as differences in suggested validation parameters. Importantly, we observed discrepancies between the parameters VCEPs specified as required for approved assay instances and the fulfillment of these requirements in the individual assays cited in pilot variant interpretation. Interpretation of the intricacies of functional assays often requires expert-level knowledge of the gene and disease, and current VCEP recommendations for functional assay evidence are a useful tool to improve the accessibility of functional data by providing a starting point for curators to identify approved functional assays and key metrics. However, our analysis suggests that further guidance is needed to standardize this process and ensure consistency in the application of functional evidence.
Pseudo-BCI algebras with derivations

In this paper we define two types of implicative derivations on pseudo-BCI algebras, we investigate their properties and we give a characterization of regular implicative derivations of type II. We also define the notion of a $d$-invariant deductive system of a pseudo-BCI algebra $A$ proving that $d$ is a regular derivation of type II if and only if every deductive system on $A$ is $d$-invariant. It is proved that a pseudo-BCI algebra is $p$-semisimple if and only if the only regular derivation of type II is the identity map. Another main result consists of proving that the set of all implicative derivations of a $p$-semisimple pseudo-BCI algebra forms a commutative monoid with respect to function composition. Two types of symmetric derivations on pseudo-BCI algebras are also introduced and it is proved that in the case of $p$-semisimple pseudo-BCI algebras the sets of type II implicative derivations and type II symmetric derivations are equal.
Computing Residual Diffusivity by Adaptive Basis Learning via Super-Resolution Deep Neural Networks

It is expensive to compute residual diffusivity in chaotic in-compressible flows by solving advection-diffusion equation due to the formation of sharp internal layers in the advection dominated regime. Proper orthogonal decomposition (POD) is a classical method to construct a small number of adaptive orthogonal basis vectors for low cost computation based on snapshots of fully resolved solutions at a particular molecular diffusivity \(D_{0}^{*}\). The quality of POD basis deteriorates if it is applied to \(D_0\ll D_{0}^{*}\). To improve POD, we adapt a super-resolution generative adversarial deep neural network (SRGAN) to train a nonlinear mapping based on snapshot data at two values of \(D_{0}^{*}\). The mapping models the sharpening effect on internal layers as \(D_0\) becomes smaller. We show through numerical experiments that after applying such a mapping to snapshots, the prediction accuracy of residual diffusivity improves considerably that of the standard POD.
Stress transmission through three-dimensional granular crystals with stacking faults

We explore the effect of stacking fault defects on the transmission of forces in three-dimensional face-centered-cubic granular crystals. An external force is applied to a small area at the top surface of a crystalline packing of granular beads containing one or two stacking faults at various depths. The response forces at the bottom surface are measured and found to correspond to predictions based on vector force balance within the geometry of the defects. We identify the elementary stacking fault as a boundary between two pure face-centered-cubic crystals with different stacking orders. Other stacking faults produce response force patterns that can be viewed as resulting from repetitions of this basic defect. As the number of stacking faults increases, the intensity pattern evolves toward that of an hexagonal-close-packed crystal. This leads to the conclusion that the force pattern of that crystal structure can be viewed as the extreme limit of a face-centered-cubic crystal with a stacking fault at every layer.
Single-Neuron Representations of Spatial Targets in Humans

The hippocampus and surrounding medial-temporal-lobe (MTL) structures are critical for both memory and spatial navigation, but we do not fully understand the neuronal representations used to support these behaviors. Much research has examined how the MTL neurally represents spatial information, such as with "place cells" that represent an animal's current location or "head-direction cells" that code for an animal's current heading. In addition to behaviors that require an animal to attend to the current spatial location, navigating to remote destinations is a common part of daily life. To examine the neural basis of these behaviors, we recorded single-neuron activity from neurosurgical patients playing Treasure Hunt, a virtual-reality spatial-memory task. By analyzing how the activity of these neurons related to behavior in Treasure Hunt, we found that the firing rates of many MTL neurons during navigation significantly changed depending on the position of the current spatial target. In addition, we observed neurons whose firing rates during navigation were tuned to specific heading directions in the environment, and others whose activity changed depending on the timing within the trial. By showing that neurons in our task represent remote locations rather than the subject's own position, our results suggest that the human MTL can represent remote spatial information according to task demands.
Trend Analysis on Adoption of Virtual and Augmented Reality in the Architecture, Engineering, and Construction Industry

With advances in Building Information Modeling (BIM), Virtual Reality (VR) and Augmented Reality (AR) technologies have many potential applications in the Architecture, Engineering, and Construction (AEC) industry. However, the AEC industry, relative to other industries, has been slow in adopting AR/VR technologies, partly due to lack of feasibility studies examining the actual cost of implementation versus an increase in profit. The main objectives of this paper are to understand the industry trends in adopting AR/VR technologies and identifying gaps within the industry. The identified gaps can lead to opportunities for developing new tools and finding new use cases. To achieve these goals, two rounds of a survey at two different time periods (a year apart) were conducted. Responses from 158 industry experts and researchers were analyzed to assess the current state, growth, and saving opportunities for AR/VR technologies for the AEC industry. The findings demonstrate that older generations are significantly more confident about the future of AR/VR technologies and they see more benefits in AR/VR utilization. Furthermore, the research results indicate that Residential and commercial sectors have adopted these tools the most, compared to other sectors and institutional and transportation sectors had the highest growth from 2017 to 2018. Industry experts anticipated a solid growth in the use of AR/VR technologies in 5 to 10 years, with the highest expectations towards healthcare. Ultimately, the findings show a significant increase in AR/VR utilization in the AEC industry from 2017 to 2018.
Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation

Summary Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others’ closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation.
Orbital transmutation and the electronic spectrum of FeSe in the nematic phase

The authors discuss recent experimental observations on the nematic phase of FeSe in terms of an orbital transmutation of the low-energy excitations between the normal state and the nematic phase
Weighted Completion Time Minimization for Unrelated Machines via Iterative Fair Contention Resolution.

We give a 1.488-approximation for the classic scheduling problem of minimizing total weighted completion time on unrelated machines. This is a considerable improvement on the recent breakthrough of $(1.5 - 10^{-7})$-approximation (STOC 2016, Bansal-Srinivasan-Svensson) and the follow-up result of $(1.5 - 1/6000)$-approximation (FOCS 2017, Li). Bansal et al. introduced a novel rounding scheme yielding strong negative correlations for the first time and applied it to the scheduling problem to obtain their breakthrough, which resolved the open problem if one can beat out the long-standing $1.5$-approximation barrier based on independent rounding. Our key technical contribution is in achieving significantly stronger negative correlations via iterative fair contention resolution, which is of independent interest. Previously, Bansal et al. obtained strong negative correlations via a variant of pipage type rounding and Li used it as a black box.
A Two-Tiered Welfare State

The eligibility rules, sanctions, and privacy intrusions discussed in previous chapters only exist in programs aimed at low-income families. None of these features can be found in programs aimed at middle- or upper-income families, which constitute much greater proportions of the total federal budget. Possible explanations for this double standard include the application of ascetic values to needy families and lower levels of empathy across racial groups. The two tiers of social policy have detrimental effects to all Americans. Basic-income advocates argue that the only way to address unfair social policy is to replace significant pieces of it with one, universal system.
Sleeve gastrectomy enhances glucose utilization and remodels adipose tissue independent of weight loss

Sleeve gastrectomy (SG) induces weight loss-independent improvements in glucose homeostasis by unknown mechanisms. We sought to identify the metabolic adaptations responsible for these improvements. Nonobese C57BL/6J mice on standard chow underwent SG or sham surgery. Functional testing and indirect calorimetry were used to capture metabolic phenotypes. Tissue-specific glucose uptake was assessed by 18-fluorodeoxyglucose (18-FDG) PET/computed tomography, and RNA sequencing was used for gene-expression analysis. In this model, SG induced durable improvements in glucose tolerance in the absence of changes in weight, body composition, or food intake. Indirect calorimetry revealed that SG increased the average respiratory exchange ratio toward 1.0, indicating a weight-independent, systemic shift to carbohydrate utilization. Following SG, orally administered 18-FDG preferentially localized to white adipose depots, showing tissue-specific increases in glucose utilization induced by surgery. Transcriptional analysis with RNA sequencing demonstrated that increased glucose uptake in the visceral adipose tissue was associated with upregulation in transcriptional pathways involved in energy metabolism, adipocyte maturation, and adaptive and innate immune cell chemotaxis and differentiation. SG induces a rapid, weight loss-independent shift toward glucose utilization and transcriptional remodeling of metabolic and immune pathways in visceral adipose tissue. Continued study of this early post-SG physiology may lead to a better understanding of the anti-diabetic mechanisms of bariatric surgery.
Iroki: automatic customization and visualization of phylogenetic trees

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
Drug Abuse and the Internet: Evidence from Craigslist

The United States is in the midst of a drug overdose epidemic. Although the online availability of drugs has been a growing concern with considerable speculation that digital platforms are contribu...
The Structure of Radiatively Inefficient Black Hole Accretion Flows

We run three long-timescale general-relativistic magnetohydrodynamic simulations of radiatively inefficient accretion flows onto non-rotating black holes. Our aim is to achieve steady-state behavior out to large radii and understand the resulting flow structure. A simulation with adiabatic index Gamma = 4/3 and small initial alternating poloidal magnetic field loops is run to a time of 440,000 GM/c^3, reaching inflow equilibrium inside a radius of 370 GM/c^2. Variations with larger alternating field loops and with Gamma = 5/3 are run to 220,000 GM/c^3, attaining equilibrium out to 170 GM/c^2 and 440 GM/c^2. There is no universal self-similar behavior obtained at radii in inflow equilibrium: the Gamma = 5/3 simulation shows a radial density profile with power law index ranging from -1 in the inner regions to -1/2 in the outer regions, while the others have a power-law slope ranging from -1/2 to close to -2. Both simulations with small field loops reach a state with polar inflow of matter, while the more ordered initial field has polar outflows. However, unbound outflows remove only a factor of order unity of the inflowing material over a factor of ~300 in radius. Our results suggest that the dynamics of radiatively inefficient accretion flows are sensitive to how the flow is fed from larger radii, and may differ appreciably in different astrophysical systems. Millimeter images appropriate for Sgr A* are qualitatively (but not quantitatively) similar in all simulations, with a prominent asymmetric image due to Doppler boosting.
Identification of a PRC2 Accessory Subunit Required for Subtelomeric H3K27 Methylation in Neurospora crassa.

Polycomb repressive complex 2 (PRC2) catalyzes methylation of histone H3 at lysine 27 (H3K27) in genomic regions of most eukaryotes and is critical for maintenance of the associated transcriptional repression. However, the mechanisms that shape the distribution of H3K27 methylation, such as recruitment of PRC2 to chromatin and/or stimulation of PRC2 activity, are unclear. Here, using a forward genetic approach in the model organism Neurospora crassa, we identified two alleles of a gene, NCU04278, encoding an unknown P RC2 a ccessory s ubunit (PAS). Loss of PAS resulted in losses of H3K27 methylation concentrated near the chromosome ends and derepression of a subset of associated subtelomeric genes. Immunoprecipitation followed by mass spectrometry confirmed reciprocal interactions between PAS and known PRC2 subunits, and sequence similarity searches demonstrated that PAS is not unique to N. crassa PAS homologs likely influence the distribution of H3K27 methylation and underlying gene repression in a variety of fungal lineages.
A Benchmark Suite for Evaluating Caches' Vulnerability to Timing Attacks

Based on improvements to an existing three-step model for cache timing-based attacks, this work presents 88 Strong types of theoretical timing-based vulnerabilities in processor caches. It also presents and implements a new benchmark suite that can be used to test if processor cache is vulnerable to one of the attacks. In total, there are 1094 automatically-generated test programs which cover the 88 Strong theoretical vulnerabilities. The benchmark suite generates the Cache Timing Vulnerability Score (CTVS) which can be used to evaluate how vulnerable a specific cache implementation is to different attacks. A smaller CTVS means the design is more secure. Evaluation is conducted on commodity Intel and AMD processors and shows how the differences in processor implementations can result in different types of attacks that they are vulnerable to. Further, the benchmarks and the CTVS can be used in simulation to help designers of new secure processors and caches evaluate their designs' susceptibility to cache timing-based attacks.
Defense-VAE: A Fast and Accurate Defense Against Adversarial Attacks

Deep neural networks (DNNs) have been enormously successful across a variety of prediction tasks. However, recent research shows that DNNs are particularly vulnerable to adversarial attacks, which poses a serious threat to their applications in security-sensitive systems. In this paper, we propose a simple yet effective defense algorithm Defense-VAE that uses variational autoencoder (VAE) to purge adversarial perturbations from contaminated images. The proposed method is generic and can defend white-box and black-box attacks without the need of retraining the original CNN classifiers, and can further strengthen the defense by retraining CNN or end-to-end finetuning the whole pipeline. In addition, the proposed method is very efficient compared to the optimization-based alternatives, such as Defense-GAN, since no iterative optimization is needed for online prediction. Extensive experiments on MNIST, Fashion-MNIST, CelebA and CIFAR-10 demonstrate the superior defense accuracy of Defense-VAE compared to Defense-GAN, while being 50x faster than the latter. This makes Defense-VAE widely deployable in real-time security-sensitive systems. Our source code can be found at https://github.com/lxuniverse/defense-vae.
Network cross-validation by edge sampling

Summary While many statistical models and methods are now available for network analysis, resampling of network data remains a challenging problem. Cross-validation is a useful general tool for model selection and parameter tuning, but it is not directly applicable to networks since splitting network nodes into groups requires deleting edges and destroys some of the network structure. In this paper we propose a new network resampling strategy, based on splitting node pairs rather than nodes, that is applicable to cross-validation for a wide range of network model selection tasks. We provide theoretical justification for our method in a general setting and examples of how the method can be used in specific network model selection and parameter tuning tasks. Numerical results on simulated networks and on a statisticians’ citation network show that the proposed cross-validation approach works well for model selection.
Robust window operators

It is a common practice in computer vision and image processing to convolve rectangular constant coefficient windows with digital images to perform local smoothing and derivative estimation for edge detection and other purposes. If all data points in each image window belong to the same statistical population, this practice is reasonable and fast. But, as is well known, constant coefficient window operators produce incorrect results if more than one statistical population is present within a window, for example, if a gray-level or gradient discontinuity is present. This paper shows one way to apply the theory of robust statistics to the data smoothing and derivative estimation problem. A robust window operator is demonstrated that preserves gray-level and gradient discontinuities in digital images as it smooths and estimates derivatives.
Rollout Algorithms for Stochastic Scheduling Problems

Stochastic scheduling problems are difficult stochastic control problems with combinatorial decision spaces. In this paper we focus on a class of stochastic scheduling problems, the quiz problem and its variations. We discuss the use of heuristics for their solution, and we propose rollout algorithms based on these heuristics which approximate the stochastic dynamic programming algorithm. We show how the rollout algorithms can be implemented efficiently, with considerable savings in computation over optimal algorithms. We delineate circumstances under which the rollout algorithms are guaranteed to perform better than the heuristics on which they are based. We also show computational results which suggest that the performance of the rollout policies is near-optimal, and is substantially better than the performance of their underlying heuristics.
Regulation of the ER stress response by a mitochondrial microprotein

Cellular homeostasis relies on having dedicated and coordinated responses to a variety of stresses. The accumulation of unfolded proteins in the endoplasmic reticulum (ER) is a common stress that triggers a conserved pathway called the unfolded protein response (UPR) that mitigates damage, and dysregulation of UPR underlies several debilitating diseases. Here, we discover that a previously uncharacterized 54-amino acid microprotein PIGBOS regulates UPR. PIGBOS localizes to the mitochondrial outer membrane where it interacts with the ER protein CLCC1 at ER-mitochondria contact sites. Functional studies reveal that the loss of PIGBOS leads to heightened UPR and increased cell death. The characterization of PIGBOS reveals an undiscovered role for a mitochondrial protein, in this case a microprotein, in the regulation of UPR originating in the ER. This study demonstrates microproteins to be an unappreciated class of genes that are critical for inter-organelle communication, homeostasis, and cell survival.
Edge states and the valley Hall effect

Abstract We study energy propagation along line-defects (edges) in two dimensional continuous, energy preserving periodic media. The unperturbed medium (bulk) is modeled by a honeycomb Schroedinger operator, which is periodic with respect to the triangular lattice, invariant under parity, P , and complex-conjugation, C . A honeycomb operator has Dirac points in its band structure: two dispersion surfaces touch conically at an energy level, E D [25] , [27] . Periodic perturbations which break P or C open a gap in the essential spectrum about energy E D . Such operators model an insulator near energy E D . Our edge operator is a small perturbation of the bulk and models a transition (via a domain wall) between distinct periodic, P or C breaking perturbations. The edge operator permits energy transport along the line-defect. The associated energy channels are called edge states. They are time-harmonic solutions of the underlying wave equation, which are localized near and propagating along the line-defect. They are of great scientific interest due to their remarkable stability, and are a key property of topological insulators. We completely characterize the edge state spectrum within the bulk spectral gap about E D . At the center of our analysis is an expansion of the edge operator resolvent for energies near E D . The leading term features the resolvent of an effective Dirac operator. Edge state eigenvalues are poles of the resolvent, which bifurcate from the Dirac point. The corresponding eigenstates have the multiscale structure identified in [23] . We extend earlier work on zigzag-type edges [14] to all rational edges. We elucidate the role in edge state formation played by the type of symmetry-breaking and the orientation of the edge. We prove the resolvent expansion by a new direct and transparent strategy. Our results also provide a rigorous explanation of the numerical observations in [22] , [38] ; see also the photonic experimental study in [42] . Finally we discuss implications for the Valley Hall Effect, which concerns quantum Hall-like energy transport in honeycomb structures.
Justice, mercy and equality in discretionary criminal justice decision-making

This essay examines whether, in exercising their discretion, criminal justice officials should do justice, grant mercy, and treat alleged or convicted offenders equally. Although it endorses doing justice, the essay maintains that officials should almost never reduce a just punishment simply to be merciful. Public officials are fiduciaries, and they ordinarily have no authority to make unmerited gifts. Sometimes, however, deciding not to inflict a just penalty can reflect the willingness of an entire society to forgive. That may be the case, for example, when truth and reconciliation commissions approve amnesties. The essay focuses on the teachings of Jesus Christ and questions some of them. It asks, for example, whether a modern chief executive would merit praise or condemnation if this executive followed Jesus's example in the case of the woman taken in adultery. The essay also suggests that—unlike other officials—chief executives exercising their pardon power need not act affirmatively to treat like cases alike. A conclusion notes that it would have been out of character for Jesus Christ to refuse a plea for mercy. Nevertheless, few Christians have endorsed an implication of his willingness to forgive—the abolition of criminal punishment.
The Photospheric Convection Spectrum

Spectra of the cellular photospheric flows are determined from observations acquired by the MDI instrument on the SOHO spacecraft. Spherical harmonic spectra are obtained from the full-disk observations. Fourier spectra are obtained from the high-resolution observations. The p-mode oscillation signal and instrumental artifacts are reduced by temporal filtering of the Doppler data. The resulting spectra give power (kinetic energy) per wave number for effective spherical harmonic degrees from 1 to over 3000. Significant power is found at all wavenumbers, including the small wavenumbers representative of giant cells. The time evolution of the spectral coefficients indicates that these small wavenumber components rotate at the solar rotation rate and thus represent a component of the photospheric cellular flows. The spectra show distinct peaks representing granules and supergranules but no distinct features at wavenumbers representative of mesogranules or giant cells. The observed cellular patterns and spectra are well represented by a model that includes two distinct modes – granules and supergranules.
Chapter 5 – Agonists: The Measurement of Affinity and Efficacy in Functional Assays

The use of cellular response to agonists is considered from the standpoint of optimal assays for measurement of agonism, recombinant assays, and the impact of real time kinetics. The chapter then discusses the practical us of the Black/Leff operational model for the quantification of agonist efficacy and the use of the model to predict agonism in all systems. The relevance and quantitative measurement of biased agonism is then considered.
PROTECTION AGAINST UVA-INDUCED PHOTOOXIDATIVE DAMAGE IN MAMMALIAN CELL LINES EXPRESSING INCREASED LEVELS OF METALLOTHIONEIN

Metallothionein (MT) is an endogenous low molecular weight protein that is inducible in a variety of eukaryotic cells and has the ability to selectivity bind heavy metal ions such as zinc and the cadmium. Although the exact physiological role of MT is still not understood, there is strong evidence that MT is involved in providing cellular resistance against the damaging effects of heavy metals and in the regulation of intracellular zinc and copper. Recently, it has been demonstrated that MT can scavenge radiation-induced reactive oxygen intermediates in vitro, specifically hydroxyl and superoxide radicals, and because of these observations it has been suggested that MT may provide protection against radiation-induced oxidative stress in vivo. Cell lines expressing increased levels of MT have demonstrated resistance to ionizing radiation, to ultraviolet radiation, and also to various DNA damaging agents including melphalan and cis-diaminedichloroplatinum. It is therefore important to gain some insight into the relationship between cellular MT content and cellular resistance to radiation and other DNA damaging agents. In this study we investigated the role of MT in providing protection against monochromatic 365-nm UVA radiation, which is known to generate intracellular reactive oxygen species that are involved in both DNA damage and cellmore » killing. For this purpose, we used zinc acetate, a potent inducer of MT, to elevate MT levels in V79 Chinese hamster fibroblasts prior to UVA exposure and determined cell survival for uninduced and induced cultures. In order to eliminate any zinc effects other than MT induction, we also isolated and characterized cadmium chloride-resistant clones of V79 cells that have increased steady-state levels of both MT mRNA and protein, and we examined their survival characteristics against 365-nm radiation in the absence of zinc acetate. 14 refs., 3 figs.« less
Characterization of the Relationship between the Chaperone and Lipid-Binding Functions of the 70-kDa Heat-Shock Protein, HspA1A

HspA1A, a molecular chaperone, translocates to the plasma membrane (PM) of stressed and cancer cells. This translocation results in HspA1A's cell-surface presentation, which renders tumors radiation insensitive. To specifically inhibit the lipid-driven HspA1A's PM translocation and devise new therapeutics it is imperative to characterize the unknown HspA1A's lipid-binding regions and determine the relationship between the chaperone and lipid-binding functions. To elucidate this relationship, we determined the effect of phosphatidylserine (PS)-binding on the secondary structure and chaperone functions of HspA1A. Circular dichroism revealed that binding to PS resulted in minimal modification on HspA1A's secondary structure. Measuring the release of inorganic phosphate revealed that PS-binding had no effect on HspA1A's ATPase activity. In contrast, PS-binding showed subtle but consistent increases in HspA1A's refolding activities. Furthermore, using a Lysine-71-Alanine mutation (K71A; a null-ATPase mutant) of HspA1A we show that although K71A binds to PS with affinities similar to the wild-type (WT), the mutated protein associates with lipids three times faster and dissociates 300 times faster than the WT HspA1A. These observations suggest a two-step binding model including an initial interaction of HspA1A with lipids followed by a conformational change of the HspA1A-lipid complex, which accelerates the binding reaction. Together these findings strongly support the notion that the chaperone and lipid-binding activities of HspA1A are dependent but the regions mediating these functions do not overlap and provide the basis for future interventions to inhibit HspA1A's PM-translocation in tumor cells, making them sensitive to radiation therapy.
Lattice calculation of the lowest-order hadronic contribution to the muon anomalous magnetic moment.

We present a quenched lattice calculation of the lowest order (alpha^2) hadronic contribution to the anomalous magnetic moment of the muon which arises from the hadronic vacuum polarization. A general method is presented for computing entirely in Euclidean space, obviating the need for the usual dispersive treatment which relies on experimental data for e^+e^- annihilation to hadrons. While the result is not yet of comparable accuracy to those state-of-the-art calculations, systematic improvement of the quenched lattice computation to this level of accuracy is straightforward and well within the reach of present computers. Including the effects of dynamical quarks is conceptually trivial, the computer resources required are not.