cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
NudgeRank: Digital Algorithmic Nudging for Personalized Health
Creators: name: Chiam, Jodi
name: Lim, Aloysius
name: Teredesai, Ankur
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computers and Society (cs.CY)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: In this paper we describe NudgeRank, an innovative digital algorithmic nudging system designed to foster positive health behaviors on a population-wide scale. Utilizing a novel combination of Graph Neural Networks augmented with an extensible Knowledge Graph, this Recommender System is operational in production, delivering personalized and context-aware nudges to over 1.1 million care recipients daily. This enterprise deployment marks one of the largest AI-driven health behavior change initiatives, accommodating diverse health conditions and wearable devices. Rigorous evaluation reveals statistically significant improvements in health outcomes, including a 6.17% increase in daily steps and 7.61% more exercise minutes. Moreover, user engagement and program enrollment surged, with a 13.1% open rate compared to baseline systems' 4%. Demonstrating scalability and reliability, NudgeRank operates efficiently on commodity compute resources while maintaining automation and observability standards essential for production systems.
description: To be published in Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD '24)
Lasso adjustments of treatment effect estimates in randomized experiments
Creators: name: Bloniarz, Adam
name: Liu, Hanzhong
name: Zhang, Cun-Hui
name: Sekhon, Jasjeet
name: Yu, Bin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: We provide a principled way for investigators to analyze randomized experiments when the number of covariates is large. Investigators often use linear multivariate regression to analyze randomized experiments instead of simply reporting the difference of means between treatment and control groups. Their aim is to reduce the variance of the estimated treatment effect by adjusting for covariates. If there are a large number of covariates relative to the number of observations, regression may perform poorly because of overfitting. In such cases, the Lasso may be helpful. We study the resulting Lasso-based treatment effect estimator under the Neyman-Rubin model of randomized experiments. We present theoretical conditions that guarantee that the estimator is more efficient than the simple difference-of-means estimator, and we provide a conservative estimator of the asymptotic variance, which can yield tighter confidence intervals than the difference-of-means estimator. Simulation and data examples show that Lasso-based adjustment can be advantageous even when the number of covariates is less than the number of observations. Specifically, a variant using Lasso for selection and OLS for estimation performs particularly well, and it chooses a smoothing parameter based on combined performance of Lasso and OLS.
Phonon mechanism in the most dilute superconductor: n-type SrTiO3
Creators: name: Gor'kov, Lev P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Superconductivity of doped SrTiO3 is proven to be a particular case of the broader concept of the non-adiabatic pairing mediated by phonons with frequency comparable or larger the Fermi energy. We argue that, for carrier concentrations exceeding that of the mobility edge, the superconductivity of doped SrTiO3 is mediated by interaction of electrons with several longitudinal (LO) optical polar phonons. The electronic spectrum of SrTiO3 consists at low temperatures of three conduction bands which are successively doped. Each band contributes to the Cooper instability and exhibits a superconducting gap in the energy spectrum. The theory presented below predicts maxima in dependence of Tc(n)-the transition temperature on n, the number of electrons owing to the following mechanism. Doping by electrons increases density of states at the Fermi surface and Tc initially grows up. At the same time, screening on the part of accumulating charges tends to reduce amplitude of the electrical fields inherent in LO phonon modes and at larger concentrations the matrix element of interaction between electrons and LO phonons decreases. The compromise between the two tendencies leads to maxima in the Tc(n)-dependence providing interpretation to one of the most intriguing experimental findings in Xiao Lin et al [Phys. Rev. Lett. 112, 207002 (2014)]. Having reached a maximum in the third band, the superconducting transition finally decreases, rounding out the Tc(n)-dome, the three maxima in Tc(n)with accompanying superconducting gaps emerging consecutively as electrons fill successive bands. This arises from attributes of the LO optical phonon pairing mechanism. More generally, the mechanism opens prospect of increasing temperature of the superconducting transition in transition-metals oxides and other polar crystals.
description: 5 figures
From A-to-Z Review of Clustering Validation Indices
Creators: name: Hassan, Bryar A.
name: Tayfor, Noor Bahjat
name: Hassan, Alla A.
name: Ahmed, Aram M.
name: Rashid, Tarik A.
name: Abdalla, Naz N.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Data clustering involves identifying latent similarities within a dataset and organizing them into clusters or groups. The outcomes of various clustering algorithms differ as they are susceptible to the intrinsic characteristics of the original dataset, including noise and dimensionality. The effectiveness of such clustering procedures directly impacts the homogeneity of clusters, underscoring the significance of evaluating algorithmic outcomes. Consequently, the assessment of clustering quality presents a significant and complex endeavor. A pivotal aspect affecting clustering validation is the cluster validity metric, which aids in determining the optimal number of clusters. The main goal of this study is to comprehensively review and explain the mathematical operation of internal and external cluster validity indices, but not all, to categorize these indices and to brainstorm suggestions for future advancement of clustering validation research. In addition, we review and evaluate the performance of internal and external clustering validation indices on the most common clustering algorithms, such as the evolutionary clustering algorithm star (ECA*). Finally, we suggest a classification framework for examining the functionality of both internal and external clustering validation measures regarding their ideal values, user-friendliness, responsiveness to input data, and appropriateness across various fields. This classification aids researchers in selecting the appropriate clustering validation measure to suit their specific requirements.
Alyssum bungei Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum bungei

description: Alyssum bungei Boiss., Fl. Orient. 1: 274. 1867.
Type: “Hab. in Persiâ inter Ispahan et Teheran (Bunge!)”.
Holotypus: IRAN: “inter Isfahan et Teheran ”, V.1859, Bunge s.n. (G-BOIS [G00332364]; iso-: K [K000484971], P [P2272229, P2272230, P2272231]).
= Meniocus heterotrichus (Boiss.) Hadač & Chrtek in Acta Univ. Carol., Biol. 1971: 260. 1973.
Note. – Boissier somehow did not realize that the material he received from and named after Bunge was at a much younger stage of development than the mature material of conspecific Alyssum heterotrichum that he described 21 years earlier.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on pages 93-94, DOI: 10.5281/zenodo.7630433
Ant-Inspired Density Estimation via Random Walks
Creators: name: Musco, Cameron
name: Su, Hsin-Hao
name: Lynch, Nancy
Publisher: name: arXiv
Year: 2016
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences

description: Many ant species employ distributed population density estimation in applications ranging from quorum sensing [Pra05], to task allocation [Gor99], to appraisal of enemy colony strength [Ada90]. It has been shown that ants estimate density by tracking encounter rates -- the higher the population density, the more often the ants bump into each other [Pra05,GPT93]. We study distributed density estimation from a theoretical perspective. We prove that a group of anonymous agents randomly walking on a grid are able to estimate their density within a small multiplicative error in few steps by measuring their rates of encounter with other agents. Despite dependencies inherent in the fact that nearby agents may collide repeatedly (and, worse, cannot recognize when this happens), our bound nearly matches what would be required to estimate density by independently sampling grid locations. From a biological perspective, our work helps shed light on how ants and other social insects can obtain relatively accurate density estimates via encounter rates. From a technical perspective, our analysis provides new tools for understanding complex dependencies in the collision probabilities of multiple random walks. We bound the strength of these dependencies using $local\ mixing\ properties$ of the underlying graph. Our results extend beyond the grid to more general graphs and we discuss applications to size estimation for social networks and density estimation for robot swarms.
Alyssum montanum var. hymettium Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum montanum
Alyssum montanum var. hymettium boiss., fl.

description: Alyssum montanum var. hymettium Boiss., Fl. Orient. 1: 274. 1867.
Type: “Hab. in Graeciae monte Hymetto (Auch. exs. 276! Spr.!), Parnasso (Heldr!)”.
Lectotypus (designated by ŠPANIEL et al., 2017: 1438): GREECE: “in Mte Hymetto”, s.d., Aucher-Eloy 276 (G-BOIS [G00332365]; isolecto-: BM [BM000750107], G [G00388918, G00446161, G00446162], K [K000484576], P [P05426246, P05426263, P05426422]). Syntypi: GREECE: “In monte Parnasso. reg. alpina”, 11.VIII.1852, Heldreich s.n. (G-BOIS [G00332366], WU [WU0076265]); “Gipsel d‘Hymetteri”, s.d., Spruner s.n. (G-BOIS [G00332367]).
= Alyssum montanum L., Sp. Pl.: 650. 1753.
Notes. – Alyssum montanum is the most variable species in the genus, and numerous infraspecific taxa at various ranks have been recognized.
HARTVIG (2002: 210) accepted var. hymettium solely on morphological grounds within Greece, but without extensive population-based and detailed morphological and molecular studies. It is then advisable to reduce the variety to synonymy within subsp. montanum, as done in BRASSIBASE (2019).
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 94, DOI: 10.5281/zenodo.7630433
A Variational Perspective on Accelerated Methods in Optimization
Creators: name: Wibisono, Andre
name: Wilson, Ashia C.
name: Jordan, Michael I.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Optimization and Control (math.OC)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Accelerated gradient methods play a central role in optimization, achieving optimal rates in many settings. While many generalizations and extensions of Nesterov's original acceleration method have been proposed, it is not yet clear what is the natural scope of the acceleration concept. In this paper, we study accelerated methods from a continuous-time perspective. We show that there is a Lagrangian functional that we call the \emph{Bregman Lagrangian} which generates a large class of accelerated methods in continuous time, including (but not limited to) accelerated gradient descent, its non-Euclidean extension, and accelerated higher-order gradient methods. We show that the continuous-time limit of all of these methods correspond to traveling the same curve in spacetime at different speeds. From this perspective, Nesterov's technique and many of its generalizations can be viewed as a systematic way to go from the continuous-time curves generated by the Bregman Lagrangian to a family of discrete-time accelerated algorithms.
description: 38 pages. Subsumes an earlier working draft arXiv:1509.03616
Multimode optomechanical system in the quantum regime
Creators: name: Nielsen, William H. P.
name: Tsaturyan, Yeghishe
name: Møller, Christoffer B.
name: Polzik, Eugene S.
name: Schliesser, Albert
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We realise a simple and robust optomechanical system with a multitude of long-lived ($Q>10^7$) mechanical modes in a phononic-bandgap shielded membrane resonator. An optical mode of a compact Fabry-Perot resonator detects these modes' motion with a measurement rate ($96~\mathrm{kHz}$) that exceeds the mechanical decoherence rates already at moderate cryogenic temperatures ($10\,\mathrm{K}$). Reaching this quantum regime entails, i.~a., quantum measurement backaction exceeding thermal forces, and thus detectable optomechanical quantum correlations. In particular, we observe ponderomotive squeezing of the output light mediated by a multitude of mechanical resonator modes, with quantum noise suppression up to -2.4 dB (-3.6 dB if corrected for detection losses) and bandwidths $\lesssim 90\,\mathrm{ kHz}$. The multi-mode nature of the employed membrane and Fabry-Perot resonators lends itself to hybrid entanglement schemes involving multiple electromagnetic, mechanical, and spin degrees of freedom.
description: 19 pages, 9 figures
Alyssum montanum var. ochroleucum Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum montanum
Alyssum montanum var. ochroleucum (boiss. & a. huet) boiss.

description: Alyssum montanum var. ochroleucum (Boiss. & A. Huet) Boiss., Fl. Orient. 1: 274. 1867.
 Alyssum ochroleucum Boiss. & A. Huet in Boiss., Diagn. Pl. Orient. ser. 2, 5: 36. 1856.
Type: “Hab. in Armeniâ propè Tortoum cl. Huet du Pavillon”.
Holotypus: TURKEY: “inter Hako et Tortoum”, VI.1853, Huet du Pavillon s.n. (G-BOIS [G00332368]; iso-: G [G00388911, G00388912], K [K000484908], KW [KW000127917], W [W18890093875]).
Notes. – There is only one sheet in G-BOIS and two duplicates in G. “In montibus inter Erzeroum et Ispir. In arenosis torrentium propè Tortum. 4–5000 p.s.m. Jun. 1853 ” is indicated for G [G00388911] and KW [KW000127917] and “circà Tortum. Jun. 1853 ” for G [G00388912], K [K000484908] and W [W18890093875].
Boissier in Flora Orientalis reduced the species to a variety of Alyssum montanum but changed his mind again in the Supplementum and re-recognized it as a distinct species.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 94, DOI: 10.5281/zenodo.7630433
Data-driven parameterization of the generalized Langevin equation
Creators: name: Lei, Huan
name: Baker, Nathan
name: Li, Xiantao
Publisher: name: arXiv
Year: 2016
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: We present a data-driven approach to determine the memory kernel and random noise in generalized Langevin equations. To facilitate practical implementations, we parameterize the kernel function in the Laplace domain by a rational function, with coefficients directly linked to the equilibrium statistics of the coarse-grain variables. We show that such an approximation can be constructed to arbitrarily high order and the resulting generalized Langevin dynamics can be embedded in an extended stochastic model without explicit memory. We demonstrate how to introduce the stochastic noise so that the second fluctuation-dissipation theorem is exactly satisfied. Results from several numerical tests are presented to demonstrate the effectiveness of the proposed method.
Alyssum suffrutescens Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum suffrutescens

description: Alyssum suffrutescens Boiss., Fl. Orient. 1: 275. 1867[nom. illeg.].
 Alyssum erosulum Gennari & Pestal. ex Clementi in Mem. Reale Accad. Sci. Torino ser. 2, 16: 248. 1855.
Note. – Alyssum suffrutescens is illegitimate because Boissier in Flora Orientalis listed the earlier published Alyssum erosulum Gennari & Pestal. ex Clementi as a synonym and indicated that it is a “nomen improprium”.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 94, DOI: 10.5281/zenodo.7630433
Additional file 1 of PCYT1A deficiency disturbs fatty acid metabolism and induces ferroptosis in the mouse retina
Creators: name: Wang, Kaifang
name: Xu, Huijuan
name: Zou, Rong
name: Zeng, Guangqun
name: Yuan, Ye
name: Zhu, Xianjun
name: Zhao, Xiaohui
name: Li, Jie
name: Zhang, Lin
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Cancer
subject: Computational Biology

description: Additional file 1: Fig S1. Single-cell RNA sequencing analysis of the mouse eye. Fig S2. Construction strategy and validation of retina-specific knockout of Pcyt1a mouse model. Fig S3. OCT images of two-month-old mice. Fig S4. H&E staining of retinas from 10-month-old mice. Fig S5. Immunofluorescence staining of retina in 2-month-old mice. Fig S6. Transmission electron microscopy of retinas from RKO and Ctl mice at 8-month of age. Fig S7. Detection of ferroptosis indicators in ARPE-19 cells without OA induction.
High-dimensional regression adjustments in randomized experiments
Creators: name: Wager, Stefan
name: Du, Wenfei
name: Taylor, Jonathan
name: Tibshirani, Robert
Publisher: name: arXiv
Year: 2016
Subjects: subject: Methodology (stat.ME)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: We study the problem of treatment effect estimation in randomized experiments with high-dimensional covariate information, and show that essentially any risk-consistent regression adjustment can be used to obtain efficient estimates of the average treatment effect. Our results considerably extend the range of settings where high-dimensional regression adjustments are guaranteed to provide valid inference about the population average treatment effect. We then propose cross-estimation, a simple method for obtaining finite-sample-unbiased treatment effect estimates that leverages high-dimensional regression adjustments. Our method can be used when the regression model is estimated using the lasso, the elastic net, subset selection, etc. Finally, we extend our analysis to allow for adaptive specification search via cross-validation, and flexible non-parametric regression adjustments with machine learning methods such as random forests or neural networks.
description: To appear in the Proceedings of the National Academy of Sciences. The present draft does not reflect final copyediting by the PNAS staff
Assessing significance in a Markov chain without mixing
Creators: name: Chikina, Maria
name: Frieze, Alan
name: Pegden, Wesley
Publisher: name: arXiv
Year: 2016
Subjects: subject: Probability (math.PR)
subject: Methodology (stat.ME)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: We present a new statistical test to detect that a presented state of a reversible Markov chain was not chosen from a stationary distribution. In particular, given a value function for the states of the Markov chain, we would like to demonstrate rigorously that the presented state is an outlier with respect to the values, by establishing a $p$-value for observations we make about the state under the null hypothesis that it was chosen uniformly at random. A simple heuristic used in practice is to sample ranks of states from long random trajectories on the Markov chain, and compare these to the rank of the presented state; if the presented state is a $0.1\%$-outlier compared to the sampled ranks (i.e., its rank is in the bottom $0.1\%$ of sampled ranks) then this should correspond to a $p$-value of $0.001$. This test is not rigorous, however, without good bounds on the mixing time of the Markov chain, as one must argue that the observed states on the trajectory approximate the stationary distribution. Our test is the following: given the presented state in the Markov chain, take a random walk from the presented state for any number of steps. We prove that observing that the presented state is an $\varepsilon$-outlier on the walk is significant at $p=\sqrt {2\varepsilon}$, under the null hypothesis that the state was chosen from a stationary distribution. Our result assumes nothing about the structure of the Markov chain beyond reversibility, and we construct examples to show that significance at $p\approx\sqrt \varepsilon$ is essentially best possible in general. We illustrate the use of our test with a potential application to the rigorous detection of gerrymandering in Congressional districtings.
description: 15 pages, 3 figures
Alyssum suffrutescens var. olympicum Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum suffrutescens
Alyssum suffrutescens var. olympicum boiss.

description: Alyssum suffrutescens var. olympicum Boiss., Fl. Orient. 1: 276. 1867 [nom. illeg.].
 Alyssum wulfenianum var. suffruticosum Boiss. ex Clementi in Mem. Reale Accad. Sci. Torino ser. 2, 16: 248. 1855.
Type: “[Aucher-Eloy] n. 275, Olympus Bithynus”.
Lectotypus (designated here): TURKEY: “Olymp. Bith.”, s.d., Aucher-Eloy 275 (G-BOIS [G00332374]; isolecto-: A [A00018615], BM [BM000582930], G [G00388578, G00388579, G00388580], K [K000484913, K000484914], P [P2272342, P05444992]).
= Alyssum erosulum Gennari & Pestal. ex Clementi in Mem. Reale Accad. Sci. Torino ser. 2, 16: 248. 1855.
Notes. – Alyssum suffrutescens var. olympicum is illegitimate because it is superfluous for A. wulfenianum var. suffruticosum. Although Boissier in Flora Orientalis recognized this and the above entry as different taxa, they belong to the same taxon.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 95, DOI: 10.5281/zenodo.7630433
Brownian motion of solitons in a Bose-Einstein Condensate
Creators: name: Aycock, L. M.
name: Hurst, H. M.
name: Efimkin, D. K.
name: Genkina, D.
name: Lu, H. -I
name: Galitski, V.
name: Spielman, I. B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: For the first time, we observed and controlled the Brownian motion of solitons. We launched solitonic excitations in highly elongated $^{87}\rm{Rb}$ BECs and showed that a dilute background of impurity atoms in a different internal state dramatically affects the soliton. With no impurities and in one-dimension (1-D), these solitons would have an infinite lifetime, a consequence of integrability. In our experiment, the added impurities scatter off the much larger soliton, contributing to its Brownian motion and decreasing its lifetime. We describe the soliton's diffusive behavior using a quasi-1-D scattering theory of impurity atoms interacting with a soliton, giving diffusion coefficients consistent with experiment.
description: 4 figures
Additional file 3 of PCYT1A deficiency disturbs fatty acid metabolism and induces ferroptosis in the mouse retina
Creators: name: Wang, Kaifang
name: Xu, Huijuan
name: Zou, Rong
name: Zeng, Guangqun
name: Yuan, Ye
name: Zhu, Xianjun
name: Zhao, Xiaohui
name: Li, Jie
name: Zhang, Lin
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Cancer
subject: Computational Biology

description: Additional file 3. Uncropped blots. The raw blots corresponding with Figs. 5, 7 and Fig S2 are shown with molecular weight indicators.
Commensurate $4a_0$ period Charge Density Modulations throughout the $Bi_2Sr_2CaCu_2O_{8+x}$ Pseudogap Regime
Creators: name: Mesaros, A.
name: Fujita, K.
name: Edkins, S. D.
name: Hamidian, M. H.
name: Eisaki, H.
name: Uchida, S.
name: Davis, J. C. Séamus
name: Lawler, M. J.
name: Kim, Eun-Ah
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Theories based upon strong real space (r-space) electron electron interactions have long predicted that unidirectional charge density modulations (CDM) with four unit cell (4$a_0$) periodicity should occur in the hole doped cuprate Mott insulator (MI). Experimentally, however, increasing the hole density p is reported to cause the conventionally defined wavevector $Q_A$ of the CDM to evolve continuously as if driven primarily by momentum space (k-space) effects. Here we introduce phase resolved electronic structure visualization for determination of the cuprate CDM wavevector. Remarkably, this new technique reveals a virtually doping independent locking of the local CDM wavevector at $|Q_0|=2π/4a_0$ throughout the underdoped phase diagram of the canonical cuprate $Bi_2Sr_2CaCu_2O_8$. These observations have significant fundamental consequences because they are orthogonal to a k-space (Fermi surface) based picture of the cuprate CDM but are consistent with strong coupling r-space based theories. Our findings imply that it is the latter that provide the intrinsic organizational principle for the cuprate CDM state.
Alyssum praecox Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum praecox

description: Alyssum praecox Boiss., Fl. Orient. 1: 275. 1867.
Type: “Hab. in monte Tchoschdagh Ciliciae Kurdicae (Ky exs. 95! spec. florifera), Tauro Cilicico circa Gülekboghas (Bal!), et montibus inter Aintab et Marasch (Haussk! spec. fructifera). Fl. Maio”.
Lectotypus (designated by DUDLEY, 1965b: 388): TURKEY: “Coteaux calcaires entourant de village de Gulek-Boghas, à 10 lieues au nord de Tarsous”, 26.VI.1855, Balansa 166 (G-BOIS [G00332371]; isolecto-: E [E00386023], G [G00388900]). Syntypi: TURKEY: “Taurus Cataonicus. Artrihakôi inter Aintab & Marasch”, 12.VII.1865, Haussknecht s.n. (G-BOIS [G00332370], W [W0075794, W18890055594]); “In jugis montis Tschosch Dagh versus Bakhyr Dagh.”, 5600' [1705 m], 15.V.1859, Kotschy 95 (A [A00018576], BM [BM000582933, BM000582934], G-BOIS [G00332369], JE [JE00024513], K [K000484912], P [P05444874], W [W0075779, W18890058110]).
Notes. – DUDLEY (1965b) narrowed the selection of three syntypes in the original publication to one and he listed a G sheet as the lectotype. He annotated in 1961 the G-BOIS sheet as syntype. This sheet, which is taken here as the lectotype, is with a label that carries the species name in Boissier’s handwriting and the rest of the data in Balansa’s handwritten label, including the field number 166.
Labels of the isolectotypes are printed, and they carry the exact collection data as the lectotype but without a collection or field number.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 94, DOI: 10.5281/zenodo.7630433
Selective Purcell enhancement of two closely linked zero-phonon transitions of a silicon carbide color center
Creators: name: Bracher, David O.
name: Zhang, Xingyu
name: Hu, Evelyn L.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Point defects in silicon carbide are rapidly becoming a platform of great interest for single photon generation, quantum sensing, and quantum information science. Photonic crystal cavities (PCC) can serve as an efficient light-matter interface both to augment the defect emission and to aid in studying the defects' properties. In this work, we fabricate 1D nanobeam PCCs in 4H-silicon carbide with embedded silicon vacancy centers. These cavities are used to achieve Purcell enhancement of two closely spaced defect zero-phonon lines (ZPL). Enhancements of >80-fold are measured using multiple techniques. Additionally, the nature of the cavity coupling to the different ZPLs is examined.
description: 15 pages, 5 figures
A High Efficiency Aluminum-Ion Battery Using an AlCl3-Urea Ionic Liquid Analogue Electrolyte
Creators: name: Angell, Michael
name: Pan, Chun-Jern
name: Rong, Youmin
name: Yuan, Chunze
name: Lin, Meng-Chang
name: Hwang, BingJoe
name: Dai, Hongjie
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: In recent years, impressive advances in harvesting renewable energy have led to pressing demand for the complimentary energy storage technology. Here, a high coulombic efficiency (~ 99.7%) Al battery is developed using earth-abundant aluminum as the anode, graphite as the cathode, and a cheap ionic liquid analogue electrolyte made from a mixture of AlCl3 and urea in 1.3 : 1 molar ratio. The battery displays discharge voltage plateaus around 1.9 V and 1.5 V (average discharge = 1.73 V) and yielded a specific cathode capacity of ~73 mAh g-1 at a current density of 100 mA g-1 (~ 1.4 C). High coulombic efficiency over a range of charge-discharge rates and stability over ~150-200 cycles was easily demonstrated. In-situ Raman spectroscopy clearly showed chloroaluminate anion intercalation/deintercalation of graphite in the cathode side during charge/discharge and suggested the formation of a stage 2 graphite intercalation compound when fully charged. Raman spectroscopy and nuclear magnetic resonance suggested the existence of AlCl4-, Al2Cl7- anions, and [AlCl2. (urea)n]+ cations in the urea/AlCl3 electrolyte when an excess of AlCl3 was present. Aluminum deposition therefore proceeded through two pathways, one involving Al2Cl7- anions and the other involving [AlCl2.(urea)n]+ cations. This battery is a promising prospect for a future high performance, low cost energy storage device.
Overcoming catastrophic forgetting in neural networks
Creators: name: Kirkpatrick, James
name: Pascanu, Razvan
name: Rabinowitz, Neil
name: Veness, Joel
name: Desjardins, Guillaume
name: Rusu, Andrei A.
name: Milan, Kieran
name: Quan, John
name: Ramalho, Tiago
name: Grabska-Barwinska, Agnieszka
name: Hassabis, Demis
name: Clopath, Claudia
name: Kumaran, Dharshan
name: Hadsell, Raia
Publisher: name: arXiv
Year: 2016
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: The ability to learn tasks in a sequential fashion is crucial to the development of artificial intelligence. Neural networks are not, in general, capable of this and it has been widely thought that catastrophic forgetting is an inevitable feature of connectionist models. We show that it is possible to overcome this limitation and train networks that can maintain expertise on tasks which they have not experienced for a long time. Our approach remembers old tasks by selectively slowing down learning on the weights important for those tasks. We demonstrate our approach is scalable and effective by solving a set of classification tasks based on the MNIST hand written digit dataset and by learning several Atari 2600 games sequentially.
A simple AF algebra not isomorphic to its opposite
Creators: name: Farah, Ilijas
name: Hirshberg, Ilan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Operator Algebras (math.OA)
subject: Logic (math.LO)
subject: FOS: Mathematics

description: We show that it is consistent with ZFC that there is a simple nuclear non-separable C*-algebra which is not isomorphic to its opposite algebra. We can furthermore guarantee that this example is an inductive limit of unital copies of the Cuntz algebra O_2, or of the CAR algebra.
description: 13 pages. To appear in PNAS
Collective force generation by groups of migrating bacteria
Creators: name: Sabass, Benedikt
name: Stone, Howard A.
name: Shaevitz, Joshua W.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: From biofilm and colony formation in bacteria to wound healing and embryonic development in multicellular organisms, groups of living cells must often move collectively. While considerable study has probed the biophysical mechanisms of how eukaryotic cells generate forces during migration, little such study has been devoted to bacteria, in particular with regard to the question of how bacteria generate and coordinate forces during collective motion. This question is addressed here for the first time using traction force microscopy. We study two distinct motility mechanisms of Myxococcus xanthus, namely twitching and gliding. For twitching, powered by type-IV pilus retraction, we find that individual cells exert local traction in small hotspots with forces on the order of 50 pN. Twitching of bacterial groups also produces traction hotspots, however with amplified forces around 100 pN. Although twitching groups migrate slowly as a whole, traction fluctuates rapidly on timescales <1.5 min. Gliding, the second motility mechanism, is driven by lateral transport of substrate adhesions. When cells are isolated, gliding produces low average traction on the order of 1 Pa. However, traction is amplified in groups by a factor of ~5. Since advancing protrusions of gliding cells push on average in the direction of motion, we infer a long-range compressive load sharing among sub-leading cells. Together, these results show that the forces generated during twitching and gliding have complementary characters and both forces are collectively amplified in groups.
Alyssum sphacioticum Boiss. & Heldr.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum sphacioticum

description: Alyssum sphacioticum Boiss. & Heldr. in Boiss., Diagn. Pl. Orient. 8: 35. 1849.
Type: “Hab. in monte Stravopodia cacumine excelso jugi Sphaciotici rarum (Heldreich)”.
Holotypus: GREECE: “Mt Stravopodia (les plus hautes sommités d’Sphakia)”, 6500' [1980 m], 10.VII.1846, Heldreich 1509 (G-BOIS [G00332375]; iso-: B [B100244953]).
Note. – This Greek endemic is highly restricted to W Crete.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 95, DOI: 10.5281/zenodo.7630433
EVALUATION AND OPTIMIZATION OF LOW IMPACT DEVELOPMENT DESIGNS FOR SUSTAINABLE STORMWATER MANAGEMENT IN A CHANGING CLIMATE
Creators: name: Abduljaleel, Yasir Qasim
Publisher: name: Washington State University
Year: 2023
Subjects: Water resources management

description: The intensity and frequency of extreme storms have been increasing due to possible climate change, making it challenging to manage stormwaters in highly urbanized areas. Without an adequate and appropriate stormwater system, these storms may cause major floods and damages. Low Impact Development (LID) has gained acceptance as an alternative for managing the increased stormwater. However, there is limited understanding of their effectiveness and optimize the LIDs with conventional stormwater systems (CSSs) under current and future climates. This dissertation aims to evaluate the performance of several LIDs under current and future storm conditions, identify the best performing mixes of LIDs and CCSs, and provide a decision-making tool for urban stormwater management. The Stormwater Management Model (SWMM) was used to simulate the rainfall-runoff under conventional and LIDs-based stormwater systems. A multi-objective Genetic Algorithm (MOGA) was used to optimize the LID and CCS further, considering the reduction in runoff and installation costs. The type, size, location, and the number of different LIDs were considered as decision variables.the methodologies have been tested for Renton City, located in King County, one of the fastest growing area in the US Pacific Northwest and often impacted by floods. The overall results show that the LID practices are more effective in reducing total runoff compared to peak flow. The reduction from the 50- and 100-years flood events ranges 30% - 75% for total runoff volume and 25% - 55% for peak flow depending on LIDs’ types and combinations. The optimum combination of LIDs in the study area can reduce the peak flow and total runoff volume by up to 13% and 29% under future climate change and by up to 62% and 80% under the current storm conditions. The framework introduced in this study will help the local authorities and practitioners to implement appropriate climate change adaptation strategies by maximizing the benefit from LIDs and ensuring sustainable stormwater management for the current and future climates.
Alyssum aizoides Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum aizoides

description: Alyssum aizoides Boiss. in Ann. Sci. Nat., Bot. ser. 2, 17: 153. 1842.
Type: “[Aucher-Eloy] N. 271 Armenia ”.
Lectotypus (designated here): TURKEY: sine loco, s.d., Aucher-Eloy 271 (G-BOIS [G00332380]; isolecto-: BM [BM000583935], G [G00429197, G00446165], K [K000484926], MPU [MPU017013], P [P00868521, P05372727]).
Note. – Lectotypification of the name is justified because Boissier based the original species description on G00446165 and the specimen in his herbarium.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 95, DOI: 10.5281/zenodo.7630433
Random Subsets of Structured Deterministic Frames have MANOVA Spectra
Creators: name: Haikin, Marina
name: Zamir, Ram
name: Gavish, Matan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: We draw a random subset of $k$ rows from a frame with $n$ rows (vectors) and $m$ columns (dimensions), where $k$ and $m$ are proportional to $n$. For a variety of important deterministic equiangular tight frames (ETFs) and tight non-ETF frames, we consider the distribution of singular values of the $k$-subset matrix. We observe that for large $n$ they can be precisely described by a known probability distribution -- Wachter's MANOVA spectral distribution, a phenomenon that was previously known only for two types of random frames. In terms of convergence to this limit, the $k$-subset matrix from all these frames is shown to be empirically indistinguishable from the classical MANOVA (Jacobi) random matrix ensemble. Thus empirically the MANOVA ensemble offers a universal description of the spectra of randomly selected $k$-subframes, even those taken from deterministic frames. The same universality phenomena is shown to hold for notable random frames as well. This description enables exact calculations of properties of solutions for systems of linear equations based on a random choice of $k$ frame vectors out of $n$ possible vectors, and has a variety of implications for erasure coding, compressed sensing, and sparse recovery. When the aspect ratio $m/n$ is small, the MANOVA spectrum tends to the well known Marcenko-Pastur distribution of the singular values of a Gaussian matrix, in agreement with previous work on highly redundant frames. Our results are empirical, but they are exhaustive, precise and fully reproducible.
iMapD: intrinsic Map Dynamics exploration for uncharted effective free energy landscapes
Creators: name: Chiavazzo, Eliodoro
name: Coifman, Ronald R.
name: Covino, Roberto
name: Gear, C. William
name: Georgiou, Anastasia S.
name: Hummer, Gerhard
name: Kevrekidis, Ioannis G.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extraction of coarse-grained, macroscopic information from atomistic or stochastic (here Molecular Dynamics, MD) simulations. The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator towards new, unexplored phase space regions by exploiting the smoothness of the (gradually, as the exploration progresses) revealed intrinsic low-dimensional geometry of the FES.
The Energetic Cost of Building a Virus
Creators: name: Mahmoudabadi, Gita
name: Milo, Ron
name: Phillips, Rob
Publisher: name: arXiv
Year: 2017
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Populations and Evolution (q-bio.PE)
subject: Subcellular Processes (q-bio.SC)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the host's molecular resources, a detailed estimate for the energetic cost of viral synthesis is largely lacking. To quantify the energetic cost of viruses to their hosts, we enumerated the costs associated with two very distinct but representative DNA and RNA viruses, namely T4 and influenza. We found that for these viruses, translation of viral proteins is the most energetically expensive process. Interestingly, the cost of building a T4 phage and a single influenza virus are nearly the same. Due to influenza's higher burst size, however, the overall cost of a T4 phage infection is only 2-3% of the cost of an influenza infection. The costs of these infections relative to their host's estimated energy budget during the infection reveal that a T4 infection consumes about a third of its host's energy budget, where as an influenza infection consumes only 1%. Building on our estimates for T4, we show how the energetic costs of double-stranded DNA viruses scale with virus size, revealing that the dominant cost of building a virus can switch from translation to genome replication above a critical virus size. Lastly, using our predictions for the energetic cost of viruses, we provide estimates for the strengths of selection and genetic drift acting on newly incorporated genetic elements in viral genomes, under conditions of energy limitation.
FMRI Clustering and False Positive Rates
Creators: name: Cox, Robert W.
name: Chen, Gang
name: Glen, Daniel R.
name: Reynolds, Richard C.
name: Taylor, Paul A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: Applications (stat.AP)
subject: FOS: Biological sciences
subject: FOS: Computer and information sciences

description: Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false positive rates (FPRs) in traditional approaches are greatly inflated, questioning the validity of "countless published fMRI studies"; 2) nonparametric methods produce valid, but slightly conservative, FPRs; 3) a common flawed assumption is that the spatial autocorrelation function (ACF) of FMRI noise is Gaussian-shaped; and 4) a 15-year-old bug in AFNI's 3dClustSim significantly contributed to producing "particularly high" FPRs compared to other software. We repeated simulations from [1] (Beijing-Zang data [2], see [3]), and comment on each point briefly.
description: 3 pages, 1 figure. A Letter accepted in PNAS
Alyssum aurantiacum Boiss.
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum aurantiacum

description: Alyssum aurantiacum Boiss., Fl. Orient. 1: 276. 1867.
Type: “Hab. in regione alpinâ montis Akgadh Lyciae (Bourg. exs. 20! sub A. lepidoto)”.
Holotypus: TURKEY: “In glareosis regionis alpinae montis Ak-Dagh”, 5.VII.1860, Bourgeau 20 (G-BOIS [G00332376]; iso-: B [B100241659, B100241660], E [E00386024], G [G00446163, G00446164], GOET [GOET002675], JE [JE00003021, JE00003022], K [K000484917, K000484919, K000484920], P [P06681528], W [W0050688, W18890016459]).
Notes. – Boissier based the species description solely on the unicate in his herbarium and, therefore, the name does not need lectotypification.
description: Published as part of AL-Shehbaz, Ihsan A. & Barriera, Gabrielle, 2019, Typification of Edmond Boissier's Cruciferae (Brassicaceae) names enumerated in Flora Orientalis, pp. 1-193 in Boissiera 72 on page 95, DOI: 10.5281/zenodo.7630433