cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Using Deep Learning and Google Street View to Estimate the Demographic Makeup of the US
Creators: name: Gebru, Timnit
name: Krause, Jonathan
name: Wang, Yilun
name: Chen, Duyun
name: Deng, Jia
name: Aiden, Erez Lieberman
name: Fei-Fei, Li
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: The United States spends more than $1B each year on initiatives such as the American Community Survey (ACS), a labor-intensive door-to-door study that measures statistics relating to race, gender, education, occupation, unemployment, and other demographic factors. Although a comprehensive source of data, the lag between demographic changes and their appearance in the ACS can exceed half a decade. As digital imagery becomes ubiquitous and machine vision techniques improve, automated data analysis may provide a cheaper and faster alternative. Here, we present a method that determines socioeconomic trends from 50 million images of street scenes, gathered in 200 American cities by Google Street View cars. Using deep learning-based computer vision techniques, we determined the make, model, and year of all motor vehicles encountered in particular neighborhoods. Data from this census of motor vehicles, which enumerated 22M automobiles in total (8% of all automobiles in the US), was used to accurately estimate income, race, education, and voting patterns, with single-precinct resolution. (The average US precinct contains approximately 1000 people.) The resulting associations are surprisingly simple and powerful. For instance, if the number of sedans encountered during a 15-minute drive through a city is higher than the number of pickup trucks, the city is likely to vote for a Democrat during the next Presidential election (88% chance); otherwise, it is likely to vote Republican (82%). Our results suggest that automated systems for monitoring demographic trends may effectively complement labor-intensive approaches, with the potential to detect trends with fine spatial resolution, in close to real time.
description: 41 pages including supplementary material. Under review at PNAS
Additional file 1 of Genomic analysis based on chromosome-level genome assembly reveals Myrtaceae evolution and terpene biosynthesis of rose myrtle
Creators: name: Yang, Ling
name: Jin, Jingjing
name: Lyu, Shanwu
name: Zhang, Fangqiu
name: Cao, Peijian
name: Qin, Qiaomei
name: Zhang, Guanghui
name: Feng, Chen
name: Lu, Peng
name: Li, Huiguang
name: Deng, Shulin
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1: Fig S1. K-mer frequency distribution curve of Illumina short reads for the R. tomentosa genome by GenomeScope. Fig S2. Chromosome karyotype analysis of R. tomentosa. 2n = 2X = 22. Bar = 10 μM. Fig S3. Hi-C contact data mapped to the R. tomentosa chromosome. Fig S4. Merqury assembly spectrum plots for evaluating k-mer completeness to the R. tomentosa chromosome. Fig S5. Comparison of gene models between R. tomentosa with those in other species. Fig S6. Distribution of synonymous substitution levels (Ks) of paralogous (A) and orthologous genes (B). Fig S7. Go analysis of positively selected genes in R. tomentosa. Fig S8. Chromosomal location of TPSs on chromosomes in R. tomentosa.
Microscopic dynamics of charge separation at the aqueous electrochemical interface
Creators: name: Kattirtzi, John A.
name: Limmer, David T.
name: Willard, Adam P.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We have used molecular simulation and methods of importance sampling to study the thermodynamics and kinetics of ionic charge separation at a liquid water-metal interface. We have considered this process using canonical examples of two different classes of ions: a simple alkali-halide pair, Na$^+$I$^-$, or classical ions, and the products of water autoionization, H$_3$O$^+$OH$^-$, or water ions. We find that for both ion classes, the microscopic mechanism of charge separation, including water's collective role in the process, is conserved between the bulk liquid and the electrode interface. Despite this, the thermodynamic and kinetic details of the process differ between these two environments in a way that depends on ion type. In the case of the classical ion pairs, a higher free energy barrier to charge separation and a smaller flux over that barrier at the interface, results in a rate of dissociation that is 40x slower relative to the bulk. For water ions, a slightly higher free energy barrier is offset by a higher flux over the barrier from longer lived hydrogen bonding patters at the interface, resulting in a rate of association that is similar both at and away from the interface. We find that these differences in rates and stabilities of charge separation are due to the altered ability of water to solvate and reorganize in the vicinity of the metal interface.
description: 6 pages, 3 figures + SI
Alyssum mouradicum Boiss. & Balansa
Creators: name: AL-Shehbaz, Ihsan A.
name: Barriera, Gabrielle
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Brassicales
Brassicaceae
Alyssum
Alyssum mouradicum

description: Alyssum mouradicum Boiss. & Balansa in Boiss., Diagn. Pl. Orient. ser. 2, 6: 16. 1859.
Type: “Hab. in regione alpinâ montis Mouraddagh Phrygiae alt. 2400 metr. ubi fine Junii floriferum et cum fruct. immaturis legit cl. Balansa”.
Holotypus: TURKEY: “Région alpine du MouradDagh (Phrygià)”, c. 2400 m, 27.VI.1857, Balansa 373 (G-BOIS [G00332381]; iso-: A [A00018523], G [G00388917]).
Notes. – The A isotype was taken by Dudley from the G specimen(s).
The G00388917 duplicate was not examined by Boissier and does not have the collector’s 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 pages 95-96, DOI: 10.5281/zenodo.7630433
FARG'ONA VILOYATI TUPROQLARINING O'RGANILISH TARIXI
Creators: name: Karimova, Dilnozaxon
Publisher: name: Zenodo
Year: 2025

description: Fargʻona vodiysi Oʻzbekistonning eng muhim qishloq xoʻjalik mintaqalaridan biri boʻlib, uning tuproqlari qadim zamonlardan buyon iqtisodiy va ekologik ahamiyatga ega boʻlib kelgan. Sugʻoriladigan yerlarda paxta, gʻalla va boshqa qishloq xoʻjalik ekinlarini yetishtirish ushbu hududning agrar rivojlanishida asosiy oʻrinni egallaydi. Tuproq unumdorligini aniqlash va yaxshilash boʻyicha olib borilgan izlanishlar nafaqat qishloq xoʻjaligi mahsuldorligini oshirish, balki ekologik barqarorlikni taʼminlash uchun ham muhimdir.Fargʻona viloyati tuproqlari tarixan turli davrlarda oʻrganilib, ulardan samarali foydalanish uchun ilmiy asoslar ishlab chiqilgan. Dastlabki tadqiqotlar Rossiya imperiyasi davrida boshlanib, Sovet Ittifoqi davrida esa keng koʻlamli melioratsiya va shoʻrlanishni bartaraf etishga qaratilgan ishlanmalar olib borildi. Mustaqillik yillarida esa tuproq resurslarining ekologik va iqtisodiy ahamiyati, shuningdek, iqlim oʻzgarishlari sharoitida ulardan foydalanish masalalari alohida eʼtibor qozondi.Mazkur maqolada Fargʻona viloyati tuproqlarining oʻrganilish tarixi, tadqiqot yoʻnalishlari va ularning hudud qishloq xoʻjaligiga taʼsiri tahlil qilinadi. Ushbu izlanishlarning natijalari nafaqat ilmiy qiymatga ega, balki hududning iqtisodiy va ekologik barqarorligini taʼminlashga xizmat qiladi.
Discrete modes of social information processing predict individual behavior of fish in a group
Creators: name: Harpaz, Roy
name: Tkačik, Gašper
name: Schneidman, Elad
Publisher: name: arXiv
Year: 2017
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Biological Physics (physics.bio-ph)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an active mode in which they are sensitive to the swimming patterns of conspecifics, and a passive mode where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors behavior. At the group level, switching between active and passive modes is uncorrelated among fish, yet correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates, as well as to other species.
An Algorithm for Cellular Reprogramming
Creators: name: Ronquist, Scott
name: Patterson, Geoff
name: Brown, Markus
name: Chen, Haiming
name: Bloch, Anthony
name: Muir, Lindsey
name: Brockett, Roger
name: Rajapakse, Indika
Publisher: name: arXiv
Year: 2017
Subjects: subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences

description: The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to develop better predictions about and methods for control over specific biological processes and system-wide cell behavior. In this paper we describe an approach to optimizing the use of transcription factors in the context of cellular reprogramming. We construct an approximate model for the natural evolution of a synchronized population of fibroblasts, based on data obtained by sampling the expression of some 22,083 genes at several times along the cell cycle. (These data are based on a colony of cells that have been cell cycle synchronized) In order to arrive at a model of moderate complexity, we cluster gene expression based on the division of the genome into topologically associating domains (TADs) and then model the dynamics of the expression levels of the TADs. Based on this dynamical model and known bioinformatics, we develop a methodology for identifying the transcription factors that are the most likely to be effective toward a specific cellular reprogramming task. The approach used is based on a device commonly used in optimal control. From this data-guided methodology, we identify a number of validated transcription factors used in reprogramming and/or natural differentiation. Our findings highlight the immense potential of dynamical models models, mathematics, and data guided methodologies for improving methods for control over biological processes.
Osmotaxis in Escherichia coli through changes in motor speed
Creators: name: Rosko, Jerko
name: Martinez, Vincent
name: Poon, Wilson
name: Pilizota, Teuta
Publisher: name: arXiv
Year: 2017
Subjects: subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: Bacterial motility, and in particular repulsion or attraction towards specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory network in many bacterial species. For Escherichia coli most of the current understanding comes from the experiments with low levels of chemotactically-active ligands. However, chemotactically-inactive chemical species at concentrations found in the human gastrointestinal tract produce significant changes in E. coli's osmotic pressure, and have been shown to lead to taxis. To understand how these nonspecific physical signals influence motility, we look at the response of individual bacterial flagellar motors under step-wise changes in external osmolarity. We combine these measurements with a population swimming assay under the same conditions. Unlike for chemotactic response, a long-term increase in swimming/motor speeds is observed, and in the motor rotational bias, both of which scale with the osmotic shock magnitude. We discuss how the speed changes we observe can lead to steady state bacterial accumulation.
description: 24 pages, 11 figures
Alyssum lepidotum 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 lepidotum

description: Alyssum lepidotum Boiss., Diagn. Pl. Orient. 1: 73. 1843.
Type: “Hab. in regione alpinâ summâ Cariae, montes propè Moglah Aucher No 299, Cadmus suprà Gheyra ego Junio 1842 [Boissier]”.
Lectotypus (first step designated by DUDLEY, 1965b: 390; second step designated here): TURKEY: “ Pic de Geyra ”, VI.1842, Boissier s.n. (G-BOIS [G00332378]; isolecto-: A [A00018554], B [B100244986], JE [JE00002999], W). Syntypus: TURKEY: “Mouglah”, s.d., Aucher-Eloy 252 (G-BOIS [G00332377], K [K000484921, K000484922], P [P00868514, P05330196]).
Notes. – DUDLEY (1965b) selected one of the two syntypes cited in the original publication but did not indicate which of the four herbaria he cited house the lectotype, and therefore a second step is done here. Dudley listed K among the isolectotypes, but the two duplicates by Boissier K000484923 and K000484924 were collected from “Mesogis cacumen suprà Tralles ” and are not recognized here as part of the type collection.
The lectotype is a collection folder of three sheets, of which one is unlabeled, and the barcoded sheet has the species name, locality, and month and collection year. The third sheet has four rows of plants with the locality “Pic de Geyra” on the second row and collection year on the other three rows.
BOISSIER (1843) erroneously cited the syntype as Aucher-Eloy 299, but he later corrected it to 252 (BOISSIER, 1867a).
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
Locally embedded presages of global network bursts
Creators: name: Tajima, Satohiro
name: Mita, Takeshi
name: Bakkum, Douglas J.
name: Takahashi, Hirokazu
name: Toyoizumi, Taro
Publisher: name: arXiv
Year: 2017
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Dynamical Systems (math.DS)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Biological sciences
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: I.2.0
subject: 92-02

description: Spontaneous, synchronous bursting of neural population is a widely observed phenomenon in nervous networks, which is considered important for functions and dysfunctions of the brain. However, how the global synchrony across a large number of neurons emerges from an initially non-bursting network state is not fully understood. In this study, we develop a new state-space reconstruction method combined with high-resolution recordings of cultured neurons. This method extracts deterministic signatures of upcoming global bursts in "local" dynamics of individual neurons during non-bursting periods. We find that local information within a single-cell time series can compare with or even outperform the global mean field activity for predicting future global bursts. Moreover, the inter-cell variability in the burst predictability is found to reflect the network structure realized in the non-bursting periods. These findings demonstrate the deterministic mechanisms underlying the locally concentrated early-warnings of the global state transition in self-organized networks.
Alyssum idaeum 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 idaeum

description: Alyssum idaeum Boiss. & Heldr. in Boiss., Diagn. Pl. Orient. 8: 35. 1849.
Type: “Hab. ad saxa cacuminum montis Idae act 6000' rarum (Heldreich)”.
Holotypus: GREECE: “ Creta in saxosis montis Ida ”, 6000' [1830 m], 28.V.1846, Heldreich 1509 (G-BOIS [G00332382]; iso-: B [B100244988], BM [BM000750129], G [G00389046, G00446190], GH [GH00018547], GOET [GOET002688], K [K000484586, K000484587, K000484588, K000484589], W [W00075613], WU [WU0076290]).
Notes. – The holotype sheet has two labels, of which the one written by Heldreich (“in saxis. Mt Ida – sommités”) has the collection number and day, and the other is mimeographed written by Boissier as above but lacks both. However, the locality, elevation, month, and year in both are identical.
All isotypes, except for the BM and K000484588 that carry Heldreich’s writing, have the mimeographed Boissier label.
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 96, DOI: 10.5281/zenodo.7630433
Introduzione alla Fisica Ambientale
Creators: name: Vitali, Giuliano
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2018
Subjects: AGR/02 Agronomia e coltivazioni erbacee
FIS/07 Fisica applicata (a beni culturali, ambientali, biologia e medicina)

description: L'introduzione alla Fisica Ambientale è scritta per studenti dei primi anni di università,  scritto allo scopo di dare una linea di studio dei concetti chiave e cercando di stimolare approfondimenti.
Si affrontano a livello elementare i concetti di base della fisica dell'atmosfera, meteorologia e climatologia, idrologia e fisica del suolo, privilegiando la descrizione dei processi che caratterizzano gli ambienti terrestri.
Il testo inizia col descrivere gli aspetti strutturali dell'ambiente, diviso nei suoi elementi classici sole, aria, acqua e terra; nella seconda parte si affrontano gli aspetti dinamici e quindi i flussi all'interno e tra i vari comparti, assieme al fenomeno del trasporto; nella terza parte sono invece introdotti i concetti di base relativi alle principali trasformazioni fisiche e chimiche associate alle interazioni tra energia e materia; infine nella quarta parte si affrontano i processi associati agli organismi viventi, per concludere con una introduzione alla climatologia.
Introduzione alla Fisica del Terreno
Creators: name: Vitali, Giuliano
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2018
Subjects: AGR/02 Agronomia e coltivazioni erbacee
FIS/07 Fisica applicata (a beni culturali, ambientali, biologia e medicina)

description: Dispense di Fisica del Terreno per i primi anni di università
Glass transitions may be similar in 2 and 3 dimensions, after all
Creators: name: Tarjus, Gilles
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: This is a commentary on two recent experimental papers in PNAS by Vivek et al. and Illing et al. that convincingly address an issue at the junction of two fundamental questions in glass physics: the role of the dimensionality of space on the glass transition and the possible existence of long wavelength fluctuations in two-dimensional amorphous solids.
description: 3-page Commentary
Model of Brain Activation Predicts the Neural Collective Influence Map of the Brain
Creators: name: Morone, Flaviano
name: Roth, Kevin
name: Min, Byungjoon
name: Stanley, H. Eugene
name: Makse, Hernán A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Efficient complex systems have a modular structure, but modularity does not guarantee robustness, because efficiency also requires an ingenious interplay of the interacting modular components. The human brain is the elemental paradigm of an efficient robust modular system interconnected as a network of networks (NoN). Understanding the emergence of robustness in such modular architectures from the interconnections of its parts is a long-standing challenge that has concerned many scientists. Current models of dependencies in NoN inspired by the power grid express interactions among modules with fragile couplings that amplify even small shocks, thus preventing functionality. Therefore, we introduce a model of NoN to shape the pattern of brain activations to form a modular environment that is robust. The model predicts the map of neural collective influencers (NCIs) in the brain, through the optimization of the influence of the minimal set of essential nodes responsible for broadcasting information to the whole-brain NoN. Our results suggest new intervention protocols to control brain activity by targeting influential neural nodes predicted by network theory.
description: 18 pages, 5 figures
Alyssum ruprechtii 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 ruprechtii

description: Alyssum ruprechtii Boiss., Fl. Orient. Suppl.: 51. 1888
[nom. illeg.].
 Alyssum andinum Rupr., Fl. Caucasi: 103. 1869.
Lectotypus: designated by DOROFEYEV (2012: 414).
Notes. – Alyssum ruprechtii is illegitimate because the earlier published A. andinum was listed as its synonym. BOISSIER (1888) apparently did not like the name A. andinum and indicated that it is “nomen absurdum, etenim Andes sunt Alpes Americae nec Orbis veteris”.
DOROFEYEV (2012: 414) did not list Alyssum ruprechtii, though he accepted A. andinum and lectotypified it.
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 96, DOI: 10.5281/zenodo.7630433
Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport
Creators: name: Blau, Samuel M.
name: Bennett, Doran I. G.
name: Kreisbeck, Christoph
name: Scholes, Gregory D.
name: Aspuru-Guzik, Alán
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in two-dimensional electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct down-conversion from the highest-energy states to the lowest-energy pigments. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio QM/MM nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We demonstrate that bilin solvation controls EET pathways and that direct down-conversion proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We thus suggest that engineering local solvation dynamics represents a potential design principle for nanoscale control of EET.
Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues
Creators: name: Yang, Xingbo
name: Bi, Dapeng
name: Czajkowski, Michael
name: Merkel, Matthias
name: Manning, M. Lisa
name: Marchetti, M. Cristina
Publisher: name: arXiv
Year: 2017
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: Cell Behavior (q-bio.CB)
subject: Tissues and Organs (q-bio.TO)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Collective cell migration is a highly regulated process involved in wound healing, cancer metastasis and morphogenesis. Mechanical interactions among cells provide an important regulatory mechanism to coordinate such collective motion. Using a Self-Propelled Voronoi (SPV) model that links cell mechanics to cell shape and cell motility, we formulate a generalized mechanical inference method to obtain the spatio-temporal distribution of cellular stresses from measured traction forces in motile tissues and show that such traction-based stresses match those calculated from instantaneous cell shapes. We additionally use stress information to characterize the rheological properties of the tissue. We identify a motility-induced swim stress that adds to the interaction stress to determine the global contractility or extensibility of epithelia. We further show that the temporal correlation of the interaction shear stress determines an effective viscosity of the tissue that diverges at the liquid-solid transition, suggesting the possibility of extracting rheological information directly from traction data.
description: 12 pages, 9 figures
Effect Of Diffusion-Induced Element Accumulation On The Opacity Inside B Stars
Creators: name: Alain, Hui-Bon-Hoa
name: Vauclair Sylvie
Publisher: name: Zenodo
Year: 2018

description: Stellar models with homogeneous abundances fail to reproduce the pulsation frequencies of early B-type stars. Their oscillations are excited by kappa-mechanism involving the Fe-peak elements where they are main contributors to the opacity (the "Z-bump") and a ad hoc increase of the opacity in these layers is necessary to match the observations.

We test whether atomic diffusion can induce such an opacity increase through Fe and Ni accumulations in the Z-bump. With models computed using the Toulouse–Geneva Evolution Code, we show that atomic diffusion changes the abundance profiles inside the star, leading to an overabundance of the iron-peak elements in the upper envelope. The opacity may reach the amount required by seismic studies, provided that fingering mixing, which extends the size of the overabundance zone, is taken into account. Mass-loss is also required to evolve the model until the end of the main sequence.
Alyssum tetrastemon 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 tetrastemon

description: Alyssum tetrastemon Boiss. in Ann. Sci. Nat., Bot. ser. 2, 17: 153. 1842.
Type: “[Aucher-Eloy] N. 279, Cilicia ”.
Holotypus: TURKEY: “ Cilicia ”, s.d., Aucher-Eloy 279 (G-BOIS [G00332384]; iso-: G [G00446166], P [P02272277]).
Note. – Boissier did not examine or annotate the duplicates at G and P.
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 96, DOI: 10.5281/zenodo.7630433
title: Weyl Darstellung der metaplektischen Operatoren und die fraktionale Fourier Transformation der Gaussfunktion
Creators: name: Duzelovic, Jasminko
Year: 2010

description: Das Bestreben dieser Diplomarbeit ist es, die metaplektische Darstellung vom Standpunkt des Weyl Calculus der Pseudodifferential Operatoren zu untersuchen. Die Resultate dieser Untersuchungen führen zu der quadratischen Fourier Transformation, die einfach einen Spezialfall der metaplektischen Operatoren darstellt. Der Zugang den ich in dieser Diplomarbeit gewählt habe, ist dank der symplektischen Cayley Transformation sehr direkt. Vereinfacht gesagt, die Betonung liegt auf dem Zusammenhang zwischen der symplektischen Gruppe und der Fourier Transformation. Beispielsweise assoziiert die metaplektische Gruppe zu der Fourier Transformation die standard symplektische Rotation. Auf mathematisch etwas anspruchsvollerem Niveau kann die metaplektische Gruppe Mp(d) auf zwei verschiedenen Wegen de…niert werden. Hier eine kurze Zusammenfassung dieser möglichen Zugänge zur metaplektischen Gruppe: Die symplektische Gruppe Sp(d) besitzt Überdeckungsgruppen der Ordnung q = 2,3,...,... . Die Überdeckungsgruppe Sp2(d) mit der Ordnung 2, kann mit der Gruppe der unitären Operatoren wirkend auf L2(Rd) identifiziert werden: Diese Gruppe ist die metaplektische Gruppe, bezeichnet mit Mp(d): Ein anderer Zugang zur metaplektischen Gruppe Mp(d) ist durch direkte Konstruktion: -eine Familie von unitären Operatoren auf L2(Rd) kann durch erzeugende Funktionen der symplektischen Matrizen konstruiert werden. Auf diesem Wege wird eine Gruppe erzeugt, die metaplektische Gruppe Mp(d) ; -das ist auch der Zugang den ich in dieser Diplomarbeit gewählt habe. Meine Arbeit ist wie folgt strukturiert : Nach Einführung der relevanten Grundbegrie, wird die Theorie der metaplektischen Gruppe vom Standpunkt der quadratischen Fourier Transformation betrachtet. Als ein wichtiges Resultat in diesem Abschnitt zeigt sich die Tatsache, dass jeder metaplektische Operator in genau zwei quadratische Fourier Transformationen faktorisiert werden kann. An dieser Stelle gebe ich eine sehr kurze Verbindung zu entsprechendem Gebiet der Maslov Indizes. Danach werden die Elemente der metaplektischen Gruppe Mp(d) vom pseudodifferentionellen Standpunkt untersucht.
Modeling and replicating statistical topology, and evidence for CMB non-homogeneity
Creators: name: Adler, Robert J.
name: Agami, Sarit
name: Pranav, Pratyush
Publisher: name: arXiv
Year: 2017
Subjects: subject: Methodology (stat.ME)
subject: Applications (stat.AP)
subject: Other Statistics (stat.OT)
subject: FOS: Computer and information sciences

description: Under the banner of `Big Data', the detection and classification of structure in extremely large, high dimensional, data sets, is, one of the central statistical challenges of our times. Among the most intriguing approaches to this challenge is `TDA', or `Topological Data Analysis', one of the primary aims of which is providing non-metric, but topologically informative, pre-analyses of data sets which make later, more quantitative analyses feasible. While TDA rests on strong mathematical foundations from Topology, in applications it has faced challenges due to an inability to handle issues of statistical reliability and robustness and, most importantly, in an inability to make scientific claims with verifiable levels of statistical confidence. We propose a methodology for the parametric representation, estimation, and replication of persistence diagrams, the main diagnostic tool of TDA. The power of the methodology lies in the fact that even if only one persistence diagram is available for analysis -- the typical case for big data applications -- replications can be generated to allow for conventional statistical hypothesis testing. The methodology is conceptually simple and computationally practical, and provides a broadly effective statistical procedure for persistence diagram TDA analysis. We demonstrate the basic ideas on a toy example, and the power of the approach in a novel and revealing analysis of CMB non-homogeneity.
Composition of Early Planetary Atmospheres II: Coupled Dust and Chemical Evolution in Protoplanetary Disks
Creators: name: Cridland, A. J.
name: Pudritz, Ralph E.
name: Birnstiel, Tilman
name: Cleeves, L. Ilsedore
name: Bergin, Edwin A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present the next step in a series of papers devoted to connecting the composition of the atmospheres of forming planets with the chemistry of their natal evolving protoplanetary disks. The model presented here computes the coupled chemical and dust evolution of the disk and the formation of three planets per disk model. Our three canonical planet traps produce a Jupiter near 1 AU, a Hot Jupiter and a Super-Earth. We study the dependency of the final orbital radius, mass, and atmospheric chemistry of planets forming in disk models with initial disk masses that vary by 0.02 $M_\odot$ above and below our fiducial model ($M_{disk,0} = 0.1 ~M_\odot$). We compute C/O and C/N for the atmospheres formed in our 3 models and find that C/O$_{\rm planet}\sim$ C/O$_{\rm disk}$, which does not vary strongly between different planets formed in our model. The nitrogen content of atmospheres can vary in planets that grow in different disk models. These differences are related to the formation history of the planet, the time and location that the planet accretes its atmosphere, and are encoded in the bulk abundance of NH$_3$. These results suggest that future observations of atmospheric NH$_3$ and an estimation of the planetary C/O and C/N can inform the formation history of particular planetary systems.
description: Accepted for publication in MNRAS
Additional file 1 of Validation of the Health Assessment Tool (HAT) based on four aging cohorts from the Swedish National study on Aging and Care
Creators: name: Abbadi, Ahmad
name: Kokoroskos, Emmanouil
name: Stamets, Matthew
name: Vetrano, Davide L.
name: Orsini, Nicola
name: Elmståhl, Sölve
name: Fagerström, Cecilia
name: Wimo, Anders
name: Sköldunger, Anders
name: Berglund, Johan Sanmartin
name: Olsson, Christina B.
name: Wachtler, Caroline
name: Fratiglioni, Laura
name: Calderón-Larrañaga, Amaia
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 1: Document S1, Tables S1–S9, Figures S1–S4. Document S1 Calculation of HAT scores, Table S1 Baseline characteristics of the study population across SNAC sites stratified by sex, Table S2 Baseline characteristics of the study population across SNAC sites stratified by age, Table S3 Individual health indicator cut-off points, Table S4 Most frequent health indicator categories by HAT score in SNAC-K, Table S5 Most frequent health indicator categories by HAT score in SNAC-B, Table S6 Most frequent health indicator categories by HAT score in SNAC-GÅS, Table S7 Most frequent health indicator categories by HAT score in SNAC-N, Table S8 Most frequent health indicator categories by HAT score in harmonized dataset, Figure S1 Test information function, Figure S2 Individual and meta-analyzed predictive capacity of the HAT across all SNAC sites except for SNAC-B, Table S9 Predictive capacity of the HAT, Figure S3 HAT-based geriatric charts and risk of 5-year mortality, Figure S4 Reliability plots.
Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting
Creators: name: Bennett, Doran I. G.
name: Fleming, Graham R.
name: Amarnath, Kapil
Publisher: name: arXiv
Year: 2017
Subjects: subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the PSII yield, which only emerges on the 100 nm scale of the grana membrane and determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 nm x 200 nm patch of the grana membrane. We demonstrate that single molecule measurements of qE are consistent with a weak-quenching regime. Consequently, excitation transport can be rigorously coarse-grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. A diffusion-corrected lake model substantially improves the PSII yield determined from variable chlorophyll fluorescence measurements and offers an improved model of PSII for photosynthetic metabolism.
description: 19 pages, 4 figures, 3 supplementary figures
Topological localization in out-of-equilibrium dissipative systems
Creators: name: Dasbiswas, Kinjal
name: Mandadapu, Kranthi K.
name: Vaikuntanathan, Suriyanarayanan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: In this paper we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We show this for physically two disparate cases : stochastic networks governed by microscopic single particle dynamics as well as collections of driven, interacting particles described by coarse-grained hydrodynamic theory. In both cases, the presence of dissipative couplings to the environment that break time reversal symmetry are crucial to ensuring topologically protection. These examples constitute proof of principle that notions of topological protection, established in the context of electronic and mechanical systems, do indeed extend generically to processes that operate out of equilibrium. Such topologically robust boundary modes have implications for both biological and synthetic systems.
description: 11 pages, 4 figures (SI: 8 pages 3 figures)
Alyssum tetrastemon var. cappadocicum 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 tetrastemon
Alyssum tetrastemon var. cappadocicum boiss.

description: Alyssum tetrastemon var. cappadocicum Boiss. in Ann. Sci. Nat., Bot. ser. 2, 17: 153. 1842.
Type: “[Aucher-Eloy] n. 270 Akdag”.
Holotypus: TURKEY: “Ak Dagh”, s.d., Aucher-Eloy 270 (G-BOIS [G00332385]; iso-: G [G00446168, G00446167], K [K000364807], MPU [MPU013463]).
= Alyssum tetrastemon Boiss. in Ann. Sci. Nat., Bot. ser. 2, 17: 153. 1842.
Notes. – Boissier in Flora Orientalis erroneously maintained var. cappadocicum despite citing its type under the collections of Alyssum tetrastemon and listed a different collection under that variety.
He did not annotate the duplicate G00446167, and his Flora Orientalis varietal concept was the basis for DUDLEY’S (1964a: 72) A. corningii T.R. Dudley.
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 96, DOI: 10.5281/zenodo.7630433
Fluctuation-enhanced electric conductivity in electrolyte solutions
Creators: name: Péraud, Jean-Philippe
name: Nonaka, Andy
name: Bell, John B.
name: Donev, Aleksandar
name: Garcia, Alejandro L.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In this letter we analyze the effects of an externally applied electric field on thermal fluctuations for a fluid containing charged species. We show in particular that the fluctuating Poisson-Nernst-Planck equations for charged multispecies diffusion coupled with the fluctuating fluid momentum equation, result in enhanced charge transport. Although this transport is advective in nature, it can macroscopically be represented as electrodiffusion with renormalized electric conductivity. We calculate the renormalized electric conductivity by deriving and integrating the structure factor coefficients of the fluctuating quantities and show that the renormalized electric conductivity and diffusion coefficients are consistent although they originate from different noise terms. In addition, the fluctuating hydrodynamics approach recovers the electrophoretic and relaxation corrections obtained by Debye-Huckel-Onsager theory, and provides a quantitative theory that predicts a non-zero cross-diffusion Maxwell-Stefan coefficient that agrees well with experimental measurements. Finally, we show that strong applied electric fields result in anisotropically enhanced velocity fluctuations and reduced fluctuations of salt concentrations.
description: 12 pages, 1 figure
MANFAATLAR TO'QNASHUVI TUSHUNCHASI VA UNING HUQUQIY TABIATI
Creators: name: Najimova, Jamola
name: Bokiyev, Jahongir
Publisher: name: Zenodo
Year: 2025

description: Mazkur maqolada O‘zbekiston Respublikasidagi davlat boshqaruvida manfaatlar to‘qnashuvi va korrupsiyaning oldini olish masalalari tahlil qilinadi. Maqolada manfaatlar to‘qnashuvi tushunchasi, uning huquqiy tabiati, xalqaro tajribalar va O‘zbekistonning amaldagi huquqiy tizimi o‘rganiladi. Bunda, korrupsiya va manfaatlar to‘qnashuvi jamiyatda tengsizlik, o‘zaro nizolarni keltirib chiqarishi, davlat boshqaruvidagi ishonchsizlikni kuchaytirishi mumkinligi ta’kidlanadi. Shu sababli, davlat boshqaruvini shaffoflashtirish, korrupsiyaga qarshi kurashishning samarali mexanizmlarini ishlab chiqish, davlat xizmatchilarining huquqiy savodxonligini oshirish, normativ-huquqiy hujjatlarni takomillashtirish zarurligi qayd etilgan. Maqolada xalqaro tajriba va amaliyotda olingan o‘rganishlar, shuningdek, manfaatlar to‘qnashuvi va korrupsiyaga qarshi kurashishda yuzaga kelgan muammolar va ularni bartaraf etish uchun takliflar keltirilgan.
Iterative Random Forests to detect predictive and stable high-order interactions
Creators: name: Basu, Sumanta
name: Kumbier, Karl
name: Brown, James B.
name: Yu, Bin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Machine Learning (stat.ML)
subject: Genomics (q-bio.GN)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building on Random Forests (RF), Random Intersection Trees (RITs), and through extensive, biologically inspired simulations, we developed the iterative Random Forest algorithm (iRF). iRF trains a feature-weighted ensemble of decision trees to detect stable, high-order interactions with same order of computational cost as RF. We demonstrate the utility of iRF for high-order interaction discovery in two prediction problems: enhancer activity in the early Drosophila embryo and alternative splicing of primary transcripts in human derived cell lines. In Drosophila, among the 20 pairwise transcription factor interactions iRF identifies as stable (returned in more than half of bootstrap replicates), 80% have been previously reported as physical interactions. Moreover, novel third-order interactions, e.g. between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order relationships that are candidates for follow-up experiments. In human-derived cells, iRF re-discovered a central role of H3K36me3 in chromatin-mediated splicing regulation, and identified novel 5th and 6th order interactions, indicative of multi-valent nucleosomes with specific roles in splicing regulation. By decoupling the order of interactions from the computational cost of identification, iRF opens new avenues of inquiry into the molecular mechanisms underlying genome biology.
Alyssum tetrastemon var. latifolium 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 tetrastemon
Alyssum tetrastemon var. latifolium boiss., fl.

description: Alyssum tetrastemon var. latifolium Boiss., Fl. Orient. 1: 278. 1867.
Type: “Hab. in Libani monte Sannin (Bourquenoud!), montibus Palaestinae prope Nazareth (Roth!)”.
Lectotypus (designated here): LEBANON: “Sommet du Sannine”, 14.VI.1859, Bourquenoud 2465 (G-BOIS [G00332386]; isolecto-: JE [JE00003020]). Syntypus: ISRAEL: “Nazareth”, 1858, Roth 149 (G-BOIS [G00332387], K [K000484932]).
= Alyssum baumgartnerianum Bornm. in Jahresber. K. Franz-Jos. Landesgymnas. Oberrealschule Baden 48: 16. 1911.
Note. – This small perennial is distributed from south central Turkey southward into Lebanon, Israel, and W Syria.
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 96, DOI: 10.5281/zenodo.7630433
Chance, long tails, and inference: a non-Gaussian, Bayesian theory of vocal learning in songbirds
Creators: name: Zhou, Baohua
name: Hofmann, David
name: Pinkoviezky, Itai
name: Sober, Samuel J.
name: Nemenman, Ilya
Publisher: name: arXiv
Year: 2017
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Biological sciences

description: Traditional theories of sensorimotor learning posit that animals use sensory error signals to find the optimal motor command in the face of Gaussian sensory and motor noise. However, most such theories cannot explain common behavioral observations, for example that smaller sensory errors are more readily corrected than larger errors and that large abrupt (but not gradually introduced) errors lead to weak learning. Here we propose a new theory of sensorimotor learning that explains these observations. The theory posits that the animal learns an entire probability distribution of motor commands rather than trying to arrive at a single optimal command, and that learning arises via Bayesian inference when new sensory information becomes available. We test this theory using data from a songbird, the Bengalese finch, that is adapting the pitch (fundamental frequency) of its song following perturbations of auditory feedback using miniature headphones. We observe the distribution of the sung pitches to have long, non-Gaussian tails, which, within our theory, explains the observed dynamics of learning. Further, the theory makes surprising predictions about the dynamics of the shape of the pitch distribution, which we confirm experimentally.
Additional file 2 of Validation of the Health Assessment Tool (HAT) based on four aging cohorts from the Swedish National study on Aging and Care
Creators: name: Abbadi, Ahmad
name: Kokoroskos, Emmanouil
name: Stamets, Matthew
name: Vetrano, Davide L.
name: Orsini, Nicola
name: Elmståhl, Sölve
name: Fagerström, Cecilia
name: Wimo, Anders
name: Sköldunger, Anders
name: Berglund, Johan Sanmartin
name: Olsson, Christina B.
name: Wachtler, Caroline
name: Fratiglioni, Laura
name: Calderón-Larrañaga, Amaia
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 2: TRIPOD checklist.
D3.7 Dataset from farm pilot cases and product health-promoting features of UCs for business cases and RADIANT LCA
Creators: name: Krenz, Lina
name: Pleissner, Daniel
name: Moreira, Diana
name: Nunes da Silva, Marta
name: Santos, Carla
name: Vasconcelos, Marta W.
Publisher: name: Zenodo
Year: 2024

description: This document demonstrates the datasets from farm pilot cases and product health-promoting features of UCs for business cases and RADIANT LCA.  This report consolidates multiple datasets generated during the RADIANT project, encompassing analyses from farm pilot cases, Life Cycle Assessments, and business cases development to promote the sustainability, innovation and market integration of underutilized crops (UCs) as well as data on their health-promoting properties.