bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher-order adaptive methods for exit times of Itô diffusions
Authors: Hoel Håkon , Ragunathan Sankarasubramanian 
Published: October 2023

Abstract
We construct a higher-order adaptive method for strong approximations of exit times of Itô stochastic differential equations (SDEs). The method employs a strong Itô–Taylor scheme for simulating SDE paths, and adaptively decreases the step size in the numerical integration as the solution approaches the boundary of the domain. These techniques complement each other nicely: adaptive timestepping improves the accuracy of the exit time by reducing the magnitude of the overshoot of the numerical solution when it exits the domain, and higher-order schemes improve the approximation of the state of the diffusion process. We present two versions of the higher-order adaptive method. The first one uses the Milstein scheme as the numerical integrator and two step sizes for adaptive timestepping: $h$ when far away from the boundary and $h^2$ when close to the boundary. The second method is an extension of the first one using the strong Itô–Taylor scheme of order 1.5 as the numerical integrator and three step sizes for adaptive timestepping. Under some regularity assumptions, we show that for any $\xi&gt;0$, the strong error is ${\mathcal{O}}(h^{1-\xi })$ and ${\mathcal{O}}(h^{3/2-\xi })$ for the first and second method, respectively. Provided quite restrictive commutativity conditions hold for the diffusion coefficient, we further show that the expected computational cost for both methods is ${\mathcal{O}}(h^{-1} \log (h^{-1}))$. This results in a near doubling/trebling of the strong error rate compared to the standard Euler–Maruyama-based approach, while the computational cost rate is kept close to order one. Numerical examples that support the theoretical results are provided, and we discuss the potential for extensions that would further improve the strong convergence rate of the method.
Transmission Dynamics and Rare Clustered Transmission Within an Urban University Population Before Widespread Vaccination
Authors: Turcinovic Jacquelyn , Kuhfeldt Kayla , Sullivan Madison , Landaverde Lena , Platt Judy T , Alekseyev Yuriy O , Doucette-Stamm Lynn , Hamer Davidson H , Klapperich Catherine , Landsberg Hannah E , Connor John H 
Published: October 2023

Abstract

Background
Universities returned to in-person learning in 2021 while SARS-CoV-2 spread remained high. At the time, it was not clear whether in-person learning would be a source of disease spread.

Methods
We combined surveillance testing, universal contact tracing, and viral genome sequencing to quantify introductions and identify likely on-campus spread.

Results
Ninety-one percent of viral genotypes occurred once, indicating no follow-on transmission. Less than 5% of introductions resulted in &gt;3 cases, with 2 notable exceptions of 40 and 47 cases. Both partially overlapped with outbreaks defined by contact tracing. In both cases, viral genomics eliminated over half the epidemiologically linked cases but added an equivalent or greater number of individuals to the transmission cluster.

Conclusions
Public health interventions prevented within-university transmission for most SARS-CoV-2 introductions, with only 2 major outbreaks being identified January to May 2021. The genetically linked cases overlap with outbreaks identified by contact tracing; however, they persisted in the university population for fewer days and rounds of transmission than estimated via contact tracing. This underscores the effectiveness of test-trace-isolate strategies in controlling undetected spread of emerging respiratory infectious diseases. These approaches limit follow-on transmission in both outside-in and internal transmission conditions.
Loop-mediated isothermal amplification of economically important Ceratitis species (Diptera: Tephritidae)
Authors: Zhang Yue , Li Weisong , Virgilio Massimiliano , De Meyer Marc , Li Zhihong 
Published: October 2023

Abstract
Ceratitis is an economically important genus of fruit flies that originated in Africa, has a wide host range, and causes serious economic losses due to its invasive damage. As a result, it is critical to identify them accurately and quickly in the world. Loop-mediated isothermal amplification (LAMP), as one of the representatives of isothermal amplification technology, has been widely used in the rapid nucleic acid detection of human pathogens and has shown its advantages in the identification of insect agricultural pests. In this study, using the mitochondrial cox1 and cob genes as target genes, the rapid molecular identification of the Ceratitis FARQ complex, C. cosyra, and C. capitata was realized based on LAMP. The experimental conditions optimization results showed that F3/B3:FIP/BIP = 1:8 was the optimal primer concentration ratio and 63 °C was the optimal reaction temperature. The sensitivity of the primers obtained in this study can reach up to 0.01 ng/μl DNA. A loop-mediated isothermal amplification identification technology system was established based on rapid, rough DNA extraction and visual detection of Ceratitis economically important fruit flies. The positive reaction system changed from pink to khaki by visual detection. The identification flow can be completed within 1 hour, including sample processing, DNA extraction, and LAMP visual detection.
Low-noise chopper amplifier design for low-frequency induction magnetometers
Authors: Tang Yao , Xi Zhenzhu , Chen Xingpeng , Long Xia 
Published: October 2023

Abstract
Induction magnetometers (IM) are commonly used in the magnetotelluric method for exploration. 1/f noise in the low-frequency band of the preamplifier reduces the signal-to-noise ratio of IM, thus affecting the exploration results. We designed a low-noise chopper amplifier with equivalent input voltage noise of 9.8 nV/√Hz at 1 mHz, 2.1 nV/√Hz at 0.01 Hz, and 1.9 nV/√Hz at 0.1 Hz; 1/f noise corner frequency of 8 mHz, and equivalent input current noise of 200 fA/√Hz at 1 mHz, 100 fA/√Hz at 0.01 Hz, and 60 fA/√Hz at 0.1 Hz. The IM using this chopper amplifier is 85.5 cm long, 6.0 cm in diameter, and has a total weight of 4.8 kg. Its sensitivity is 300 mV/nT during 20 Hz and 1 kHz, with a theoretical equivalent input magnetic field noise of 0.3 pT/√Hz at 1 Hz and a measurement frequency range of 1 mHz to 1 kHz.
Ultrasonic P-wave to determine pore parameters of Spergen limestone
Authors: Li Guangquan , Liu Zhongyuan , Li Bohua 
Published: October 2023

AbstractUltrasonic waves are capable of helping characterize pores of rocks. A model of viscous squirt is used to simulate phase velocity and the quality factor of ultrasonic P-wave measured in water-saturated Spergen limestone, thus determining pore parameters of the limestone. The measured P-wave had a centroid frequency of ∼0.75 MHz, and two simulations are conducted in this paper. The first simulation yields a dispersion curve with a dipping spike followed by a rising spike. However, it cannot yield the measured quality factor. Another drawback is that one of the pore parameters violates rock physics. The second simulation yields a dispersion curve with a small velocity depression followed by an upward velocity concave; the measured phase velocity and quality factor are simultaneously predicted. The resulting dimensions of the rock unit are 0.3 by 0.333 mm, which is consistent with the mean grain diameter of 0.3 mm. The relative first and second porosities are ascertained to be 0.97 and 0.03, respectively. The aperture distance at contact of grains is inverted as 1.8 µm. Remarkably, the minimum phase velocity of the water-saturated limestone is lower than the Gassmann velocity.
An improved Compton parameter map of thermal Sunyaev–Zeldovich effect from Planck PR4 data
Authors: Chandran Jyothis , Remazeilles Mathieu , Barreiro R B 
Published: October 2023

ABSTRACT
Taking advantage of the reduced levels of noise and systematics in the data of the latest Planck release (PR4, also known as NPIPE), we construct a new all-sky Compton-y parameter map (hereafter, y-map) of the thermal Sunyaev–Zeldovich (SZ) effect from the Planck PR4 data. A tailored Needlet Internal Linear Combination (NILC) pipeline, first validated on detailed sky simulations, is applied to the nine single-frequency Planck PR4 sky maps, ranging from 30 to 857 GHz, to produce the PR4 y-map over 98 per cent of the sky. Using map comparisons, angular power spectra, and one-point statistics, we show that the PR4 NILC y-map is of improved quality compared to that of the previous PR2 release. The new y-map shows reduced levels of large-scale striations associated with 1/f noise in the scan direction. Regions near the Galactic plane also show lower residual contamination by Galactic thermal dust emission. At small angular scales, the residual contamination by thermal noise and cosmic infrared background (CIB) emission is found to be reduced by around 7 and 34 per cent, respectively, in the PR4 y-map. The PR4 NILC y-map is made publicly available for astrophysical and cosmological analyses of the thermal SZ effect.
Mini-quenching of z = 4–8 galaxies by bursty star formation
Authors: Dome Tibor , Tacchella Sandro , Fialkov Anastasia , Ceverino Daniel , Dekel Avishai , Ginzburg Omri , Lapiner Sharon , Looser Tobias J 
Published: October 2023

ABSTRACT
The recent reported discovery of a low-mass z = 5.2 and an intermediate-mass z = 7.3 quenched galaxy with JWST/NIRSpec is the first evidence of halted star formation above z ≈ 5. Here, we show how bursty star formation at z = 4–8 gives rise to temporarily quenched, or mini-quenched galaxies in the mass range M⋆ = 107–109 M⊙ using four models of galaxy formation: the periodic box simulation IllustrisTNG, the zoom-in simulations vela and FirstLight and an empirical halo model. The main causes for mini-quenching are stellar feedback, lack of gas accretion onto galaxies, and galaxy–galaxy interactions. The abundance of (mini-)quenched galaxies agrees across the models: the population first appears below z ≈ 8, after which their proportion increases with cosmic time, from ∼0.5–1.0 per cent at z = 7 to ∼2–4 per cent at z = 4, corresponding to comoving number densities of ∼10−5 and ∼10−3 Mpc−3, respectively. These numbers are consistent with star formation rate duty cycles inferred for vela and FirstLight galaxies. Their star formation histories (SFHs) suggest that mini-quenching at z = 4–8 is short-lived with a duration of ∼20–40 Myr, which is close to the free-fall time-scale of the inner halo. However, mock spectral energy distributions of mini-quenched galaxies in IllustrisTNG and vela do not match JADES-GS-z7-01-QU photometry, unless their SFHs are artificially altered to be more bursty on time-scales of ∼40 Myr. Studying mini-quenched galaxies might aid in calibrating sub-grid models governing galaxy formation, as these may not generate sufficient burstiness at high redshift to explain the SFH inferred for JADES-GS-z7-01-QU.
Ribocentre-switch: a database of riboswitches
Authors: Bu Fan , Lin Xiaowei , Liao Wenjian , Lu Zhizhong , He Yuanlin , Luo Yuhang , Peng Xuemei , Li Mengxiao , Huang Yuanyin , Chen Xiaoxue , Xiao Bowen , Jiang Jiuhong , Deng Jie , Huang Jian , Lin Tianxin , Miao Zhichao , Huang Lin 
Published: October 2023

Abstract
Riboswitches are regulatory elements found in the untranslated regions (UTRs) of certain mRNA molecules. They typically comprise two distinct domains: an aptamer domain that can bind to specific small molecules, and an expression platform that controls gene expression. Riboswitches work by undergoing a conformational change upon binding to their specific ligand, thus activating or repressing the genes downstream. This mechanism allows gene expression regulation in response to metabolites or small molecules. To systematically summarise riboswitch structures and their related ligand binding functions, we present Ribocentre-switch, a comprehensive database of riboswitches, including the information as follows: sequences, structures, functions, ligand binding pockets and biological applications. It encompasses 56 riboswitches and 26 orphan riboswitches from over 430 references, with a total of 89 591 sequences. It serves as a good resource for comparing different riboswitches and facilitating the identification of potential riboswitch candidates. Therefore, it may facilitate the understanding of RNA structural conformational changes in response to ligand signaling. The database is publicly available at https://riboswitch.ribocentre.org.
Added prognostic value of 3D deep learning-derived features from preoperative MRI for adult-type diffuse gliomas
Authors: Lee Jung Oh , Ahn Sung Soo , Choi Kyu Sung , Lee Junhyeok , Jang Joon , Park Jung Hyun , Hwang Inpyeong , Park Chul-Kee , Park Sung Hye , Chung Jin Wook , Choi Seung Hong 
Published: October 2023

Abstract

Background
To investigate the prognostic value of spatial features from whole-brain MRI using a three-dimensional (3D) convolutional neural network for adult-type diffuse gliomas.

Methods
In a retrospective, multicenter study, 1925 diffuse glioma patients were enrolled from 5 datasets: SNUH (n = 708), UPenn (n = 425), UCSF (n = 500), TCGA (n = 160), and Severance (n = 132). The SNUH and Severance datasets served as external test sets. Precontrast and postcontrast 3D T1-weighted, T2-weighted, and T2-FLAIR images were processed as multichannel 3D images. A 3D-adapted SE-ResNeXt model was trained to predict overall survival. The prognostic value of the deep learning-based prognostic index (DPI), a spatial feature-derived quantitative score, and established prognostic markers were evaluated using Cox regression. Model evaluation was performed using the concordance index (C-index) and Brier score.

Results
The MRI-only median DPI survival prediction model achieved C-indices of 0.709 and 0.677 (BS = 0.142 and 0.215) and survival differences (P &lt; 0.001 and P = 0.002; log-rank test) for the SNUH and Severance datasets, respectively. Multivariate Cox analysis revealed DPI as a significant prognostic factor, independent of clinical and molecular genetic variables: hazard ratio = 0.032 and 0.036 (P &lt; 0.001 and P = 0.004) for the SNUH and Severance datasets, respectively. Multimodal prediction models achieved higher C-indices than models using only clinical and molecular genetic variables: 0.783 vs. 0.774, P = 0.001, SNUH; 0.766 vs. 0.748, P = 0.023, Severance.

Conclusions
The global morphologic feature derived from 3D CNN models using whole-brain MRI has independent prognostic value for diffuse gliomas. Combining clinical, molecular genetic, and imaging data yields the best performance.
Acceptability and feasibility of assisted telepsychiatry in routine healthcare settings in India: a qualitative study
Authors: Nadkarni Abhijit , Garg Ankur , Agrawal Ravindra , Sambari Seema , Mirchandani Kedar , Velleman Richard , Gupta Devika , Bhatia Urvita , Fernandes Godwin , D’souza Ethel , Amonkar Akshada , Rane Anil 
Published: October 2023

Abstract
Technology-enabled interventions are often recommended to overcome geographical barriers to access and inequitable distribution of mental healthcare workers. The aim of this study was to examine the acceptability and feasibility of an assisted telepsychiatry model implemented in primary care settings in India. In-depth interviews were conducted with patients who received telepsychiatry consultations. Data were collected about domains such as experience with communicating with psychiatrists over a video call and feasibility of accessing services. Data were analysed using a thematic analysis approach. Patients recognized that technology enabled them to access treatment and appreciated its contribution to the improvement in their mental health condition. They reported that the telepsychiatry experience was comparable to face-to-face consultations. They had a positive experience of facilitation by counsellors and found treatment delivery in primary care non-stigmatizing. While some adapted easily to the technology platform because of increased access to technology in their daily lives, others struggled to communicate over a screen. For some, availability of care closer to their homes was convenient; for others, even the little travel involved posed a financial burden. In some cases, the internet connectivity was poor and interfered with the video calls. Patients believed that scale could be achieved through adoption of this model by the public sector, collaboration with civil society, enhanced demand generation strategies and leveraging platforms beyond health systems. Assisted telepsychiatry integrated in routine healthcare settings has the potential to make scarce specialist mental health services accessible in low resource settings by overcoming geographical and logistical barriers.
Time Travel without Hyperkinesis
Authors: Lewis David 
Published: October 2023

Abstract
This is the first chapter of The Paradoxes of Time Travel. In The Paradoxes of Time Travel Lewis argues that time travel as it is imagined in certain science fiction narratives is a genuine possibility. In his own words, Lewis aimed, ‘(1) to solve a philosophical problem hitherto largely ignored or casually mis-solved by philosophers […]; (2) to introduce the layman to various topics in metaphysics, since our problem turns out to connect with many more familiar ones; and (3) to show several of my favorite doctrines and methods in metaphysics’. In the course of his 6 lectures, Lewis lays out his Quinean four-dimensionalist metaphysics and explains how our ordinary concept of person allows for causal loops. This requires a notion of ‘reverse causation’ which Lewis explains by analysing causation in counterfactual terms. Finally, Lewis elaborates on the sense in which we can and cannot be intelligibly said to be free to change the past.
Rational Belief: Statics
Authors: Lewis David 
Published: October 2023

Abstract
This is the second chapter of Confirmation Theory. Confirmation Theory is a book manuscript that Lewis wrote in 1969 on the basis of a course he’d given at UCLA. He submitted the manuscript to Harvard University Press who expressed an interest. It consists of seven chapters covering intensional semantics, probability measures, rational belief, principles of indifference and Carnap and Hintikka’s inductive systems. The work was intended to be accessible to students with, as Lewis put it, ‘hairy high-school algebra’. He described the manuscript to Richard Jeffrey as ‘Mathematically self-contained, with proofs for the major theorems’. Lewis originally envisaged that Carnap’s The Continuum of Inductive Methods (1952) be used as an accompanying text. Lewis focused on Carnap and Hintikka in particular because he believed that their work constituted the attractive core of what competing theories of confirmation had in common.
Reply to Sommers’ “Composite Things” (1969)
Authors: Lewis David 
Published: October 2023

Abstract
This is a brief draft reply to Fred Sommers’ ‘Structural Ontology’. The paper, dating from 1969, was handwritten by Lewis, and apparently never fully finished. In this reply Lewis grapples with the extensions required for Sommers’ distinction between being P and un-P for some predicate P, and raises some sceptical questions about Sommers’ argument for phenomenalism, suggesting that it would generalise to apply to machines as well as persons.
Insatiable Quantifiers (1972)
Authors: Lewis David 
Published: October 2023

Abstract
This short paper, dating from 1972, is related in its content to Lewis’s 1975 paper ‘Adverbs of Quantification’. In it Lewis lays out the semantic advantages of ‘insatiable quantifiers’, namely quantifiers which bind all variables in their scope. Lewis discusses the application of such quantifiers to donkey sentences.
To the Thursday Logic Seminar (1976)
Authors: Lewis David 
Published: October 2023

Abstract
This is a short note, written by Lewis in 1976. It is inspired by Lewis’s contribution to the discussion session of a paper by Richard Epstein at Victoria University of Wellington in 1976. Lewis’s note is a brief but specific proposal working out his suggestion to Epstein that in relevance logics, the relevance relation between sentences could be modelled as a relation of subject matter overlap: Lewis proposes an assignment of subject matters to sentences such that sentences are relevant iff their subject matters overlap.
Modal Demifictionalism (1994)
Authors: Lewis David 
Published: October 2023

Abstract
In this short paper, dating from 1994, Lewis considers the question whether his opponents, Pettit and Menzies, who take a fictionalist attitude towards possible worlds, can state their view in such a way that the truth of ‘necessarily, if pigs fly, then there are many worlds’ or some equivalent statement is accounted for. He concludes that they cannot.
Quick Impact Projects
Authors: Oksamytna Kseniya 
Published: October 2023

AbstractQuick impact projects emerged in the early 2000s due to the Brahimi Panel’s ‘authority talk’. The Panel operated under favourable circumstances. It had an image as an independent, representative, knowledgeable, and cohesive group of experts led by a figure of significant international stature. While the chair and the panellists enjoyed an image of impartiality, they also had an insider status in UN circles due to their long and distinguished careers in diplomacy, peacekeeping, and humanitarian affairs. Quick impact projects were a specific and not very salient recommendation, coming across as intuitive and commonsensical. Quick impact projects’ low salience compared favourably with the more significant and controversial Brahimi Report’s recommendation on mission integration, so humanitarian and development actors focused their energy on opposing the latter rather than the former. The absence of other voices discussing the issue made the Brahimi Panel the only source of information, adding to its authoritativeness. Other favourable conditions included a cultural match with UN values of assistance and the crisis of peacekeeping. The Secretariat developed unofficial guidance on quick impact projects in 2006 and official policy in 2007. While there were posts, units, and committees at the mission level to select and manage quick impact projects, there was no dedicated section at headquarters. Some financial contributors questioned the necessity of quick impact projects beyond the start-up stage, yet quick impact projects grew in size and scope. They also contributed to the legitimization of programmatic funding in peacekeeping.
Vegetable Genius
Authors: Biagioli Mario 
Published: October 2023

Abstract
Over time, many scholars have looked at how breeders, farmers, and scientists have attempted to codify and protect the value they saw in the plants they had selectively bred or modified. This chapter looks at this process from a different direction: analysing the role that the figure of the plant has played in the conceptual development of intellectual property law. Through an analysis of eighteenth-century theoretical works on literary originality, it argues that the very notion of genius—the romantic trope central to the development of copyright law—has vegetable roots. The chapter also argues that what made the figure of the plant and of organic growth remarkable is its enduring capacity to capture the conceptual conundrums embedded in intellectual property law, for both supporters and critics, from the eighteenth century to the present.