cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of SAMHD1 silencing cooperates with radiotherapy to enhance anti-tumor immunity through IFI16-STING pathway in lung adenocarcinoma
Creators: name: Li, Yangyi
name: Gao, Yuke
name: Jiang, Xueping
name: Cheng, Yajie
name: Zhang, Jianguo
name: Xu, Liexi
name: Liu, Xinyu
name: Huang, Zhengrong
name: Xie, Conghua
name: Gong, Yan
Publisher: name: figshare
Year: 2024
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: Table S1. Primer sequences used for amplification and the targeting siRNA sequences. Table S2. Antibodies used in this study. Figure S1. Functional enrichment analysis to confirm the association of SAMHD1 with immunity. Figure S2. SAMHD1 inhibited TBK1-IRF3-IFN-I pathway in LUAD cells. Figure S3. SAMHD1 silencing synergized with radiotherapy to induce ssDNA accumulation and activate TBK1-IRF3-IFN-I signaling. Figure S4. SAMHD1 overexpression alleviated radiation-induced inhibition of LUAD cells growth. Figure S5. SAMHD1 silencing synergized with radiotherapy to regulate CD3+ and CD8+ T cell infiltration in spleen.
Figure_S1_xyz153701c28279b – Supplemental material for A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis
Creators: name: Sheng, Mengying
name: Xie, Xueying
name: Wang, Jun
name: Gu, Wanjun
Publisher: name: SAGE Journals
Year: 2019
Subjects: Cell Biology

description: Supplemental material, Figure_S1_xyz153701c28279b for A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis by Mengying Sheng, Xueying Xie, Jun Wang and Wanjun Gu in Evolutionary Bioinformatics
Reholttumia micropaleata S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Reholttumia
Reholttumia micropaleata

description: Reholttumia micropaleata (Holttum) S.E. Fawc. & A.R. Sm., comb. nov.
— Pneumatopteris micropaleata Holttum, Blumea 21:319. 1973.
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 78, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
AIM818286_Supplemental_material_SP1 – Supplemental material for Acupuncture for the treatment of lower limb diabetic peripheral neuropathy: a systematic review
Creators: name: Nash, Jane
name: Armour, Mike
name: Penkala, Stefania
Publisher: name: SAGE Journals
Year: 2019
Subjects: Medicine

description: Supplemental material, AIM818286_Supplemental_material_SP1 for Acupuncture for the treatment of lower limb diabetic peripheral neuropathy: a systematic review by Jane Nash, Mike Armour and Stefania Penkala in Acupuncture in Medicine
Dynamic interventions with limited knowledge in network games
Creators: name: Shakarami, Mehran
name: Cherukuri, Ashish
name: Monshizadeh, Nima
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: Systems and Control (eess.SY)
subject: FOS: Mathematics
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: This paper studies the problem of intervention design for steering the actions of noncooperative players in quadratic network games to the social optimum. The players choose their actions with the aim of maximizing their individual payoff functions, while a central regulator uses interventions to modify their marginal returns and maximize the social welfare function. This work builds on the key observation that the solution to the steering problem depends on the knowledge of the regulator on the players' parameters and the underlying network. We, therefore, consider different scenarios based on limited knowledge and propose suitable static, dynamic and adaptive intervention protocols. We formally prove convergence to the social optimum under the proposed mechanisms. We demonstrate our theoretical findings on a case study of Cournot competition with differentiated goods.
Appendix – Supplemental material for Comparison of Periodontal Status Between Male Exclusive Narghile Smokers and Male Exclusive Cigarette Smokers
Creators: name: Khemiss, Mehdi
name: Fekih, Dalila Ben
name: Khelifa, Mohamed Ben
name: Saad, Helmi Ben
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: 111099 Nursing not elsewhere classified
subject: 111799 Public Health and Health Services not elsewhere classified

description: Supplemental material, Appendix for Comparison of Periodontal Status Between Male Exclusive Narghile Smokers and Male Exclusive Cigarette Smokers by Mehdi Khemiss, Dalila Ben Fekih, Mohamed Ben Khelifa and Helmi Ben Saad in American Journal of Men’s Health
Dealing with missing data under stratified sampling designs where strata are study domains
Creators: name: Rodríguez, Carlos
name: Nieto-Barajas, Luis
name: Pérez-Pérez, Carlos
Publisher: name: arXiv
Year: 2022
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: A quick count seeks to estimate the voting trends of an election and communicate them to the population on the evening of the same day of the election. In quick counts, the sampling is based on a stratified design of polling stations. Voting information is gathered gradually, often with no guarantee of obtaining the complete sample or even information in all the strata. However, accurate interval estimates with partial information must be obtained. Furthermore, this becomes more challenging if the strata are additionally study domains. To produce partial estimates, two strategies are proposed: 1) A Bayesian model using a dynamic post-stratification strategy and a single imputation process defined after a thorough analysis of historic voting information. Additionally, a credibility level correction is included to solve the underestimation of the variance; 2) a frequentist alternative that combines standard multiple imputation ideas with classic sampling techniques to obtain estimates under a missing information framework. Both solutions are illustrated and compared using information from the 2021 quick count. The aim was to estimate the composition of the Chamber of Deputies in Mexico.
Reholttumia novae-caledoniae S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Reholttumia
Reholttumia novae-Caledoniae

description: Reholttumia novae-caledoniae (Holttum) S.E. Fawc. & A.R. Sm., comb. nov.
— Pneumatopteris novae-caledoniae Holttum, Blumea 21:313.1973.
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 78, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
DS_10.1177_0022034519835204 – Supplemental material for Crucial and Overlapping Roles of Six1 and Six2 in Craniofacial Development
Creators: name: Z. Liu
name: C. Li
name: J. Xu
name: Y. Lan
name: H. Liu
name: X. Li
name: P. Maire
name: X. Wang
name: R. Jiang
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 110599 Dentistry not elsewhere classified
subject: FOS: Clinical medicine
subject: 91299 Materials Engineering not elsewhere classified
subject: FOS: Materials engineering

description: Supplemental material, DS_10.1177_0022034519835204 for Crucial and Overlapping Roles of Six1 and Six2 in Craniofacial Development by Z. Liu, C. Li, J. Xu, Y. Lan, H. Liu, X. Li, P. Maire, X. Wang and R. Jiang in Journal of Dental Research
A hyperbolic-elliptic PDE model and conservative numerical method for gravity-dominated variably-saturated groundwater flow
Creators: name: Shadab, Mohammad Afzal
name: Hesse, Marc Andre
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: Richards equation is often used to represent two-phase fluid flow in an unsaturated porous medium when one phase is much heavier and more viscous than the other. However, it cannot describe the fully saturated flow for some capillary functions without specialized treatment due to degeneracy in the capillary pressure term. Mathematically, gravity-dominated variably saturated flows are interesting because their governing partial differential equation switches from hyperbolic in the unsaturated region to elliptic in the saturated region. Moreover, the presence of wetting fronts introduces strong spatial gradients often leading to numerical instability. In this work, we develop a robust, multidimensional mathematical model and implement a well-known efficient and conservative numerical method for such variably saturated flow in the limit of negligible capillary forces. The elliptic problem in saturated regions is integrated efficiently into our framework by solving a reduced system corresponding only to the saturated cells using fixed head boundary conditions in the unsaturated cells. In summary, this coupled hyperbolic-elliptic PDE framework provides an efficient, physics-based extension of the hyperbolic Richards equation to simulate fully saturated regions. Finally, we provide a suite of easy-to-implement yet challenging benchmark test problems involving saturated flows in one and two dimensions. These simple problems, accompanied by their corresponding analytical solutions, can prove to be pivotal for the code verification, model validation (V&V) and performance comparison of simulators for variably saturated flow. Our numerical solutions show an excellent comparison with the analytical results for the proposed problems. The last test problem on two-dimensional infiltration in a stratified, heterogeneous soil shows the formation and evolution of multiple disconnected saturated regions.
description: 28 pages, 15 figures
Exploration of disease phenotype variation in equid trypanosomiasis
Creators: name: Raftery, Alexandra
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 300909
subject: Veterinary parasitology
classificationCode: 300906
subject: Veterinary immunology
classificationCode: 300904
subject: Veterinary diagnosis and diagnostics

description: Supplementary data files for PhD
Double and Quadruple Flat Bands tuned by Alternative magnetic Fluxes in Twisted Bilayer Graphene
Creators: name: Le, Congcong
name: Zhang, Qiang
name: Fan, Cui
name: Wu, Xianxin
name: Chiu, Ching-Kai
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Twisted bilayer graphene (TBG) can host the moiré energy flat bands with two-fold degeneracy serving as a fruitful playground for strong correlations and topological phases. However, the number of degeneracy is not limited to two. Introducing a spatially alternative magnetic field, we report that the induced magnetic phase becomes an additional controllable parameter and leads to an undiscovered generation of four-fold degenerate flat bands. This emergence stems from the band inversion at $Γ$ point near the Fermi level with a variation of both twisted angle and magnetic phase. We present the conditions for the emergence of multi-fold degenerate flat bands, which are associated with the eigenvalue degeneracy of a Birman-Schwinger operator. Using holomorphic functions, which explain the origin of the double flat bands in the conventional TBG, we can generate analytical wave functions in the magnetic TBG to show absolute flatness with four-fold degeneracy. Moreover, we identify an orbital-related intervalley coherent state as the many-body ground state at charge neutrality. In contrast, the conventional TBG has only two moiré energy flat bands, and the highly degenerate flat bands with additional orbital channels in this magnetic platform might bring richer correlation physics.
description: 15 pages and 8 figures
DS_10.1177_0022034519835205 – Supplemental material for Phenotype and Variant Spectrum in the LAMB3 Form of Amelogenesis Imperfecta
Creators: name: C.E.L. Smith
name: J.A. Poulter
name: S.J. Brookes
name: G. Murillo
name: S. Silva
name: C.J. Brown
name: A. Patel
name: H. Hussain
name: J. Kirkham
name: C.F. Inglehearn
name: A.J. Mighell
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 110599 Dentistry not elsewhere classified
subject: FOS: Clinical medicine
subject: 91299 Materials Engineering not elsewhere classified
subject: FOS: Materials engineering

description: Supplemental material, DS_10.1177_0022034519835205 for Phenotype and Variant Spectrum in the LAMB3 Form of Amelogenesis Imperfecta by C.E.L. Smith, J.A. Poulter, S.J. Brookes, G. Murillo, S. Silva, C.J. Brown, A. Patel, H. Hussain, J. Kirkham, C.F. Inglehearn and A.J. Mighell in Journal of Dental Research
MSJ837706_supplementary_figures – Supplemental material for Functional neuroplasticity in response to cerebello-thalamic injury underpins the clinical presentation of tremor in multiple sclerosis
Creators: name: Boonstra, Frederique MC
name: Noffs, Gustavo
name: Perera, Thushara
name: Jokubaitis, Vilija G
name: Vogel, Adam P
name: Moffat, Bradford A
name: Butzkueven, Helmut
name: Evans, Andrew
name: van der Walt, Anneke
name: Kolbe, Scott C
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: Aged Health Care

description: Supplemental material, MSJ837706_supplementary_figures for Functional neuroplasticity in response to cerebello-thalamic injury underpins the clinical presentation of tremor in multiple sclerosis by Frederique MC Boonstra, Gustavo Noffs, Thushara Perera, Vilija G Jokubaitis, Adam P Vogel, Bradford A Moffat, Helmut Butzkueven, Andrew Evans, Anneke van der Walt and Scott C Kolbe in Multiple Sclerosis Journal
Ultrafast Opto-magnetic Effects in the Extreme Ultraviolet Spectral Range
Creators: name: Hennecke, Martin
name: Schmising, Clemens von Korff
name: Yao, Kelvin
name: Jal, Emmanuelle
name: Vodungbo, Boris
name: Chardonnet, Valentin
name: Légaré, Katherine
name: Capotondi, Flavio
name: Naumenko, Denys
name: Pedersoli, Emanuele
name: Lopez-Quintas, Ignacio
name: Nikolov, Ivaylo P.
name: Raimondi, Lorenzo
name: De Ninno, Giovanni
name: Salemi, Leandro
name: Ruta, Sergiu
name: Chantrell, Roy
name: Ostler, Thomas
name: Pfau, Bastian
name: Engel, Dieter
name: Oppeneer, Peter M.
name: Eisebitt, Stefan
name: Radu, Ilie
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Coherent light-matter interactions mediated by opto-magnetic phenomena like the inverse Faraday effect (IFE) are expected to provide a non-thermal pathway for ultrafast manipulation of magnetism on timescales as short as the excitation pulse itself. As the IFE scales with the spin-orbit coupling strength of the involved electronic states, photo-exciting the strongly spin-orbit coupled core-level electrons in magnetic materials appears as an appealing method to transiently generate large opto-magnetic moments. Here, we investigate this scenario in a ferrimagnetic GdFeCo alloy by using intense and circularly polarized pulses of extreme ultraviolet radiation. Our results reveal ultrafast and strong helicity-dependent magnetic effects which are in line with the characteristic fingerprints of an IFE, corroborated by ab initio opto-magnetic IFE theory and atomistic spin dynamics simulations.
Discrete fragmentation equations with time-dependent coefficients
Creators: name: Kerr, Lyndsay
name: Lamb, Wilson
name: Langer, Matthias
Publisher: name: arXiv
Year: 2022
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 34G10, 47D06, 80A30, 34D05

description: We examine an infinite, linear system of ordinary differential equations that models the evolution of fragmenting clusters, where each cluster is assumed to be composed of identical units. In contrast to previous investigations into such discrete-size fragmentation models, we allow the fragmentation coefficients to vary with time. By formulating the initial-value problem for the system as a non-autonomous abstract Cauchy problem, posed in an appropriately weighted $\ell^1$ space, and then applying results from the theory of evolution families, we prove the existence and uniqueness of physically relevant, classical solutions for suitably constrained coefficients.
description: to appear in "Discrete and Continuous Dynamical Systems - Series S
Reholttumia oxyoura S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Reholttumia
Reholttumia oxyoura

description: Reholttumia oxyoura (Copel.) S.E. Fawc. & A.R. Sm., comb. nov.
— Dryopteris oxyoura Copel., Philipp. J. Sci. 60:107. 1936.— Cyclosorus oxyourus (Copel.) Copel. — Pneumatopteris oxyoura (Copel.) Holttum — Thelypteris oxyoura (Copel.) C.F.Reed
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 78, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
Measurement of Lepton Mass Squared Moments in $B \to X_c \ell \bar \nu_{\ell}$ Decays with the Belle II Experiment
Creators: name: Belle-II Collaboration
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2022
Subjects: lepton, mass
GeV
BELLE
Upsilon(10570)
decay modes
hadronic decay
quark
charm
electron positron
meson
phase space

description: We present measurements of the first to fourth moments of the lepton mass squared $q^2$ of \mbox{$B \to X_c \, \ell\, \bar \nu_{\ell}$} decays for $\ell = e, \mu$ and with $X_c$ a hadronic system containing a charm quark. These results use a sample of electron-positron collisions at the $\Upsilon(4S)$ resonance corresponding to $62.8 \, \mathrm{fb}^{-1}$ of integrated luminosity and collected by the Belle II experiment in 2019 and 2020. To identify the $X_c$ system and reconstruct $q^2$, one of the $B$ mesons from an $\Upsilon(4S) \to B \kern 0.18em\overline{\kern -0.18em B}$ decay is fully reconstructed in a hadronic decay mode using a multivariate $B$ tagging algorithm. We report raw and central moments for $ q^2 > 1.5 \; \mathrm{GeV^2/c^4}$ up to $q^2 > 8.5 \; \mathrm{GeV^2/c^4}$, probing up to 77% of the accessible \mbox{$B \to X_c \, \ell\, \bar \nu_{\ell}$} phase space. This is the first measurement of moments in the experimentally challenging range of $[ 1.5, 2.5 ] \, \mathrm{GeV^2/c^4}$.
Robust superconducting correlation against inter-site interactions in the extended two-leg Hubbard ladder
Creators: name: Zhou, Zongsheng
name: Ye, Weinan
name: Luo, Hong-Gang
name: Zhao, Jize
name: Chang, Jun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The Hubbard and related models serve as a fundamental starting point in understanding the novel experimental phenomena in correlated electron materials, such as superconductivity, Mott insulator, magnetism and stripe phases. Recent numerical simulations indicate that the emergence of superconductivity is connected with the next nearest-neighbor hopping $t^\prime$ in the Hubbard model. However, the impacts of complex inter-site electron interaction in the $t^\prime$-Hubbard model are less explored. Utilizing the state-of-art density-matrix renormalization group method, we investigate the $t^\prime$-Hubbard model on a two-leg ladder with inter-site interactions extended to the fourth neighbor sites. The accurate numerical results show that the quasi-long-range superconducting correlation remains stable under the repulsive nearest-neighbor and the next nearest-neighbor interactions though these interactions are against the superconductivity. The ground state properties are also undisturbed by the longer-range repulsive interactions. In addition, inspired by recent experiments on one-dimensional cuprates chain $\mathrm{Ba}_{2-x}\mathrm{Sr}_x\mathrm{CuO}_{3+δ}$, which implies an effective attraction between the nearest neighbors may exist in the cuprates superconductors, we also show that the attractive interaction between the nearest neighbors significantly enhances the superconducting correlation when it is comparable to the strength of the nearest-neighbor hopping $t^\prime$. Stronger attraction drives the system into a Luther-Emery liquid phase. Nevertheless, with the attraction further increasing, the system enters an electron-hole phase separation and the superconducting correlation is destroyed. Finally, we investigate the effects of on-site Coulomb interaction on superconductivity.
Exceptional directions for the Teichmüller geodesic flow and Hausdorff dimension
Creators: name: Al-Saqban, Hamid
name: Apisa, Paul
name: Erchenko, Alena
name: Khalil, Osama
name: Mirzadeh, Shahriar
name: Uyanik, Caglar
Publisher: name: arXiv
Year: 2017
Subjects: subject: Dynamical Systems (math.DS)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics

description: We prove that for every flat surface $ω$, the Hausdorff dimension of the set of directions in which Teichmüller geodesics starting from $ω$ exhibit a definite amount of deviation from the correct limit in Birkhoff's and Oseledets' Theorems is strictly less than $1$. This theorem extends a result by Chaika and Eskin where they proved that such sets have measure $0$. We also prove that the Hausdorff dimension of the directions in which Teichmüller geodesics diverge on average in a stratum is bounded above by $1/2$, strengthening a classical result due to Masur. Moreover, we show that the Hausdorff codimension of the set of non-weakly mixing IETs with permutation $(d, d-1, \dots, 1)$, where $d$ is an odd number, is exactly $1/2$ and strengthen a result by Avila and Leguil.
description: 47 pages, strengthened main theorems and added an application to IETs
Reholttumia papuana S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Reholttumia
Reholttumia papuana

description: Reholttumia papuana (Holttum) S.E. Fawc. & A.R. Sm., comb. nov.
— Pneumatopteris papuana Holttum,Blumea 21:311.1973.
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 78, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
Some remarks on expansive mappings in metric spaces
Creators: name: Popescu, Ovidiu
name: Pacurar, Cristina Maria
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Topology (math.GN)
subject: FOS: Mathematics

description: The aim of this paper is to generalize the results on expansive mappings of Yesilkaya and Aydin from \cite{Yesilkaya}. We give some fixed point results for q-expansive mappings in metric spaces and prove some fixed point theorems for this class of mappings. Finally, we present some examples to support the new results.
Spiking activity in the ventral visual pathway under delayed match-to-sample task
Creators: name: Gilbert, Charles
name: Siebert Altavini, Tiago
Publisher: name: Zenodo
Year: 2025
Subjects: Electrophysiology
Psychophysics
Neuroscience
Vision
Top-down

description: The hierarchical view of the ventral object recognition pathway is primarily based on feedforward mechanisms, starting from a fixed basis set of object primitives and ending on a representation of whole objects in the inferotemporal cortex. Here we provide a different view. Rather than being a fixed "labeled line" for a specific feature, neurons are continually changing their stimulus selectivities on a moment-to-moment basis, as dictated by top-down influences of object expectation and perceptual task. Here we also derive the selectivity for stimulus features from an ethologically curated stimulus set, based on a delayed match-to-sample task, that finds components that are informative for object recognition.
description: Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: PHY1532846
Funding provided by: Leon Levy FoundationROR ID: https://ror.org/033hnyq61Award Number:
description: We implanted microelectrode arrays (Blackrock) in different parts of the ventral visual pathway in the left hemisphere. In animal MJ we implanted four arrays, three 6 x 6 and one 4 x 5, for a total of 128 electrodes with 400 µm spacing between electrodes. All electrodes were 1 mm long. One 6 x 6 array was implanted in opercular V1 representing 2° eccentricity in a lower visual field quadrant; the others were implanted at three positions along the prelunate gyrus. Animal MR was implanted with three arrays: one 6 x 8 array in opercular V1 representing 2° eccentricity in the lower visual field quadrant, and two 5 x 8 arrays in the prelunate gyrus. With the arrays we were able to record single unit and multiunit action potentials and local field potentials. Multiunit activity was manually sorted offline with SpikeSort software (Plexon). Sorted spikes are binned in 1ms bins.

The animals were given an initial cue or sample consisting of a full object for 500 msec, a mask consisting of a jumbled image between 400 and 800 msec, and a target consisting of a full object or object component for 500 msec. The components consisted of cropped parts of the object images. We collected data on how successful each animal was in recognizing whether the first image (cue) and second image (target) corresponded to the same object.
Cameron-Liebler Line Classes with parameter $x=\frac{(q+1)^2}{3}$
Creators: name: Feng, Tao
name: Momihara, Koji
name: Rodgers, Morgan
name: Xiang, Qing
name: Zou, Hanlin
Publisher: name: arXiv
Year: 2020
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05E30, 51E20

description: Cameron-Liebler line classes were introduced in \cite{CL}, and motivated by a question about orbits of collineation groups of $\PG(3,q)$. These line classes have appeared in different contexts under disguised names such as Boolean degree one functions, regular codes of covering radius one, and tight sets. In this paper we construct an infinite family of Cameron-Liebler line classes in $\PG(3,q)$ with new parameter $x=(q+1)^2/3$ for all prime powers $q$ congruent to 2 modulo 3. The examples obtained when $q$ is an odd power of two represent the first infinite family of Cameron-Liebler line classes in $\PG(3,q)$, $q$ even.
description: 22 pages, submitted
Reholttumia pergamacea S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Reholttumia
Reholttumia pergamacea

description: Reholttumia pergamacea (Holttum) S.E. Fawc. & A.R. Sm., comb. nov.
— Pneumatopteris pergamacea Holttum, Blumea 21:315. 1973.
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 78, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
JBD885025_supplemental_table - Stuck in the middle with you: Predictors of commitment in midlife
Creators: name: Johnson, Matthew D.
name: Somerville, Sarah D.
name: Galambos, Nancy L.
name: Krahn, Harvey J.
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology

description: JBD885025_supplemental_table for Stuck in the middle with you: Predictors of commitment in midlife by Matthew D. Johnson, Sarah D. Somerville, Nancy L. Galambos and Harvey J. Krahn in International Journal of Behavioral Development
Reholttumia psilophylla S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Reholttumia
Reholttumia psilophylla

description: Reholttumia psilophylla (Holttum) S.E. Fawc. & A.R. Sm., comb. nov.
— Pneumatopteris psilophylla Holttum. Fl. Males., Ser. 2, Pterid.1(5):427.1982.
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 78, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
Kardar-Parisi-Zhang universality in two-component driven diffusive models: Symmetry and renormalization group perspectives
Creators: name: Dolai, Pritha
name: Simha, Aditi
name: Basu, Abhik
Publisher: name: arXiv
Year: 2020
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We elucidate the universal spatio-temporal scaling properties of the time-dependent correlation functions in a class of two-component one-dimensional (1D) driven diffusive system that consists of two coupled asymmetric exclusion process. By using a perturbative renormalization group framework, we show that the relevant scaling exponents have values same as those for the 1D Kardar-Parisi-Zhang (KPZ) equation. We connect these universal scaling exponents with the symmetries of the model equations. We thus establish that these models belong to the 1D KPZ universality class.
description: Accepted for publication in Physical Review E
Fluctuation-induced Interactions in Micro- and Nano-systems: Survey of Some Basic Results
Creators: name: Dantchev, Daniel
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Soft Condensed Matter (cond-mat.soft)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: On the examples of the quantum-electrodynamical Casimir force, as well as critical Casimir and Helmholtz forces, we present a review of some results available for the class of fluctuation induced forces. In addition, we also concisely present examples of other such fluctuation-induced forces. On the instance of the Ising model we discuss the connection between the Casimir and Helmholtz forces. We discuss the importance of the presented results for the nanotechnology, and especially for devising micro- or nano-systems, and for their assembly. Some important problems for the nanotechnology, following from the currently available experimental findings, are spelled out and possible strategies for their overcoming are outlined.
description: 21 pages, 6 figures. arXiv admin note: text overlap with arXiv:2203.15050
supplementary_file – Supplemental material for The five factor model of personality and sense of coherence: A meta-analysis
Creators: name: Barańczuk, Urszula
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 110319 Psychiatry (incl. Psychotherapy)
subject: FOS: Clinical medicine
subject: 111799 Public Health and Health Services not elsewhere classified
subject: FOS: Health sciences

description: Supplemental material, supplementary_file for The five factor model of personality and sense of coherence: A meta-analysis by Urszula Barańczuk in Journal of Health Psychology
Molouki_Supplemental_Material_rev – Supplemental material for The Sign Effect in Past and Future Discounting
Creators: name: Molouki, Sarah
name: Hardisty, David J.
name: Caruso, Eugene M.
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 110319 Psychiatry (incl. Psychotherapy)
subject: Neuroscience

description: Supplemental material, Molouki_Supplemental_Material_rev for The Sign Effect in Past and Future Discounting by Sarah Molouki, David J. Hardisty and Eugene M. Caruso in Psychological Science
COVID-19 Clinical footprint to infer about mortality
Creators: name: Rodríguez, Carlos E.
name: Mena, Ramsés H.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Applications (stat.AP)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Information of 1.6 million patients identified as SARS-CoV-2 positive in Mexico is used to understand the relationship between comorbidities, symptoms, hospitalizations and deaths due to the COVID-19 disease. Using the presence or absence of these latter variables a clinical footprint for each patient is created. The risk, expected mortality and the prediction of death outcomes, among other relevant quantities, are obtained and analyzed by means of a multivariate Bernoulli distribution. The proposal considers all possible footprint combinations resulting in a robust model suitable for Bayesian inference.
description: 23 pages and 6 figures
Ordered Locales
Creators: name: Heunen, Chris
name: van der Schaaf, Nesta
Publisher: name: arXiv
Year: 2023
Subjects: subject: Category Theory (math.CT)
subject: General Topology (math.GN)
subject: FOS: Mathematics

description: We extend the Stone duality between topological spaces and locales to include order: there is an adjunction between the category of preordered topological spaces satisfying the so-called open cone condition, and the newly defined category of ordered locales. The adjunction restricts to an equivalence of categories between spatial ordered locales and sober $T_0$-ordered spaces with open cones.
description: 23 pages, 5 figures; v2: added sections 7 and 8
Supplemental Material, Supplementary_eTable_2 - Survival Impact and Clinical Predictors of Acute Gastrointestinal Bleeding in Patients With Bloodstream Infection
Creators: name: Huang, Amy Huaishiuan
name: Liu, Ye
name: Hsien, Yenh-Chen
name: Hsu, Tzu-Chun
name: Yen, Debra
name: Hsu, Wan-Ting
name: Lin, Hsin-Yang
name: Chen, Shyr-Chyr
name: Lee, Chien-Chang
Publisher: name: SAGE Journals
Year: 2020
Subjects: Emergency Medicine
Aged Health Care
Respiratory Diseases

description: Supplemental Material, Supplementary_eTable_2 for Survival Impact and Clinical Predictors of Acute Gastrointestinal Bleeding in Patients With Bloodstream Infection by Amy Huaishiuan Huang, Ye Liu, Yenh-Chen Hsien, Tzu-Chun Hsu, Debra Yen, Wan-Ting Hsu, Hsin-Yang Lin, Shyr-Chyr Chen, Chien-Chang Lee and NTUH Health Data Science Research Group in Journal of Intensive Care Medicine
Artifact repository for the paper "Isolating Compiler Faults through Differentiated Compilation Configurations"
Creators: name: Yang, Yibiao
name: Li, Qingyang
name: Sun, Maolin
name: Yang, Jing
name: Wu, Jiangchang
name: Zhou, Yuming
Publisher: name: Zenodo
Year: 2025

description: ODFL (Option Differentiating for Fault Localization) is an innovative technique proposed in the paper "Isolating Compiler Faults through Differentiated Compilation Configurations" for effective compiler fault localization.

This implementation evaluates ODFL's performance using two major C compilers: LLVM and GCC.

Prerequisites

- Linux workstation

- Python 3.x

- GCC/LLVM build dependencies

Getting Started

1. Setting Up Bug Information

Add compiler bugs to the respective summary files using this format:

bugId,trunk_revision,non_triggering_optimization,triggering_optimization,faulty_file

Example (from gccbugs_summary.txt):

`56478,r196310,-O1+-c,-O2+-c,gcc/predict.c`

Note: Comprehensive bug information is available in the benchmark directory.

2. Installing Target Compilers

Run the appropriate installation script:

# For GCC
python gcc-install.py

# For LLVM
python llvm-install.py

This will install the specified compiler versions from source.

3. Running ODFL Analysis

Execute the appropriate run script:

# For GCC
python gcc-run.py

# For LLVM
python llvm-run.py

Output:

The analysis generates Ochiai_scoredict.txt, containing suspiciousness scores for compiler source files (sorted in descending order). Higher scores indicate greater likelihood of containing the bug.

The scripts automatically process all bugs listed in the corresponding summary files.

4. Evaluating Results

Generate performance metrics with:

# For GCC
python gcc-result.py

# For LLVM
python llvm-result.py

Metrics Reported:

- Top-N (Top 1, 5, 10, 20)

- MFR (Mean First Rank)

- MAR (Mean Average Rank)

Documentation

For detailed methodology and technical background, please refer to the original paper:

"Isolating Compiler Faults through Differentiated Compilation Configurations"
Sphaerostephanos bakeri S. E. Fawc. & A. R. Sm., comb. nov.
Creators: name: Fawcett, Susan
name: Smith, Alan R.
Publisher: name: BRIT Press
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Sphaerostephanos
Sphaerostephanos bakeri

description: Sphaerostephanos bakeri (Harr.) S.E. Fawc. & A.R. Sm., comb. nov.
— Nephrodium bakeri Harr., J. Linn. Soc., Bot. 16:29. 1877.— Cyclosorus bakeri (Harr.) Copel. — Haplodictyum bakeri (Harr.) Ching — Pronephrium bakeri (Harr.)Holttum — Thelypteris bakeri (Harr.)C.F. Reed
description: Published as part of Fawcett, Susan & Smith, Alan R., 2021, A Generic Classification of the Thelypteridaceae, Fort Worth, Texas, USA :BRIT Press on page 81, DOI: 10.17348/jbrit.v15.i2.1206, http://zenodo.org/record/14111022
Neural Operators for PDE Backstepping Control of First-Order Hyperbolic PIDE with Recycle and Delay
Creators: name: Qi, Jie
name: Zhang, Jing
name: Krstic, Miroslav
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optimization and Control (math.OC)
subject: Machine Learning (cs.LG)
subject: Systems and Control (eess.SY)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The recently introduced DeepONet operator-learning framework for PDE control is extended from the results for basic hyperbolic and parabolic PDEs to an advanced hyperbolic class that involves delays on both the state and the system output or input. The PDE backstepping design produces gain functions that are outputs of a nonlinear operator, mapping functions on a spatial domain into functions on a spatial domain, and where this gain-generating operator's inputs are the PDE's coefficients. The operator is approximated with a DeepONet neural network to a degree of accuracy that is provably arbitrarily tight. Once we produce this approximation-theoretic result in infinite dimension, with it we establish stability in closed loop under feedback that employs approximate gains. In addition to supplying such results under full-state feedback, we also develop DeepONet-approximated observers and output-feedback laws and prove their own stabilizing properties under neural operator approximations. With numerical simulations we illustrate the theoretical results and quantify the numerical effort savings, which are of two orders of magnitude, thanks to replacing the numerical PDE solving with the DeepONet.
description: 20 pages
Near MDS and near quantum MDS codes via orthogonal arrays
Creators: name: Pang, Shanqi
name: Zhang, Chaomeng
name: Chen, Mengqian
name: Zhang, Miaomiao
Publisher: name: arXiv
Year: 2023
Subjects: subject: Information Theory (cs.IT)
subject: Quantum Physics (quant-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Near MDS (NMDS) codes are closely related to interesting objects in finite geometry and have nice applications in combinatorics and cryptography. But there are many unsolved problems about construction of NMDS codes. In this paper, by using symmetrical orthogonal arrays (OAs), we construct a lot of NMDS, $m$-MDS and almost extremal NMDS codes. We establish a relation between asymmetrical OAs and quantum error correcting codes (QECCs) over mixed alphabets. Since quantum maximum distance separable (QMDS) codes over mixed alphabets with the dimension equal to one have not been found in all the literature so far, the definition of a near quantum maximum distance separable (NQMDS) code over mixed alphabets is proposed. By using asymmetrical OAs, we obtain many such codes.
description: 13 pages, 0 figures
An attenuated African swine fever virus expressing the E2 glycoprotein of classical swine fever virus protects pigs against challenge of both viruses
Creators: name: Zhang, Jiwen
name: Li, Fang
name: Chen, Weiye
name: Li, Yongfeng
name: Zhang, Zhenjiang
name: Hua, Ronghong
name: Liu, Renqiang
name: Zhu, Yuanmao
name: Sun, Encheng
name: Qiu, Huaji
name: Bu, Zhigao
name: Zhao, Dongming
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: African swine fever (ASF) and classical swine fever (CSF) are highly contagious diseases with high morbidity and mortality rates resulting in an enormous impact on the global pig industry. A bivalent vaccine that simultaneously protects against both ASF and CSF is highly desirable. We previously developed a seven-gene-deleted African swine fever virus (ASFV) attenuated vaccine candidate (HLJ/18-7GD) that provides complete protection against homologous strains. Herein, we constructed a recombinant virus HLJ/18-7GD-E2 by inserting the classical swine fever virus (CSFV) E2 gene into the HLJ/18-7GD via homologous recombination. After continuous in vitro passaging, Western blotting analysis showed that the E2 gene was expressed and stably maintained within the ASFV genome. Next, the immunogenicity and protective efficacy of the recombinant HLJ/18-7GD-E2 virus was evaluated in pigs. The results revealed that a single dose of 106 TCID50 of HLJ/18-7GD-E2 induced an efficient immune response and provided complete protection against lethal challenges with ASFV or CSFV. These results demonstrate that recombinant ASFV expressing the CSFV E2 protein has potential as a bivalent live attenuated vaccine, providing solid protection against ASFV and CSFV infection in pigs.
JBR887876_Supplementary_figure_01_CLN – Supplemental material for RNA Splicing Factor Mutations That Cause Retinitis Pigmentosa Result in Circadian Dysregulation
Creators: name: Shakhmantsir, Iryna
name: Dooley, Scott J.
name: Siddharth Kishore
name: Dechun Chen
name: Pierce, Eric
name: Bennett, Jean
name: Sehgal, Amita
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 110306 Endocrinology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Neuroscience

description: Supplemental material, JBR887876_Supplementary_figure_01_CLN for RNA Splicing Factor Mutations That Cause Retinitis Pigmentosa Result in Circadian Dysregulation by Iryna Shakhmantsir, Scott J. Dooley, Siddharth Kishore, Dechun Chen, Eric Pierce, Jean Bennett and Amita Sehgal in Journal of Biological Rhythms
Degree bounds for fields of rational invariants of $\mathbb{Z}/p\mathbb{Z}$ and other finite groups
Creators: name: Blum-Smith, Ben
name: Garcia, Thays
name: Hidalgo, Rawin
name: Rodriguez, Consuelo
Publisher: name: arXiv
Year: 2023
Subjects: subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 13A50 (Primary) 20M25, 52C05, 52C07, 94A12 (Secondary)

description: Degree bounds for algebra generators of invariant rings are a topic of longstanding interest in invariant theory. We study the analogous question for field generators for the field of rational invariants of a representation of a finite group, focusing on abelian groups and especially the case of $\mathbb{Z}/p\mathbb{Z}$. The inquiry is motivated by an application to signal processing. We give new lower and upper bounds depending on the number of distinct nontrivial characters in the representation. We obtain additional detailed information in the case of two distinct nontrivial characters. We conjecture a sharper upper bound in the $\mathbb{Z}/p\mathbb{Z}$ case, and pose questions for further investigation.
description: 41 pages, 1 table. Minor corrections
Optimal transport distances to characterise electronic excitations
Creators: name: Lieberherr, Annina Z.
name: Gori-Giorgi, Paola
name: Giesbertz, Klaas J. H.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Understanding the character of electronic excitations is important in computational and reaction mechanistic studies, but their classification from simulations remains an open problem. Distances based on optimal transport have proven very useful in a plethora of classification problems and seem therefore a natural tool to try to tackle this challenge. We propose and investigate a new diagnostic $Θ$ based on the Sinkhorn divergence from optimal transport. We evaluate a $k$-NN classification algorithm on $Θ$, the popular $Λ$ diagnostic as well as their combination, and assess their performance in labelling excitations, finding that (i) The combination only slightly improves the classification, (ii) Rydberg excitations are not separated well in any setting, and (iii) $Θ$ breaks down for charge transfer in small molecules. We then define a length scale-normalised version of $Θ$ and show that the result correlates closely with $Λ$ for results obtained with Gaussian basis functions. Finally, we discuss the orbital-dependence of our approach and explore an orbital-independent version. Using an optimised combination of the optimal transport and overlap diagnostics together with a different metric is in our opinion the most promising for future classification studies.
description: 24 pages, 9 figures, 1 table