cssi/SciSciGPT-SciSciNet huggingface dataset:
Continuous factorization of the identity matrix

We investigate conditions under which the identity matrix I n can be continuously factorized through a continuous N × N matrix function A with domain in ℝ . We study the relationship of the dimension N , the diagonal entries of A , and the norm of A to the dimension n and the norms of the matrices that witness the factorization of I n through A .
Ajinomoto v. ITC, the Doctrine of Equivalents, and Biomolecule Claim Limitations at the Federal Circuit

The doctrine of equivalents (DOE) allows a court to hold an accused infringer liable for patent infringement in spite of the fact that the accused product (or process) does not fall within the literal scope of the asserted patent claim(s). Prosecution history estoppel (PHE), which can be triggered by a narrowing amendment of a patent claim during patent prosecution, or by arguments made during prosecution, imposes significant constraints on the ability of a patentee to assert the DOE. The 1990s and early 2000’s saw a proliferation of legal commentary postulating that the DOE would play an important role in protecting inventions arising out of biotechnology, particularly biomolecules (i.e., proteins and DNA/polynucleotides), and stressing the need for biotechnology patentees to avoid amendments or arguments during patent prosecution that might trigger PHE. In fact, however, prior to 2019 the Federal Circuit does not appear to have issued an opinion finding infringement under the DOE in a case in which the relevant claim limitation recites a biomolecule. It finally happened in Ajinomoto Co. v. Int'l Trade Comm'n, with a divided panel of the Federal Circuit holding that a claim limitation reciting a DNA sequence, defined in terms of the amino acid sequence of a protein encoded by the sequence, was infringed under the DOE by a DNA sequence encoding a protein having a different (but similar) amino acid sequence and equivalent function. This article begins with a brief overview of the DOE and PHE, and explains why DOE was at one time seen as particularly critical for the enforcement of patent claims reciting biomolecules. It then summarizes and analyzes the results of a Westlaw search designed to identify any and all Federal Circuit decisions applying the DOE and/or PHE to a claim limitation reciting a biomolecule, including the court’s most recent decision Ajinomoto.
An adaptive QRS detection algorithm for ultra-long-term ECG recordings.

Abstract Background Accurate detection of QRS complexes during mobile, ultra-long-term ECG monitoring is challenged by instances of high heart rate, dramatic and persistent changes in signal amplitude, and intermittent deformations in signal quality that arise due to subject motion, background noise, and misplacement of the ECG electrodes. Purpose We propose a revised QRS detection algorithm which addresses the above-mentioned challenges. Methods and results Our proposed algorithm is based on a state-of-the-art algorithm after applying two key modifications. The first modification is implementing local estimates for the amplitude of the signal. The second modification is a mechanism by which the algorithm becomes adaptive to changes in heart rate. We validated our proposed algorithm against the state-of-the-art algorithm using short-term ECG recordings from eleven annotated databases available at Physionet, as well as four ultra-long-term (14-day) ECG recordings which were visually annotated at a central ECG core laboratory. On the database of ultra-long-term ECG recordings, our proposed algorithm showed a sensitivity of 99.90% and a positive predictive value of 99.73%. Meanwhile, the state-of-the-art QRS detection algorithm achieved a sensitivity of 99.30% and a positive predictive value of 99.68% on the same database. The numerical efficiency of our new algorithm was evident, as a 14-day recording sampled at 200 Hz was analyzed in approximately 157 s. Conclusions We developed a new QRS detection algorithm. The efficiency and accuracy of our algorithm makes it a good fit for mobile health applications, ultra-long-term and pathological ECG recordings, and the batch processing of large ECG databases.
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. In this study, we assemble a comprehensive human vaginal non-redundant gene catalog (VIRGO) that includes 0.95 million non-redundant genes. The gene catalog is functionally and taxonomically annotated. We also construct a vaginal orthologous groups (VOG) from VIRGO. The gene-centric design of VIRGO and VOG provides an easily accessible tool to comprehensively characterize the structure and function of vaginal metagenome and metatranscriptome datasets. To highlight the utility of VIRGO, we analyze 1,507 additional vaginal metagenomes, and identify a high degree of intraspecies diversity within and across vaginal microbiota. VIRGO offers a convenient reference database and toolkit that will facilitate a more in-depth understanding of the role of vaginal microorganisms in women’s health and reproductive outcomes. Reference databases are essential for studies on host-microbiota interactions. Here, the authors present the construction of VIRGO, a human vaginal non-redundant gene catalog, which represents a comprehensive resource for taxonomic and functional profiling of vaginal microbiomes from metagenomic and metatranscriptomic datasets.
Pad Scratching in Chemical-Mechanical Polishing: The Effects of Mechanical and Tribological Properties

In chemical-mechanical polishing (CMP), even the soft pad asperities may, under certain conditions, generate scratches on the relatively hard surfaces being polished. In the present study, contact mechanics models of pad-induced scratching are formulated, and the effects of the hardness of the surface layers and of pad asperities as well as the interfacial friction are elucidated. Additionally, scratch-regime maps are proposed to provide criteria for scratching hard surface layers by the softer pad asperities. Furthermore, scratching indexes are introduced to predict the proportion of asperities in contact that are likely to scratch. The contact mechanics models of scratching have been validated by sliding experiments with two commercial CMP pads (Pad A and IC1000) and various thin-films (Al, Cu, SiO2, Si3N4, TiN and three low-k dielectrics) using deionized water as a “lubricant.” Both the theoretical models and the experimental results show that the number of scratches increases as the scratching index exceeds 0.33. Al and Cu layers are found to be more susceptible to pad scratching due to their low hardness and high interfacial friction. The scratch-regime maps provide practical guidelines for mitigating pad scratching in CMP. © The Author(s) 2014. 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: 10.1149/2.027405jss] All rights reserved.
Coarse free products

Abstract We define a notion of free product for coarse spaces that generalizes the corresponding notion of a free product for groups. We show that free products preserve coarse properties such as coarse property C, finite coarse decomposition complexity, and coarse property A. We also give an upper bound estimate on the dimension of a coarse free product in terms of the dimension of its factors.
Another one rides the bus? The connections between bus stop amenities, bus ridership, and ADA paratransit demand

Abstract Improving bus stops by providing shelters, seating, signage, and sidewalks is relatively inexpensive and popular among riders and local officials. Making such improvements, however, is not often a priority for U.S. transit providers because of competing demands for capital funds and a perception that amenities are not tied to measurable increases in system effectiveness or efficiency. This study analyzes recent bus stop improvements made by the Utah Transit Authority (UTA) to determine whether, and to what extent, the improvements are associated with changes in stop-level ridership and demand for Americans with Disabilities Act (ADA) paratransit service in the areas immediately surrounding improved bus stops. The study compares ridership and paratransit demand from before and after the improvements at the treated stops and at a set of unimproved stops selected using propensity score matching to control for demographic, land use, and regional accessibility influences. The analysis shows that the improved bus stops are associated with a statistically significant increase in overall ridership and a decrease in paratransit demand, compared to the control group stops. These outcomes are important for transit service providers as they seek to increase overall ridership and reduce costs associated with providing paratransit service.
Derivations and Reflection Positivity on the Quantum Cylinder

We describe the general structure of unbounded derivations in the quantum cylinder. We prove a noncommutative analog of reflection positivity for Laplace-type operators in a noncommutative cylinder following the ideas of the proof by Jaffe and Ritter (2008) of reflection positivity for Laplace operators on manifolds equipped with a reflection.
Redundant cytokine requirement for intestinal microbiota-induced Th17 cell differentiation in draining lymph nodes

Differentiation of intestinal T helper 17 (Th17) cells, which contribute to mucosal barrier protection from invasive pathogens, is dependent on colonization with distinct commensal bacteria. Segmented filamentous bacteria (SFB) are sufficient to support Th17 cell differentiation in mouse, but the molecular and cellular requirements for this process remain incompletely characterized. Here we show that intestine-draining mesenteric lymph nodes (MLN) are the dominant site of SFB-induced intestinal Th17 cell differentiation. Subsequent migration of these cells to the intestinal lamina propria is dependent on their up-regulation of integrin {beta}7. Stat3-dependent induction of ROR{gamma}t, the Th17 cell-specifying transcription factor, largely depends on IL-6, but signaling through the receptors for IL-21 and IL-23 can compensate for absence of IL-6 to promote SFB-directed Th17 cell differentiation. These results indicate that redundant cytokine signals guide commensal microbe-dependent Th17 cell differentiation in the MLN and accumulation of the cells in the lamina propria.
Where Do We Stand on Transport Infrastructure Deregulation and Public-Private Partnership?

The evolution of transport public-private partnerships (PPPs) in developing and developed countries since the early 1990s seems to be following a similar path: private initiatives work for a while but after a shock to the sector takes place the public sector returns as regulator, owner or financier; after a while the public sector runs into problems and eventually finds a hybrid solution to ensure the survival of the sector. This paper reviews the effectiveness of transport infrastructure deregulation from three angles: efficiency, fiscal and users’ viewpoint. The paper emphasizes the difficulties and strong political commitments required to make the reforms sustainable and argues that governments willing to make corrections to the reform path are faced with the need to address recurrent and emerging issues in transport systems: tariff structure, quality (timetable, safety, environment), access rules for captive shippers, the trend toward rebundling and decrease in intrasectoral competition, multimodalism and the stimulus through yardstick competition.
Vortex shedding from solid rocket propellant inhibitors

Vortex shedding frequency caused by the protrusion of inhibitors into the flow field of a solid rocket motor is investigated by experimental and mathematical models. The time dependent Navier-Stokes equations are solved using a finite difference technique assuming incompressible, two-dimensional flow under both laminar and turbulent flow conditions. For laminar flow, explicit solutions are obtained using a vorticity-transport equation in place of the Navier-Stokes equations. For turbulent flow, a two-equation (k-epsilon) model is used for turbulent modeling and the SIMPLE algorithm is employed as the computational scheme. Cold flow tests were conducted to confirm the basic flow structure and to determine the vortex shedding frequency under both laminar and turbulent flow conditions. The vortex shedding frequencies were determined using a stroboscope to measure the oscillating frequency of yarn tufts which were fastened to one inhibitor in the models. A hot-film anemometer established the velocity history behind the inhibitor. Good agreement between the theoretical results and measurements of the vortex shedding frequencies is demonstrated.
DO PATENT POOLS ENCOURAGE INNOVATION? EVIDENCE FROM THE 19TH-CENTURY SEWING MACHINE INDUSTRY

Members of a patent pool agree to use a set of patents as if they were jointly owned by all members and license them as a package to other firms. This article uses the example of the first patent pool in U.S. history, the Sewing Machine Combination (1856–1877) to perform the first empirical test of the effects of a patent pool on innovation. Contrary to theoretical predictions, the sewing machine pool appears to have discouraged patenting and innovation, in particular for the members of the pool. Data on stitches per minute, an objectively quantifiable measure of innovation, confirm these findings.
Perceptual decisions about object shape bias visuomotor coordination during rapid interception movements

Visual processing in parietal areas of the dorsal stream facilitates sensorimotor transformations for rapid movement. This action-related visual processing is hypothesized to play a distinct functional role from perception-related processing in the ventral stream. However, it is unclear how the two streams interact when perceptual identification is a prerequisite to executing an accurate movement. In the current study, we investigated how perceptual decision-making involving the ventral stream influences arm and eye movement strategies. Participants (n = 26) moved a robotic manipulandum using right whole arm movements to rapidly reach a stationary object or intercept a moving object on an augmented-reality display. On some blocks of trials, participants needed to identify the shape of the object (circle or ellipse) as a cue to either hit the object (circle) or move to a predefined location away from the object (ellipse). We found that during perceptual decision-making, there was an increased urgency to act during interception movements relative to reaching, which was associated with more decision errors. Faster hand reaction times were associated with a strategy to adjust the movement postinitiation, and this strategy was more prominent during interception. Saccadic reaction times were faster and initial saccadic peak velocity, initial gaze lags, and gains greater during decisions, suggesting that eye movements adapt to perceptual decision-making requirements. Together, our findings suggest that the integration of ventral stream information with visuomotor planning depends on imposed (or perceived) task demands.NEW & NOTEWORTHY Visual processing for perception and for action is thought to be mediated by two specialized neural pathways. Using a visuomotor decision-making task, we show that participants differentially utilized online perceptual decision-making in reaching and interception and that eye movements necessary for perception influenced motor decision strategies. These results provide evidence that task complexity modulates how pathways processing perception versus action information interact during the visual control of movement.
Optimal waveform estimation for classical and quantum systems via time-symmetric smoothing

Classical and quantum theories of time-symmetric smoothing, which can be used to optimally estimate waveforms in classical and quantum systems, are derived using a discrete-time approach, and the similarities between the two theories are emphasized. Application of the quantum theory to homodyne phase-locked loop design for phase estimation with narrowband squeezed optical beams is studied. The relation between the proposed theory and Aharonov et al.'s weak value theory is also explored.
Tetrahymena Poc5 is a transient basal body component that is important for basal body maturation

Basal bodies (BBs) are microtubule-based organelles that act as a template for and stabilize cilia at the cell surface. Centrins ubiquitously associate with BBs and function in BB assembly, maturation and stability. Human POC5 (hPOC5) is a highly conserved centrin-binding protein that binds centrins through Sfi1p-like repeats and is required for building full-length, mature centrioles. Here, we use the BB-rich cytoskeleton of Tetrahymena thermophila to characterize Poc5 BB functions. Tetrahymena Poc5 (TtPoc5) uniquely incorporates into assembling BBs and is then removed from mature BBs prior to ciliogenesis. Complete genomic knockout of TtPOC5 leads to a significantly increased production of BBs, yet a markedly reduced ciliary density, both of which are rescued by reintroduction of TtPoc5. A second Tetrahymena POC5-like gene, SFR1, is similarly implicated in modulating BB production. When TtPOC5 and SFR1 are co-deleted, cell viability is compromised and BB overproduction is exacerbated. Overproduced BBs display defective transition zone formation and a diminished capacity for ciliogenesis. This study uncovers a requirement for Poc5 in building mature BBs, providing a possible functional link between hPOC5 mutations and impaired cilia.This article has an associated First Person interview with the first author of the paper.
Improving Public Infrastructure in the Philippines

This paper explores the macroeconomic effects of improving public infrastructure in the Philippines, modeling the infrastructure scale-up plan being implemented by the current administration. After...
Detecting Deficient Coverage in Colonoscopies

Colonoscopy is tool of choice for preventing Colorectal Cancer, by detecting and removing polyps before they become cancerous. However, colonoscopy is hampered by the fact that endoscopists routinely miss 22-28% of polyps. While some of these missed polyps appear in the endoscopist’s field of view, others are missed simply because of substandard coverage of the procedure, i.e. not all of the colon is seen. This paper attempts to rectify the problem of substandard coverage in colonoscopy through the introduction of the C2D2 (Colonoscopy Coverage Deficiency via Depth) algorithm which detects deficient coverage, and can thereby alert the endoscopist to revisit a given area. More specifically, C2D2 consists of two separate algorithms: the first performs depth estimation of the colon given an ordinary RGB video stream; while the second computes coverage given these depth estimates. Rather than compute coverage for the entire colon, our algorithm computes coverage locally, on a segment-by-segment basis; C2D2 can then indicate in real-time whether a particular area of the colon has suffered from deficient coverage, and if so the endoscopist can return to that area. Our coverage algorithm is the first such algorithm to be evaluated in a large-scale way; while our depth estimation technique is the first calibration-free unsupervised method applied to colonoscopies. The C2D2 algorithm achieves state of the art results in the detection of deficient coverage. On synthetic sequences with ground truth, it is 2.4 times more accurate than human experts; while on real sequences, C2D2 achieves a 93.0% agreement with experts.
Ventral Tegmental Dopamine Neurons Control the Impulse Vector during Motivated Behavior

The ventral tegmental area (VTA) is a major source of dopamine, especially to the limbic brain regions. Despite decades of research, the function of VTA dopamine neurons remains controversial. Here, using a novel head-fixed behavioral system with five orthogonal force sensors, we show for the first time that the activity of dopamine neurons precisely represents the impulse vector (force exerted over time) generated by the animal. Distinct populations of VTA dopamine neurons contribute to components of the impulse vector in different directions. Optogenetic excitation of these neurons shows a linear relationship between signal injected and impulse generated. Optogenetic inhibition paused force generation or produced force in the backward direction. At the same time, these neurons also regulate the initiation and execution of anticipatory licking. Our results indicate that VTA dopamine controls the magnitude, direction, and duration of force used to move toward or away from any motivationally relevant stimuli.
Treatment of a high output nephrocutaneous urine leak following treatment of a giant calyceal diverticulum in a child.

Abstract Calyceal diverticula are non-secretory transitional-epithelium lined cavities that are connected to the collecting system through a small ostium. They are rarely seen in young children. Although most remain asymptomatic, the presence of stagnant urine can result in infection, stone formation and pain. Treatment may consist of percutaneous ablation or open surgical excision. Failure of the ostium to completely seal can result in a persistent leak. We present a case of a massive calyceal diverticulum in a child who developed a postsurgical nephrocutaneous fistula recalcitrant to conservative management that was successfully managed with injection of fibrin glue.
Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

ABSTRACT Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury). IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.
OSOM: A simultaneously optimal algorithm for multi-armed and linear contextual bandits

We consider the stochastic linear (multi-armed) contextual bandit problem with the possibility of hidden simple multi-armed bandit structure in which the rewards are independent of the contextual information. Algorithms that are designed solely for one of the regimes are known to be sub-optimal for the alternate regime. We design a single computationally efficient algorithm that simultaneously obtains problem-dependent optimal regret rates in the simple multi-armed bandit regime and minimax optimal regret rates in the linear contextual bandit regime, without knowing a priori which of the two models generates the rewards. These results are proved under the condition of stochasticity of contextual information over multiple rounds. Our results should be viewed as a step towards principled data-dependent policy class selection for contextual bandits.
Trump the antisemantic, and the boundaries of populism

In this article I consider Donald Trump as an “antisemantic” president, and link antisemanticism to broader forms of populism. Drawing on Stuart Hall’s analysis of Thatcherism, I explore the politi...
Smartphone-based financial incentives to promote smoking cessation during pregnancy: A pilot study

Abstract Cigarette smoking during pregnancy increases risk for pregnancy complications, growth restriction, and other adverse health outcomes. The most effective intervention for reducing smoking during pregnancy is financial incentives contingent on biochemically-verified smoking abstinence. The present study examined the efficacy of a smartphone-based intervention whereby smoking monitoring and incentive delivery occurred remotely using a mobile app. If efficacious, this remote intervention would allow pregnant women residing in geographically remote areas to benefit from incentives-based cessation interventions. Sixty U.S. pregnant smokers were recruited between May 2018 to May 2019 via obstetrical clinics, Women, Infants, and Children (WIC) offices, and Facebook. Participants were assigned sequentially to one of two treatments: best practices alone (N = 30) or best practices plus financial incentives (N = 30). Outcomes were analyzed using repeated measures analysis based on generalized estimating equations (GEE). Seven-day point prevalence abstinence rates were greater in the incentives versus best practices arms early- (46.7% vs 20.0%, OR = 3.50, 95%CI = 1.11,11.02) and late-antepartum (36.7% vs 13.3%, OR = 3.76, 95%CI = 1.04,13.65), and four- (36.7% vs 10.0%, OR = 5.21, 95%CI = 1.28,21.24) and eight-weeks postpartum (40.0% vs 6.7%, OR = 9.33, 95%CI = 1.87,46.68), although not at the 12- (23.3% vs 10.0%, OR = 2.74, 95%CI = 0.63,11.82) or 24-week (20.0% vs 6.7%, OR = 3.50, 95%CI = 0.65,18.98) postpartum assessments likely due to this pilot study being underpowered for discerning differences at the later assessments, especially 24-weeks postpartum which was three months after treatment completion. These results support the efficacy of this remote, incentives-based intervention for pregnant smokers. Further research evaluating its efficacy and cost-effectiveness in a well-powered, randomized controlled trial appears warranted.
Mechanical Characteristics of Ultrafast Zebrafish Larval Swimming Muscles

Abstract Zebrafish (Danio rerio) swim within days of fertilization, powered by muscles of the axial myotomes. Forces generated by these muscles can be measured rapidly in whole, intact larval tails by adapting protocols developed for ex vivo muscle mechanics. But it is not known how well these measurements reflect the function of the underlying muscle fibers and sarcomeres. Here we consider the anatomy of the 5-day-old, wild-type larval tail, and implement technical modifications to measuring muscle physiology in intact tails. Specifically, we quantify fundamental relationships between force, length, and shortening velocity, and capture the extreme contractile speeds required to swim with tail-beat frequencies of 80-100 Hz. Therefore, we analyze 1000 frames/second movies to track the movement of structures, visible in the transparent tail, which correlate with sarcomere length. We also characterize the passive viscoelastic properties of the preparation to isolate forces contributed by non-muscle structures within the tail. Myotomal muscles generate more than 95% of their maximum isometric stress (76±3 mN/mm2) over the range of muscle lengths used in vivo. They have rapid twitch kinetics (full width at half-maximum stress: 11±1 msec) and a high twitch to tetanus ratio (0.91±0.05), indicating adaptations for fast excitation-contraction coupling. Although contractile stress is relatively low, myotomal muscles develop high net power (134±20 W/kg at 80 Hz) in cyclical work loop experiments designed to simulate the in vivo dynamics of muscle fibers during swimming. When shortening at a constant speed of 7±1 muscle lengths/second, muscles develop 86±2% of isometric stress, while peak instantaneous power during 100Hz work loops occurs at 18±2 muscle lengths/second. These approaches can improve the usefulness of zebrafish as a model system for muscle research by providing a rapid and sensitive functional readout for experimental interventions.
Triphenyl phosphate is a selective PPARγ modulator that does not induce brite adipogenesis in vitro and in vivo.

Triphenyl phosphate (TPhP) is an environmental PPARγ ligand, and growing evidence suggests that it is a metabolic disruptor. We have shown previously that the structurally similar ligand, tributyltin, does not induce brite adipocyte gene expression. Here, using in vivo and in vitro models, we tested the hypothesis that TPhP is a selective PPARγ ligand, which fails to induce brite adipogenesis. C57BL/6 J male mice were fed either a low or very high-fat diet for 13 weeks. From weeks 7–13, mice were injected intraperitoneally, daily, with vehicle, rosiglitazone (Rosi), or TPhP (10 mg/kg). Compared to Rosi, TPhP did not induce expression of browning-related genes (e.g. Elovl3, Cidea, Acaa2, CoxIV) in mature adipocytes isolated from inguinal adipose. To determine if this resulted from an effect directly on the adipocytes, 3T3-L1 cells and primary human preadipocytes were differentiated into adipocytes in the presence of Rosi or TPhP. Rosi, but not TPhP, induced expression of brite adipocyte genes, mitochondrial biogenesis and cellular respiration. Further, Rosi and TPhP-induced distinct proteomes and phosphoproteomes; Rosi enriched more regulatory pathways related to fatty acid oxidation and mitochondrial proteins. We assessed the role of phosphorylation of PPARγ in these differences in 3T3-L1 cells. Only Rosi protected PPARγ from phosphorylation at Ser273. TPhP gained the ability to stimulate brite adipocyte gene expression in the presence of the CDK5 inhibitor and in 3T3-L1 cells expressing alanine at position 273. We conclude that TPhP is a selective PPARγ modulator that fails to protect PPARγ from phosphorylation at ser273.
A Deep Reinforced Model for Zero-Shot Cross-Lingual Summarization with Bilingual Semantic Similarity Rewards

Cross-lingual text summarization aims at generating a document summary in one language given input in another language. It is a practically important but under-explored task, primarily due to the dearth of available data. Existing methods resort to machine translation to synthesize training data, but such pipeline approaches suffer from error propagation. In this work, we propose an end-to-end cross-lingual text summarization model. The model uses reinforcement learning to directly optimize a bilingual semantic similarity metric between the summaries generated in a target language and gold summaries in a source language. We also introduce techniques to pre-train the model leveraging monolingual summarization and machine translation objectives. Experimental results in both English–Chinese and English–German cross-lingual summarization settings demonstrate the effectiveness of our methods. In addition, we find that reinforcement learning models with bilingual semantic similarity as rewards generate more fluent sentences than strong baselines.
MPC-based Vibration Control and Energy Harvesting Using an Electromagnetic Vibration Absorber With Inertia Nonlinearity.

Simultaneous vibration control and energy harvesting of vehicle suspensions has attracted great research interests over the past decades. However, existing frameworks tradeoff suspension performance for energy recovery and are only responsive to narrow-bandwidth vibrations. In this paper, a new energy-regenerative vibration absorber (ERVA) using a ball-screw mechanism is investigated. The ERVA system is based on a rotary electromagnetic generator with adjustable nonlinear rotational inertia which passively increases the moment of inertia as the vibration amplitude increases. This structure is effective for energy harvesting and vibration control without increasing the suspension size. Furthermore, a nonlinear model predictive controller (NMPC) is applied to the system for further performance enhancement where we exploit road profile information as a preview. The performance of NMPC-based ERVA is demonstrated in a number of simulations and superior performance is demonstrated.
A microscopic approach to study the onset of a highly infectious disease spreading

Abstract We combine a pedestrian dynamics model with a contact tracking method to simulate the initial spreading of a highly infectious airborne disease in a confined environment. We focus on a medium size population (up to 1000 people) with a small number of infectious people (1 or 2) and the rest of the people are divided between immune and susceptible. We adopt a space-continuous model that represents pedestrian dynamics by the forces acting on them, i.e. a microscopic force-based model. Once discretized, the model results in a high-dimensional system of second order ordinary differential equations. Before adding the contact tracking to the pedestrian dynamics model, we calibrate the model parameters, compare the model results against empirical data, and show that pedestrian self-organization into lanes can be captured. We consider an explicit approach for contact tracking by introducing a sickness domain around a sick person. A healthy but susceptible person who remains in the sickness domain for a certain amount of time may get infected (with a prescribed probability) and become a so-called secondary contact. As a concrete setting to simulate the onset of disease spreading, we consider terminals in two US airports: Hobby Airport in Houston and the Atlanta International Airport. We consider different scenarios and we quantify the increase in average number of secondary contacts as a given terminal becomes more densely populated, the percentage of immune people decreases, the number of primary contacts increases, and areas of high density (such as the boarding buses) are present.
The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

Our ability to discover effective drug combinations is limited, in part by insufficient understanding of how the transcriptional response of two monotherapies results in that of their combination. We analyzed matched time course RNAseq profiling of cells treated with single drugs and their combinations and found that the transcriptional signature of the synergistic combination was unique relative to that of either constituent monotherapy. The sequential activation of transcription factors in time in the gene regulatory network was implicated. The nature of this transcriptional cascade suggests that drug synergy may ensue when the transcriptional responses elicited by two unrelated individual drugs are correlated. We used these results as the basis of a simple prediction algorithm attaining an AUROC of 0.77 in the prediction of synergistic drug combinations in an independent dataset.
Dynamic Phase Alignment in Inertial Alfvén Turbulence

In weakly collisional plasma environments with sufficiently low electron beta, Alfv\'enic turbulence transforms into inertial Alfv\'enic turbulence at scales below the electron skin depth, ${k}_{\ensuremath{\perp}}{d}_{e}\ensuremath{\gtrsim}1$. We argue that, in inertial Alfv\'enic turbulence, both energy and generalized kinetic helicity exhibit direct cascades. We demonstrate that the two cascades are compatible due to the existence of a strong scale dependence of the phase alignment angle between velocity and magnetic field fluctuations, with the phase alignment angle scaling as $\mathrm{cos}{\ensuremath{\alpha}}_{k}\ensuremath{\propto}{k}_{\ensuremath{\perp}}^{\ensuremath{-}1}$. The kinetic and magnetic energy spectra scale as $\ensuremath{\propto}{k}_{\ensuremath{\perp}}^{\ensuremath{-}5/3}$ and $\ensuremath{\propto}{k}_{\ensuremath{\perp}}^{\ensuremath{-}11/3}$, respectively. As a result of the dual direct cascade, the generalized helicity spectrum scales as $\ensuremath{\propto}{k}_{\ensuremath{\perp}}^{\ensuremath{-}5/3}$, implying progressive balancing of the turbulence as the cascade proceeds to smaller scales in the ${k}_{\ensuremath{\perp}}{d}_{e}\ensuremath{\gg}1$ range. Turbulent eddies exhibit a phase-space anisotropy ${k}_{\ensuremath{\parallel}}\ensuremath{\propto}{k}_{\ensuremath{\perp}}^{5/3}$, consistent with critically balanced inertial Alfv\'en fluctuations. Our results may be applicable to a variety of geophysical, space, and astrophysical environments, including the Earth's magnetosheath and ionosphere, solar corona, and nonrelativistic pair plasmas, as well as to strongly rotating nonionized fluids.
Toward Autonomous Robotic Micro-Suturing using Optical Coherence Tomography Calibration and Path Planning

Robotic automation has the potential to assist human surgeons in performing suturing tasks in microsurgery, and in order to do so a robot must be able to guide a needle with sub-millimeter precision through soft tissue. This paper presents a robotic suturing system that uses 3D optical coherence tomography (OCT) system for imaging feedback. Calibration of the robot-OCT and robot-needle transforms, wound detection, keypoint identification, and path planning are all performed automatically. The calibration method handles pose uncertainty when the needle is grasped using a variant of iterative closest points. The path planner uses the identified wound shape to calculate needle entry and exit points to yield an evenly-matched wound shape after closure. Experiments on tissue phantoms and animal tissue demonstrate that the system can pass a suture needle through wounds with 0.200 mm overall accuracy in achieving the planned entry and exit points, and over 20× more precise than prior autonomous suturing robots.
GOMP: Grasp-Optimized Motion Planning for Bin Picking

Rapid and reliable robot bin picking is a critical challenge in automating warehouses, often measured in picks-per-hour (PPH). We explore increasing PPH using faster motions based on optimizing over a set of candidate grasps. The source of this set of grasps is two-fold: (1) grasp-analysis tools such as Dex-Net generate multiple candidate grasps, and (2) each of these grasps has a degree of freedom about which a robot gripper can rotate. In this paper, we present Grasp-Optimized Motion Planning (GOMP), an algorithm that speeds up the execution of a bin-picking robot’s operations by incorporating robot dynamics and a set of candidate grasps produced by a grasp planner into an optimizing motion planner. We compute motions by optimizing with sequential quadratic programming (SQP) and iteratively updating trust regions to account for the non-convex nature of the problem. In our formulation, we constrain the motion to remain within the mechanical limits of the robot while avoiding obstacles. We further convert the problem to a time-minimization by repeatedly shorting a time horizon of a trajectory until the SQP is infeasible. In experiments with a UR5, GOMP achieves a speedup of 9x over a baseline planner.
The hardest halfspace

We study the approximation of halfspaces $$h:\{0,1\}^n\to\{0,1\}$$ in the infinity norm by polynomials and rational functions of any given degree. Our main result is an explicit construction of the “hardest” halfspace, for which we prove polynomial and rational approximation lower bounds that match the trivial upper bounds achievable for all halfspaces. This completes a lengthy line of work started by Myhill and Kautz (1961). As an application, we construct a communication problem that achieves essentially the largest possible separation, of O(n) versus $$2^{-\Omega(n)}$$ , between the sign-rank and discrepancy. Equivalently, our problem exhibits a gap of log n versus $$\Omega(n)$$ between the communication complexity with unbounded versus weakly unbounded error, improving quadratically on previous constructions and completing a line of work started by Babai, Frankl, and Simon (FOCS 1986). Our results further generalize to the k-party number-on-the-forehead model, where we obtain an explicit separation of log n versus $$\Omega(n/4^{n})$$ for communication with unbounded versus weakly unbounded error.
Network clustering via kernel-ARMA modeling and the Grassmannian: The brain-network case

Abstract This paper demonstrates that all clustering tasks in a dynamic (brain) network, i.e., state clustering, community detection, and subnetwork state-sequence clustering, can be addressed by a novel unifying network-clustering framework. The connecting threads of the components of the proposed framework are: a novel kernel-based autoregressive-moving-average (ARMA) model which propels feature extraction from the network time-series, and the Riemannian geometry of the Grassmann manifold (Grassmannian) into which the extracted features are mapped. Clustering of the Grassmannian features is performed via the novel extension of a recently introduced algorithm which capitalizes on the Grassmannian distances and angular information of the point-cloud of features. Numerical tests on synthetic and real functional-magnetic-resonance-imaging (fMRI) data showcase the favorable performance of the proposed scheme against state-of-the-art network-clustering and manifold-learning methods, and corroborate the claim of this paper that the proposed framework can serve as a useful data-analytic toolbox for network(-neuroscience) research.
Leveraging functional annotation to identify genes associated with complex diseases

To increase statistical power to identify genes associated with complex traits, a number of transcriptome-wide association study (TWAS) methods have been proposed using gene expression as a mediating trait linking genetic variations and diseases. These methods first predict expression levels based on inferred expression quantitative trait loci (eQTLs) and then identify expression-mediated genetic effects on diseases by associating phenotypes with predicted expression levels. The success of these methods critically depends on the identification of eQTLs, which may not be functional in the corresponding tissue, due to linkage disequilibrium (LD) and the correlation of gene expression between tissues. Here, we introduce a new method called T-GEN (Transcriptome-mediated identification of disease-associated Genes with Epigenetic aNnotation) to identify disease-associated genes leveraging epigenetic information. Through prioritizing SNPs with tissue-specific epigenetic annotation, T-GEN can better identify SNPs that are both statistically predictive and biologically functional. We found that a significantly higher percentage (an increase of 18.7% to 47.2%) of eQTLs identified by T-GEN are inferred to be functional by ChromHMM and more are deleterious based on their Combined Annotation Dependent Depletion (CADD) scores. Applying T-GEN to 207 complex traits, we were able to identify more trait-associated genes (ranging from 7.7% to 102%) than those from existing methods. Among the identified genes associated with these traits, T-GEN can better identify genes with high (>0.99) pLI scores compared to other methods. When T-GEN was applied to late-onset Alzheimer's disease, we identified 96 genes located at 15 loci, including two novel loci not implicated in previous GWAS. We further replicated 50 genes in an independent GWAS, including one of the two novel loci.
End-to-end neural transformer based spoken language understanding

Spoken language understanding (SLU) refers to the process of inferring the semantic information from audio signals. While the neural transformers consistently deliver the best performance among the state-of-the-art neural architectures in field of natural language processing (NLP), their merits in a closely related field, i.e., spoken language understanding (SLU) have not beed investigated. In this paper, we introduce an end-to-end neural transformer-based SLU model that can predict the variable-length domain, intent, and slots vectors embedded in an audio signal with no intermediate token prediction architecture. This new architecture leverages the self-attention mechanism by which the audio signal is transformed to various sub-subspaces allowing to extract the semantic context implied by an utterance. Our end-to-end transformer SLU predicts the domains, intents and slots in the Fluent Speech Commands dataset with accuracy equal to 98.1 \%, 99.6 \%, and 99.6 \%, respectively and outperforms the SLU models that leverage a combination of recurrent and convolutional neural networks by 1.4 \% while the size of our model is 25\% smaller than that of these architectures. Additionally, due to independent sub-space projections in the self-attention layer, the model is highly parallelizable which makes it a good candidate for on-device SLU.
Stationary distributions of the Atlas model

In this article we study the Atlas model, which consists of Brownian particles on $ \mathbb{R} $, independent except that the Atlas (i.e., lowest ranked) particle $ X_{(1)}(t) $ receives drift $ \gamma dt $, $ \gamma \in \mathbb{R} $. For any fixed shape parameter $ a>2\gamma _- $, we show that, up to a shift $ \frac{a} {2}t $, the entire particle system has an invariant distribution $ \nu _a $, written in terms an explicit Radon-Nikodym derivative with respect to the Poisson point process of density $ ae^{a\xi } d\xi $. We further show that $ \nu _a $ indeed has the product-of-exponential gap distribution $ \pi _a $ derived in [ST17]. As a simple application, we establish a bound on the fluctuation of the Atlas particle $ X_{(1)}(t) $ uniformly in $ t $, with the gaps initiated from $ \pi _a $ and $ X_{(1)}(0)=0 $.
Efficient evaluation of exact exchange for periodic systems via concentric atomic density fitting.

The evaluation of the exact [Hartree–Fock (HF)] exchange operator is a crucial ingredient for the accurate description of the electronic structure in periodic systems through ab initio and hybrid density functional approaches. An efficient formulation of periodic HF exchange in a linear combination of atomic orbitals representation presented here is based on the concentric atomic density fitting approximation, a domain-free local density fitting approach in which the product of two atomic orbitals is approximated using a linear combination of fitting basis functions centered at the same nuclei as the AOs in that product. A significant reduction in the computational cost of exact exchange is demonstrated relative to the conventional approach due to avoiding the need to evaluate four-center two-electron integrals, with sub-millihartree/atom errors in absolute HF energies and good cancellation of fitting errors in relative energies. The novel aspects of the evaluation of the Coulomb contribution to the Fock operator, such as the use of real two-center multipole expansions and spheropole-compensated unit cell densities, are also described.