cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Faster Convergence of Local SGD for Over-Parameterized Models
Creators: name: Qin, Tiancheng
name: Etesami, S. Rasoul
name: Uribe, César A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Modern machine learning architectures are often highly expressive. They are usually over-parameterized and can interpolate the data by driving the empirical loss close to zero. We analyze the convergence of Local SGD (or FedAvg) for such over-parameterized models in the heterogeneous data setting and improve upon the existing literature by establishing the following convergence rates. For general convex loss functions, we establish an error bound of $Ø(1/T)$ under a mild data similarity assumption and an error bound of $Ø(K/T)$ otherwise, where $K$ is the number of local steps and $T$ is the total number of iterations. For non-convex loss functions we prove an error bound of $Ø(K/T)$. These bounds improve upon the best previous bound of $Ø(1/\sqrt{nT})$ in both cases, where $n$ is the number of nodes, when no assumption on the model being over-parameterized is made. We complete our results by providing problem instances in which our established convergence rates are tight to a constant factor with a reasonably small stepsize. Finally, we validate our theoretical results by performing large-scale numerical experiments that reveal the convergence behavior of Local SGD for practical over-parameterized deep learning models, in which the $Ø(1/T)$ convergence rate of Local SGD is clearly shown.
EARLY BUD-BREAK1 (EBB1) defines a conserved mechanism for control of bud-break in woody perennials
Creators: name: Busov, Victor
name: Carneros, Elena
name: Yakovlev, Igor
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Bud-break is an environmentally and economically important trait in trees, shrubs and vines from temperate latitudes. Poor synchronization of bud-break timing with local climates can lead to frost injuries, susceptibility to pests and pathogens and poor crop yields in fruit trees and vines. The rapid climate changes outpace the adaptive capacities of plants to respond through natural selection. This is particularly true for trees which have long generation cycle and thus the adaptive changes are significantly delayed. Therefore, to devise appropriate breeding and conservation strategies, it is imperative to understand the molecular underpinnings that govern dormancy mechanisms. We have recently identified and characterized the poplar EARLY BUD-BREAK 1 (EBB1) gene. EBB1 is a positive regulator of bud-break and encodes a transcription factor from the AP2/ERF family. Here, using comparative and functional genomics approaches we show that EBB1 function in regulation of bud-break is likely conserved across wide range of woody perennial species with importance to forestry and agriculture.
The effect of tourism arrival on CO2 emissions from transportation sector
Creators: name: Al-Mulali, Usama
name: Gholipour Fereidouni, Hassan
name: Mohammed, Abdul Hakim
Publisher: name: Swinburne
Year: 2024
Subjects: classificationCode: 3508
subject: Tourism
subject: FOS: Economics and business

description: As the second-largest aluminium user after building and construction, the transportation sector accounts for around 16%-17% of the total aluminium consumption in recent years. High speed, heavy load, weight lighting, energy saving, safety, comfort, and pollution reduction are the trends of global transportation sector which provides a good opportunity for the improving aluminum application.
Poincaré inequalities and $A_p$ weights on bow-ties
Creators: name: Björn, Anders
name: Björn, Jana
name: Christensen, Andreas
Publisher: name: arXiv
Year: 2022
Subjects: subject: Metric Geometry (math.MG)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 26D10 (Primary) 30L15, 31C15, 31C45, 31E05, 46E36 (Secondary)

description: A metric space $X$ is called a \emph{bow-tie} if it can be written as $X=X_{+} \cup X_{-}$, where $X_{+} \cap X_{-}=\{x_0\}$ and $X_{\pm} \ne \{x_0\}$ are closed subsets of $X$. We show that a doubling measure $μ$ on $X$ supports a $(q,p)$--Poincaré inequality on $X$ if and only if $X$ satisfies a quasiconvexity-type condition, $μ$ supports a $(q,p)$-Poincaré inequality on both $X_{+}$ and $X_{-}$, and a variational \p-capacity condition holds. This capacity condition is in turn characterized by a sharp measure decay condition at $x_0$.
 In particular, we study the bow-tie $X_{\mathbf{R}^n}$ consisting of the positive and negative hyperquadrants in $\mathbf{R}^n$ equipped with a radial doubling weight and characterize the validity of the \p-Poincaré inequality on $X_{\mathbf{R}^n}$ in several ways. For such weights, we also give a general formula for the capacity of annuli around the origin.
Enhancing Deformable Convolution based Video Frame Interpolation with Coarse-to-fine 3D CNN
Creators: name: Danier, Duolikun
name: Zhang, Fan
name: Bull, David
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Image and Video Processing (eess.IV)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: This paper presents a new deformable convolution-based video frame interpolation (VFI) method, using a coarse to fine 3D CNN to enhance the multi-flow prediction. This model first extracts spatio-temporal features at multiple scales using a 3D CNN, and estimates multi-flows using these features in a coarse-to-fine manner. The estimated multi-flows are then used to warp the original input frames as well as context maps, and the warped results are fused by a synthesis network to produce the final output. This VFI approach has been fully evaluated against 12 state-of-the-art VFI methods on three commonly used test databases. The results evidently show the effectiveness of the proposed method, which offers superior interpolation performance over other state of the art algorithms, with PSNR gains up to 0.19dB.
Detection of DNA damage in cumulus cells using a chromatin dispersion assay
Creators: name: Barcena, Pablo
name: López-Fernández, Carmen
name: García-Ochoa, Carlos
name: Obradors, Albert
name: Vernaeve, Valerie
name: Gosálvez, Jaime
name: Vassena, Rita
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Hematology
subject: Cancer
subject: Developmental Biology
subject: Mathematics
subject: FOS: Mathematics
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry
subject: Biophysics

description: DNA damage in cumulus cells (CCs) might be related with the developmental competence of the enclosed oocytes, however, conclusive studies are missing, partially due to the lack of a reliable, cheap, fast, and reproducible DNA damage test. We report the development of a chromatin dispersion test that allows for a fast evaluation of double strand DNA (ds-DNA) damage in CCs. The whole experiment was performed using CCs from 103 oocyte retrieval cycles evaluating the prototype D3-MAX ability (a chromatin dispersion based assay) to detect DNA breaks against in situ nick translation (ISNT) and a two tailed comet assay (TT-comet). Samples were collected from women younger than 35 years of age with a good response to stimulation. Pooled cumulus cells of MII oocytes were used. The chromatin dispersion assay results correlate with the double strand-DNA breaks values assessed by the TT-comet assay (Spearman Rho = 0.624; p = 0.003;), while the correlation was poor when compared to the single strand DNA (ss-DNA) breaks observed also with the TT-comet assay (Spearman Rho = −0.141; p = 0.554). ISNT showed a correspondence in the same cells between enzymatic incorporation of modified nucleotides and halos of chromatin dispersion. We conclude that D3-Max test detects mainly ds-DNA breaks in cumulus cells and is a reliable, fast, and easy reproducible assay suitable for routine clinical practices once the influence on oocyte quality has been established.
Third places, the connective fibre of cities and high-tech entrepreneurship
Creators: name: Credit, Kevin
name: Kekezi, Orsa
name: Mellander, Charlotta
name: Florida, Richard
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Urban ‘third places’ foster informal interactions and face-to-face contact that is critical to the development of new innovations and start-up businesses. Our research utilises extensive microdata in combination with telephone interviews with over 200 start-up companies in Stockholm, Sweden. Our findings indicate that access to third places has a significant impact on the number of new high-tech start-ups (both by entrepreneur place of residence and work) in their vicinity. This suggests that third places play a demonstrable role in innovation and economic growth.
RankDVQA: Deep VQA based on Ranking-inspired Hybrid Training
Creators: name: Feng, Chen
name: Danier, Duolikun
name: Zhang, Fan
name: Bull, David
Publisher: name: arXiv
Year: 2022
Subjects: subject: Image and Video Processing (eess.IV)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In recent years, deep learning techniques have shown significant potential for improving video quality assessment (VQA), achieving higher correlation with subjective opinions compared to conventional approaches. However, the development of deep VQA methods has been constrained by the limited availability of large-scale training databases and ineffective training methodologies. As a result, it is difficult for deep VQA approaches to achieve consistently superior performance and model generalization. In this context, this paper proposes new VQA methods based on a two-stage training methodology which motivates us to develop a large-scale VQA training database without employing human subjects to provide ground truth labels. This method was used to train a new transformer-based network architecture, exploiting quality ranking of different distorted sequences rather than minimizing the difference from the ground-truth quality labels. The resulting deep VQA methods (for both full reference and no reference scenarios), FR- and NR-RankDVQA, exhibit consistently higher correlation with perceptual quality compared to the state-of-the-art conventional and deep VQA methods, with average SROCC values of 0.8972 (FR) and 0.7791 (NR) over eight test sets without performing cross-validation. The source code of the proposed quality metrics and the large training database are available at https://chenfeng-bristol.github.io/RankDVQA.
description: 8 pages, 5 figures accepted by WACV 2024
Capital shocks, the great recession, and UK regional divergence
Creators: name: Daams, Michiel N.
name: McCann, Philip
name: Veneri, Paolo
name: Barkham, Richard
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy
subject: Mental Health

description: This paper uses uniquely detailed large-scale commercial real estate investment data to examine how financial markets perceived the attractiveness of investing in UK regions during the last two decades. Our analysis demonstrates that prior to the 2008 Global Financial Crisis all regions of the UK were perceived similarly in terms of risks, whereas the crisis engendered a flight to safety of capital into London. Other UK regions shifted rapidly into junk bond territory, and have remained there ever since. These asymmetric capital shocks led up to a profound and adverse shift in the subsequent productivity growth of the UK regional economies.
EARLY BUD-BREAK1 (EBB1) defines a conserved mechanism for control of bud-break in woody perennials
Creators: name: Busov, Victor
name: Carneros, Elena
name: Yakovlev, Igor
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Bud-break is an environmentally and economically important trait in trees, shrubs and vines from temperate latitudes. Poor synchronization of bud-break timing with local climates can lead to frost injuries, susceptibility to pests and pathogens and poor crop yields in fruit trees and vines. The rapid climate changes outpace the adaptive capacities of plants to respond through natural selection. This is particularly true for trees which have long generation cycle and thus the adaptive changes are significantly delayed. Therefore, to devise appropriate breeding and conservation strategies, it is imperative to understand the molecular underpinnings that govern dormancy mechanisms. We have recently identified and characterized the poplar EARLY BUD-BREAK 1 (EBB1) gene. EBB1 is a positive regulator of bud-break and encodes a transcription factor from the AP2/ERF family. Here, using comparative and functional genomics approaches we show that EBB1 function in regulation of bud-break is likely conserved across wide range of woody perennial species with importance to forestry and agriculture.
What determines the eﬃciency of Australian mining companies?
Creators: name: Hosseinzadeh, Ahmad
name: Smyth, Russell
name: Valadkhani, Abbas
name: Moradi, Amir
name: Hosseinzadeh, Ahmad
name: Smyth, Russell
name: Valadkhani, Abbas
name: Moradi, Amir
Publisher: name: Unknown
Year: 2017
Subjects: subject: Financial Economics
subject: Production Economics
subject: bootstrap
subject: data envelopment analysis
subject: eﬃciency determinants
subject: mining companies

description: We examine the ﬁrm-speciﬁc determinants of technical eﬃciency in Australian mining companies using data envelopment analysis (DEA). To do so, we employ panel data sourced from individual mining companies listed on the Australian Securities Exchange (ASX) over the period 2010–2014. To ensure valid statistical inference in the presence of serial correlation between DEA eﬃciency scores, we apply Simar and Wilson’s two-stage bootstrap method. We ﬁnd that ownership concentration, ﬁrm size, ﬁrm age, product portfolio, product diversiﬁcation and growth status signiﬁ-cantly contribute to eﬃciency gains. However, other ﬁrm-speciﬁc factors, such as capacity utilisation, ﬁnancial risk and overseas operations appear to have limited impact on the technical eﬃciency of mining ﬁrms.
A two-phase rank-based algorithm for low-rank matrix completion
Creators: name: Araújo, Tacildo de Souza
name: Gonçalves, Douglas S.
name: Torezzan, Cristiano
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: Matrix completion aims to recover an unknown low-rank matrix from a small subset of its entries. In many applications, the rank of the unknown target matrix is known in advance. In this paper, first we revisit a recently proposed rank-based heuristic for "known-rank" matrix completion and establish a condition under which the generated sequence is quasi-Fejér convergent to the solution set. Then, by including an acceleration mechanism similar to Nesterov's acceleration, we obtain a new heuristic. Even though the convergence of such heuristic cannot be granted in general, it turns out that it can be very useful as a warm-start phase, providing a suitable estimate for the regularization parameter and a good starting-point, to an accelerated Soft-Impute algorithm. Numerical experiments with both synthetic and real data show that the resulting two-phase rank-based algorithm can recover low-rank matrices, with relatively high precision, faster than other well-established matrix completion algorithms.
The Irish experience of Symphysiotomy: 40 years onwards
Creators: name: S. R. Shaarani
name: W. Van Eeden
name: J. M. O’Byrne
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Earth and Environmental Sciences
subject: Molecular Biology
subject: Medicine

description: The art of symphysiotomy for delivery in the instance of cephalopelvic disproportion has been a dying art since the advent of caesarean section but in Ireland this surgical procedure was not abolished until 1992. This practice is still present in the developing world and in some circumstances used in developed countries. This study offers some insights on the 40-year follow-up of patients who had undergone symphysiotomy.
External validation of a prognostic CT-based radiomic signature in oropharyngeal squamous cell carcinoma
Creators: name: Leijenaar, Ralph T. H.
name: Carvalho, Sara
name: Hoebers, Frank J. P.
name: Aerts, Hugo J. W. L.
name: Elmpt, Wouter J. C. Van
name: Huang, Shao Hui
name: Biu Chan
name: Waldron, John N.
name: O’Sullivan, Brian
name: Lambin, Philippe
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Science Policy
subject: Cancer
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cell Biology
subject: Engineering
subject: Biochemistry

description: ABSTRACTBackground. Oropharyngeal squamous cell carcinoma (OPSCC) is one of the fastest growing disease sites of head and neck cancers. A recently described radiomic signature, based exclusively on pre-treatment computed tomography (CT) imaging of the primary tumor volume, was found to be prognostic in independent cohorts of lung and head and neck cancer patients treated in the Netherlands. Here, we further validate this signature in a large and independent North American cohort of OPSCC patients, also considering CT artifacts.Methods. A total of 542 OPSCC patients were included for which we determined the prognostic index (PI) of the radiomic signature. We tested the signature model fit in a Cox regression and assessed model discrimination with Harrell's c-index. Kaplan-Meier survival curves between high and low signature predictions were compared with a log-rank test. Validation was performed in the complete cohort (PMH1) and in the subset of patients without (PMH2) and with (PMH3) visible CT artifacts within the delineated tumor region.Results. We identified 267 (49%) patients without and 275 (51%) with visible CT artifacts. The calibration slope (β) on the PI in a Cox proportional hazards model was 1.27 (H0: β = 1, p = 0.152) in the PMH1 (n = 542), 0.855 (H0: β = 1, p = 0.524) in the PMH2 (n = 267) and 1.99 (H0: β = 1, p = 0.002) in the PMH3 (n = 275) cohort. Harrell's c-index was 0.628 (p = 2.72e-9), 0.634 (p = 2.7e-6) and 0.647 (p = 5.35e-6) for the PMH1, PMH2 and PMH3 cohort, respectively. Kaplan-Meier survival curves were significantly different (p < 0.05) between high and low radiomic signature model predictions for all cohorts.Conclusion. Overall, the signature validated well using all CT images as-is, demonstrating a good model fit and preservation of discrimination. Even though CT artifacts were shown to be of influence, the signature had significant prognostic power regardless if patients with CT artifacts were included.
Regional determinants in origin–destination remittance flows from the US to Mexico: evidence from the COVID-19 pandemic
Creators: name: Flores, Miguel
name: Torre, Leonardo
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Medicine
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Information Systems not elsewhere classified
subject: Science Policy

description: Despite expectations of a decline in remittances due to rising US unemployment, total remittances to Mexico increased during the COVID-19 pandemic, although with regional disparities. Using a spatial gravity econometric model with state-level origin–destination data, we analysed these variations, considering regional economic and health conditions and demand for digital remittance services. The study focused on the second quarter of 2020, marked by lockdowns and economic disruptions. Findings suggest a strong link between employment changes and digital service demand, influencing US remittance flows. Results for Mexico support the significant impact of digital services over the altruistic hypothesis, highlighting the need for a regional approach to studying remittances.
Schizothorax intermedius McClelland & Griffith 1842
Creators: name: Sayyadzadeh, Golnaz
name: Esmaeili, Hamid Reza
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Cypriniformes
Cyprinidae
Schizothorax
Schizothorax intermedius

description: 149. Schizothorax intermedius McClelland & Griffith, 1842
Common name. Aral basin snowtrout
Taxonomy. Original description: Schizothorax intermedius McClelland & Griffith in McClelland, 1842: 579, pl. 12, fig. 1 [Cabul River at Jullalabad and Tarnuck River, Afghanistan; syntypes: (3) whereabouts unknown].
Revisions. Berg (1949: 712).
Illustrations. Berg (1949: 713, fig. 465).
Distribution in Iran. —Distribution in River Basin: Sistan.—Distribution in Ecoregions: 702-Helmand–Sistan.
Status in Iran. [Native].—Khajoo.—Listed in previous checklists from Iran by Esmaeili et al. (2017 a, 2018); Jouladeh-Roudbar et al. (2020) and Eagderi et al. (2022).—Iran material: ZM-CBSU.
Conservation. —IUCN: LC.
description: Published as part of Sayyadzadeh, Golnaz & Esmaeili, Hamid Reza, 2024, Freshwater lamprey and fishes of Iran: Reappraisal and updated checklist with a note on Eagderi et al. (2022), pp. 1-99 in Zootaxa 5402 (1) on page 50, DOI: 10.11646/zootaxa.5402.1.1, http://zenodo.org/record/10524097
Retail Beef Price Specials
Creators: name: Motes, William C.
name: Hacklander, Duane
name: Motes, William C.
name: Hacklander, Duane
Publisher: name: Unknown
Year: 1964
Subjects: subject: Demand and Price Analysis
subject: Marketing
subject: FOS: Economics and business

description: In a cooperative project with 25 retail food chains, the Economic Research Service is collecting and studying retail meat prices. Each week, these firms report regular and special prices for all cuts of meat. The following is a brief description of the patterns of beef specialing observed in this nationwide sample of chain stores. A special is here taken to mean the price reduction for the week's regular price.
description: Article Reprinted from The Marketing and Transportation Situation November 1964
The geographies of local austerity policies: a quantitative analysis of local budgets in France
Creators: name: Grandclement, Antoine
name: Halbert, Ludovic
name: Adisson, Félix
name: Lasserre-Bigorry, Vincent
name: Navarre, Françoise
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified

description: The literature acknowledges the variety of local austerity policies, but has paid less attention to their geographical diversity. This paper questions the theorisation of space in this literature and investigates the relationships between local austerity policies and the diversity of local spatial systems. By combining two fiscal and socio-economic classifications of French municipalities, it provides a comprehensive and fine-grained mapping of local austerity for an entire country. Our findings demonstrate that austerity occurs in a wide range of local spatial systems and highlight numerous instances of mundane austerity that exist between affluent areas and those most severely impacted by austerity.
Adaptive Testing for Alphas in Conditional Factor Models with High Dimensional Assets
Creators: name: Ma, Huifang
name: Feng, Long
name: Wang, Zhaojun
name: Bao, Jigang
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Science Policy

description: This article focuses on testing for the presence of alpha in time-varying factor pricing models, specifically when the number of securities N is larger than the time dimension of the return series T. We introduce a maximum-type test that performs well in scenarios where the alternative hypothesis is sparse. We establish the limit null distribution of the proposed maximum-type test statistic and demonstrate its asymptotic independence from the sum-type test statistics proposed by Ma et al. Additionally, we propose an adaptive test by combining the maximum-type test and sum-type test, and we show its advantages under various alternative hypotheses through simulation studies and two real data applications.
Bayesian Non-Homogeneous Hidden Markov Model with Variable Selection for Investigating Drivers of Seizure Risk Cycling
Creators: name: Wang, Emily T.
name: Chiang, Sharon
name: Haneef, Zulfi
name: Rao, Vikram R.
name: Moss, Robert
name: Vannucci, Marina
Publisher: name: arXiv
Year: 2022
Subjects: subject: Applications (stat.AP)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: A major issue in the clinical management of epilepsy is the unpredictability of seizures. Yet, traditional approaches to seizure forecasting and risk assessment in epilepsy rely heavily on raw seizure frequencies, which are a stochastic measurement of seizure risk. We consider a Bayesian non-homogeneous hidden Markov model for unsupervised clustering of zero-inflated seizure count data. The proposed model allows for a probabilistic estimate of the sequence of seizure risk states at the individual level. It also offers significant improvement over prior approaches by incorporating a variable selection prior for the identification of clinical covariates that drive seizure risk changes and accommodating highly granular data. For inference, we implement an efficient sampler that employs stochastic search and data augmentation techniques. We evaluate model performance on simulated seizure count data. We then demonstrate the clinical utility of the proposed model by analyzing daily seizure count data from 133 patients with Dravet syndrome collected through the Seizure Tracker TM system, a patient-reported electronic seizure diary. We report on the dynamics of seizure risk cycling, including validation of several known pharmacologic relationships. We also uncover novel findings characterizing the presence and volatility of risk states in Dravet syndrome, which may directly inform counseling to reduce the unpredictability of seizures for patients with this devastating cause of epilepsy.
description: Annals of Applied Statistics (2022)
Quantifying relation between mobility patterns and socioeconomic status of dockless sharing-bike users
Creators: name: Gao, Tianli
name: Xu, Zikun
name: Liu, Chenxin
name: Yang, Yu
name: Shang, Fan
name: Li, Ruiqi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: Bikes are among the healthiest, greenest, and most affordable means of transportation for a better future city, but mobility patterns of riders with different income were rarely studied due to limitations on collecting data. Newly emergent dockless bike-sharing platforms that record detailed information regarding each trip provide us a unique opportunity. Attribute to its better usage flexibility and accessibility, dockless bike-sharing platforms are booming over the past a few years worldwide and reviving the riding fashion in cities. In this work, by exploiting massive riding records in two megacities from a dockless bike-sharing platform, we reveal that individual mobility patterns, including radius of gyration and average travel distance, are similar among users with different income, which indicates that human beings all follow similar physical rules. However, collective mobility patterns, including average range and diversity of visitation, and commuting directions, all exhibit different behaviors and spatial patterns across income categories. Hotspot locations that attract more cycling activities are quite different over groups, and locations where users reside are of a low user ratio for both higher and lower income groups. Lower income groups are inclined to visit less flourishing locations, and commute towards the direction to the city center in both cities, and of a smaller mobility diversity in Beijing but a larger diversity in Shanghai. In addition, differences on mobility patterns among socioeconomic categories are more evident in Beijing than in Shanghai. Our findings would be helpful on designing better promotion strategies for dockless bike-sharing platforms and towards the transition to a more sustainable green transportation.
Follicular fluid alterations in endometriosis: label-free proteomics by MSE as a functional tool for endometriosis
Creators: name: Thais Regiani
name: Cordeiro, Fernanda Bertuccez
name: Costa, Lívia Do Vale Teixeira Da
name: Jéssica Salgueiro
name: Cardozo, Karina
name: Valdemir Melechco Carvalho
name: Perkel, Kayla Jane
name: Zylbersztejn, Daniel Suslik
name: Agnaldo Pereira Cedenho
name: Turco, Edson Guimarães Lo
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Developmental Biology
subject: Biological Sciences
subject: Chemistry
subject: Physiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Microbiology
subject: Biochemistry

description: Endometriosis is a chronic gynecological condition that affects 10-32% of women of reproductive age and may lead to infertility. The study of protein profiles in follicular fluid may assist in elucidating possible biomarkers related to this disease. For this, follicular fluid samples were obtained from women with tubal factor or minimal male factor infertility who had pregnancy outcomes after in vitro fertilization (IVF) treatment (control group, n = 10), women with endometriosis (endometriosis group, n = 10), along with the endometrioma from these same patients were included (endometrioma group, n = 10). For proteomic analysis, samples were pooled according to their respective groups and normalized to protein content. Proteins were analyzed by in tandem mass spectrometry (MSE) Spectra processing and the ProteinLynx Global Server v.2.5. was used for database searching. Data was submitted to the biological network analysis using Cytoscape 2.8.2 with ClueGO plugin. As a result, 535 proteins were identified among all groups. The control group differentially or uniquely expressed 33 (6%) proteins and equal expression of 98 (18%) proteins was observed in the control and endometriosis groups of which 41 (7%) proteins were further identified and/or quantified. Six (1%) proteins were observed in both the endometriosis and endometrioma groups, but 212 (39%) proteins were exclusively identified and/or quantified in the endometrioma group. There were 9 (1%) proteins observed in both the control and endometrioma groups and there were 139 (25%) proteins common among all three groups. Distinct differences among the protein profiles in the follicular fluid of patients included in this study were found, identifying proteins related to the disease progression and IVF success. Thus, some pathways related to endometriosis are associated with the presence of specific proteins, as well as the absence of others. This study provides a first step to the development of more sensitive diagnostic tests and treatment.
Nanomatrix: Scalable Construction of Crowded Biological Environments
Creators: name: Alharbi, Ruwayda
name: Strnad, Ondřej
name: Klein, Tobias
name: Viola, Ivan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Graphics (cs.GR)
subject: FOS: Computer and information sciences

description: We present a novel method for the interactive construction and rendering of extremely large molecular scenes, capable of representing multiple biological cells in atomistic detail. Our method is tailored for scenes, which are procedurally constructed, based on a given set of building rules. Rendering of large scenes normally requires the entire scene available in-core, or alternatively, it requires out-of-core management to load data into the memory hierarchy as a part of the rendering loop. Instead of out-of-core memory management, we propose to procedurally generate the scene on-demand on the fly. The key idea is a positional- and view-dependent procedural scene-construction strategy, where only a fraction of the atomistic scene around the camera is available in the GPU memory at any given time. The atomistic detail is populated into a uniform-space partitioning using a grid that covers the entire scene. Most of the grid cells are not filled with geometry, only those are populated that are potentially seen by the camera. The atomistic detail is populated in a compute shader and its representation is connected with acceleration data structures for hardware ray-tracing of modern GPUs. Objects which are far away, where atomistic detail is not perceivable from a given viewpoint, are represented by a triangle mesh mapped with a seamless texture, generated from the rendering of geometry from atomistic detail. The algorithm consists of two pipelines, the construction-compute pipeline, and the rendering pipeline, which work together to render molecular scenes at an atomistic resolution far beyond the limit of the GPU memory containing trillions of atoms. We demonstrate our technique on multiple models of SARS-CoV-2 and the red blood cell.
Agricultural economic complexity and regional inequalities: a new approach using census data from Brazil
Creators: name: de Queiroz Stein, Alexandre
name: Britto, Gustavo
name: Medeiros, Victor
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Hematology

description: The paper presents an original application of economic complexity to the agricultural sector aiming to determine its suitability to measure and depict regional structural inequalities across Brazilian regions. Using census data, we calculate agricultural complexity indexes for products (PCI-Agro) and regions (ECI-Agro) and the agricultural product space. We show that higher PCI-Agro is associated with higher levels of productivity, education, income and human development. Also, we found that ECI-Agro is associated with higher productivity in agriculture. The econometric evidence points to an inverted ‘U’-shape curve relationship between ECI-Agro and agricultural productivity, which has significant policy implications.
Symmetric doubly periodic gravity-capillary waves with small vorticity
Creators: name: Seth, Douglas Svensson
name: Varholm, Kristoffer
name: Wahlén, Erik
Publisher: name: arXiv
Year: 2022
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We construct small amplitude gravity-capillary water waves with small nonzero vorticity, in three spatial dimensions, bifurcating from uniform flows. The waves are symmetric, and periodic in both horizontal coordinates. The proof is inspired by Lortz' construction of magnetohydrostatic equilibria in reflection-symmetric toroidal domains. It relies on a global representation of the vorticity as the cross product of two gradients, and on prescribing a functional relationship between the Bernoulli function and the orbital period of the water particles. The presence of the free surface introduces significant new challenges. In particular, the resulting free boundary problem is not elliptic, and the involved maps incur a loss of regularity under Fréchet differentiation. Nevertheless, we show that a version of the Crandall-Rabinowitz local bifurcation method applies, by carefully tracking the loss of regularity.
How to Justify the Spelling of the Buddhist Hybrid Sanskrit Term Bodhisatva?
Creators: name: Bhattacharya, Gouriswar
Publisher: name: Zenodo
Year: 2010

description: Gouriswar Bhattacharya, "How to Justify the Spelling of the Buddhist Hybrid Sanskrit Term Bodhisatva?" in From Turfan to Ajanta: Festschrift for Dieter Schlingloff on the Occasion of his Eightieth Birthday, ed. Eli Franco and Monika Zin, 2 vols. (Rupandehi: Lumbini InternationalResearch Institute, 2010), 2: 35–50.
Modulational instability and wave amplification in finite water depth
Creators: name: Fernandez, L.
name: Onorato, M.
name: Monbaliu, J.
name: Toffoli, Alessandro
Publisher: name: Swinburne
Year: 2024

description: The modulational instability of a uniform wave train to side band perturbations is one of the most plausible mechanisms for the generation of rogue waves in deep water. In a condition of finite water depth, however, the interaction with the sea floor generates a wave-induced current that subtracts energy from the wave field and consequently attenuates the instability mechanism. As a result, a plane wave remains stable under the influence of collinear side bands for relative depths kh <= 1.36 (where k is the wavenumber of the plane wave and h is the water depth), but it can still destabilise due to oblique perturbations. Using direct numerical simulations of the Euler equations, it is here demonstrated that oblique side bands are capable of triggering modulational instability and eventually leading to the formation of rogue waves also for kh <= 1.36. Results, nonetheless, indicate that modulational instability cannot sustain a substantial wave growth for kh < 0.8.
First-order marginalised transition random effects models with probit link function
Creators: name: Asar, Özgür
name: Ozlem Ilk
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Marginalised models, also known as marginally specified models, have recently become a popular tool for analysis of discrete longitudinal data. Despite being a novel statistical methodology, these models introduce complex constraint equations and model fitting algorithms. On the other hand, there is a lack of publicly available software to fit these models. In this paper, we propose a three-level marginalised model for analysis of multivariate longitudinal binary outcome. The implicit function theorem is introduced to approximately solve the marginal constraint equations explicitly. probit link enables direct solutions to the convolution equations. Parameters are estimated by maximum likelihood via a Fisher–Scoring algorithm. A simulation study is conducted to examine the finite-sample properties of the estimator. We illustrate the model with an application to the data set from the Iowa Youth and Families Project. The R package pnmtrem is prepared to fit the model.
The North Sea Andrea storm and numerical simulations
Creators: name: Bitner-Gregersen, E. M.
name: Fernandez, L.
name: Lefèvre, J. M.
name: Monbaliu, J.
name: Toffoli, Alessandro
Publisher: name: Swinburne
Year: 2024

description: A coupling of a spectral wave model with a nonlinear phase-resolving model is used to reconstruct the evolution of wave statistics during a storm crossing the North Sea on 8-9 November 2007. During this storm a rogue wave (named the Andrea wave) was recorded at the Ekofisk field. The wave has characteristics comparable to the well-known New Year wave measured by Statoil at the Draupner platform 1 January 1995. Hindcast data of the storm at the nearest grid point to the Ekofisk field are here applied as input to calculate the evolution of random realizations of the sea surface and its statistical properties. Numerical simulations are carried out using the Euler equations with a higher-order spectral method (HOSM). Results are compared with some characteristics of the Andrea wave record measured by the down-looking lasers at Ekofisk.
Regional resilience and the network structure of inter-industry labour flows
Creators: name: Elekes, Zoltán
name: Tóth, Gergő
name: Eriksson, Rikard
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Cell Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: This paper explores how the network structure of local inter-industry labour flows relates to regional economic resilience across 72 local labour markets in Sweden. Drawing on recent advancements in network science, we stress test these networks against the sequential elimination of their nodes, finding substantial heterogeneity in network robustness across regions. Regression analysis with least absolute shrinkage and selection operator (LASSO) in the context of the 2008 financial crisis indicates that labour flow network robustness is a prominent structural predictor of employment change during crisis. These findings elaborate on how variation in the self-organisation of regional economies as complex systems makes for more or less resilient regions.
Text mining and integration of genetic association information
Creators: name: Rowlands, Thomas
Publisher: name: University of Leicester
Year: 2024

description: The size of biomedical data available is always increasing, yet their remains significant barriers in place to accessing this data. While research studies are published online, they are often left submitted without machine-readable versions, limiting how quickly and efficiently key information can be extracted and used via automated systems.With an emphasis on the association between genotype and phenotype, this thesis details the approaches undertaken to extract information from genome-wide association study (GWAS) publications. Using natural language processing techniques, I developed “GWAS Miner”, which utilises ontology terms to annotate and extract data from GWAS publications’ full-text and tables. This enables scalable data curation for database resources such as GWAS Central. Additionally, I developed “GWAS Tagger” for the automated annotation of a GWAS corpus which can be used for training and testing text mining machine learning models.GWAS Central is one of the largest sources of summary-level GWAS data, providing users with tools for both comparing and visualising GWAS data, along with phenotype ontologies. This thesis also describes how I extended the GWAS Central resource to integrate GWAS summary-level data with mouse disease model data from the International Mouse Phenotyping Consortium (IMPC). Combining model organism data with human GWAS, accessible via novel web interfaces, enables researchers to compare mouse gene knockout experiment data alongside human GWAS data to identify genes of interest for follow-up research and to corroborate existing findings.
External validation of a prognostic CT-based radiomic signature in oropharyngeal squamous cell carcinoma
Creators: name: Leijenaar, Ralph T. H.
name: Carvalho, Sara
name: Hoebers, Frank J. P.
name: Aerts, Hugo J. W. L.
name: Elmpt, Wouter J. C. Van
name: Huang, Shao Hui
name: Biu Chan
name: Waldron, John N.
name: O’Sullivan, Brian
name: Lambin, Philippe
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Science Policy
subject: Cancer
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cell Biology
subject: Engineering
subject: Biochemistry

description: Oropharyngeal squamous cell carcinoma (OPSCC) is one of the fastest growing disease sites of head and neck cancers. A recently described radiomic signature, based exclusively on pre-treatment computed tomography (CT) imaging of the primary tumor volume, was found to be prognostic in independent cohorts of lung and head and neck cancer patients treated in the Netherlands. Here, we further validate this signature in a large and independent North American cohort of OPSCC patients, also considering CT artifacts.Methods. A total of 542 OPSCC patients were included for which we determined the prognostic index (PI) of the radiomic signature. We tested the signature model fit in a Cox regression and assessed model discrimination with Harrell's c-index. Kaplan-Meier survival curves between high and low signature predictions were compared with a log-rank test. Validation was performed in the complete cohort (PMH1) and in the subset of patients without (PMH2) and with (PMH3) visible CT artifacts within the delineated tumor region.Results. We identified 267 (49%) patients without and 275 (51%) with visible CT artifacts. The calibration slope (β) on the PI in a Cox proportional hazards model was 1.27 (H0: β = 1, p = 0.152) in the PMH1 (n = 542), 0.855 (H0: β = 1, p = 0.524) in the PMH2 (n = 267) and 1.99 (H0: β = 1, p = 0.002) in the PMH3 (n = 275) cohort. Harrell's c-index was 0.628 (p = 2.72e-9), 0.634 (p = 2.7e-6) and 0.647 (p = 5.35e-6) for the PMH1, PMH2 and PMH3 cohort, respectively. Kaplan-Meier survival curves were significantly different (p < 0.05) between high and low radiomic signature model predictions for all cohorts.Conclusion. Overall, the signature validated well using all CT images as-is, demonstrating a good model fit and preservation of discrimination. Even though CT artifacts were shown to be of influence, the signature had significant prognostic power regardless if patients with CT artifacts were included.