bluuebunny/crossref_metadata_2025 huggingface dataset:
Does Political Equality Require Equal Power? A Pluralist Account
Authors: Mráz Attila
Published: November 2023

In this paper, I criticize two views on how political equality is related to equally distributed political power, and I offer a novel, pluralist account of political equality to address their shortcomings—in particular, concerning their implications for affirmative action in the political domain, political representation, and the situation of permanent minorities. The Equal Power View holds that political equality requires equally distributed political power. It considers affirmative action—e.g., racial or gender electoral quotas—, representation, and more-than-equal power to permanent minorities pro tanto objectionable. The Equal Status View, in contrast, holds that political equality concerns equal relations and status, and it is only contingently related to equally distributed power. I argue that while the Equal Status View is right that equal power can be insufficient for—or even objectionable from the viewpoint of—political equality, it is wrong to conclude that equal power has no independent significance in an account of political equality. My pluralist account shows that political equality entails not only status-based requirements but also independent egalitarian requirements to distribute political power equally. This account provides a finer-grained understanding of affirmative action in the political domain. It justifies affirmative action but holds that it should only be used to realize equal political status until thorough-going social reform allows us to maintain both equal political status and equally distributed political power at the same time. Similarly, representation should be amended with power-balancing institutions, and permanent minorities should enjoy equal status with minimal compromise to power equality.
Trophic relationships of translocated and indigenous chub Squalius cephalus populations with trophically analogous fishes
Authors: Warren Bertram I. C. , Pinder Adrian C. , Parker Ben , Tarkan A. Serhan , Britton J. Robert
Published: November 2023

The translocation of non-indigenous fishes into lowland rives can result in invasive populations establishing and dispersing. Because non-indigenous fishes can cause ecological harm, it is important to understand their trophic relationships and the effects they may have on native fishes. We assessed the trophic ecology of a translocated chub Squalius cephalus population in the River Frome, a lowland chalk stream in Southern England, using bulk stable isotope (δ13C, δ15N) metrics, and compared the results with those derived from indigenous chub populations. The isotopic niche sizes of all fishes in the River Frome were substantially larger in the tidal versus non-tidal site, with the δ13C values suggesting some fish were foraging further downstream of their sampling point in areas that had greater tidal and salinity influences. Inter-specific comparisons of isotopic niches revealed a consistent pattern of similar niche size and overlap between chub and the trophically analogous dace Leuciscus leuciscus. These isotopic relationships between chub and dace were then also apparent in the indigenous populations of these fishes. These results suggest that the colonisation of this lowland river by translocated chub is being facilitated by their isotopic relationships with other fishes that are similar to those observed in their native range.
Recruitment of PVT1 Enhances YTHDC1-Mediated m6A Modification of IL-33 in Hyperoxia-Induced Lung Injury During Bronchopulmonary Dysplasia
Authors: Bao Tianping , Liu Xiangye , Hu Jian , Ma Mengmeng , Li Jingyan , Cao Linxia , Yu Bingrui , Cheng Huaiping , Zhao Sai , Tian Zhaofang
Published: November 2023

Bronchopulmonary dysplasia (BPD) is a chronic lung disease that specifically affects preterm infants. Oxygen therapy administered to treat BPD can lead to hyperoxia-induced lung injury, characterized by apoptosis of lung alveolar epithelial cells. Our epitranscriptomic microarray analysis of normal mice lungs and hyperoxia-stimulated mice lungs revealed elevated RNA expression levels of IL-33, as well as increased m6A RNA methylation levels of IL-33 and PVT1 in the hyperoxia-stimulated lungs. This study aimed to investigate the role of the PVT1/IL-33 axis in BPD. A mouse model of BPD was established through hyperoxia induction, and lung histological changes were assessed by hematoxylin–eosin staining. Parameters such as radial alveolar count and mean chord length were measured to assess lung function. Mouse and human lung alveolar epithelial cells (MLE12 and A549, respectively) were stimulated with hyperoxia to create an in vitro BPD model. Cell apoptosis was detected using Western blotting and flow cytometry analysis. Our results demonstrated that silencing PVT1 suppressed apoptosis in MLE12 and A549 cells and improved lung function in hyperoxia-stimulated lungs. Additionally, IL-33 reversed the effects of PVT1 both in vivo and in vitro. Through online bioinformatics analysis and RNA-binding protein immunoprecipitation assays, YTHDC1 was identified as a RNA-binding protein (RBP) for both PVT1 and IL-33. We found that PVT1 positively regulated IL-33 expression by recruiting YTHDC1 to mediate m6A modification of IL-33. In conclusion, silencing PVT1 demonstrated beneficial effects in alleviating BPD by facilitating YTHDC1-mediated m6A modification of IL-33. Inhibition of the PVT1/IL-33 axis to suppress apoptosis in lung alveolar epithelial cells may hold promise as a therapeutic approach for managing hyperoxia-induced lung injury in BPD.
On Convergence Rates of Proximal Alternating Direction Method of Multipliers
Authors: Jin Qinian
Published: November 2023

In this paper we consider from two different aspects the proximal alternating direction method of multipliers (ADMM) in Hilbert spaces. We first consider the application of the proximal ADMM to solve well-posed linearly constrained two-block separable convex minimization problems in Hilbert spaces and obtain new and improved non-ergodic convergence rate results, including linear and sublinear rates under certain regularity conditions. We next consider the proximal ADMM as a regularization method for solving linear ill-posed inverse problems in Hilbert spaces. When the data is corrupted by additive noise, we establish, under a benchmark source condition, a convergence rate result in terms of the noise level when the number of iterations is properly chosen.
Assessing populations exposed to climate change: a focus on Africa in a global context
Authors: Ghio Daniela , Goujon Anne , Natale Fabrizio , Alfredo Alessandrini , Petroliagkis Thomas
Published: November 2023

The recent debate on population dynamics and climate change has highlighted the importance of assessing and quantifying disparities in populations’ vulnerability and adopting a forward-looking manner when considering the potential impacts of climate change on different communities and regions. In this article, we overlay demographic projections based on the Shared Socioeconomic Pathways and climate change projections derived from the Representative Concentration Pathways. We focus on populations that are likely to be the most exposed to climate change in the future, namely, African populations in a comparative global context. First, we estimate the share of populations living in rural areas, who would be more dependent on agriculture, as one of the economic sectors mostly affected by climate change. Second, we explore how climate change would worsen the condition of populations living below the poverty line. Finally, we account for low levels of education, as further factors limiting people’s adaptation ability to increasingly adverse climate circumstances. Our contribution to the literature on population, agriculture, and environmental change is twofold. Firstly, by mapping the potential populations exposed to climate change, in terms of declining agricultural yields, we identify vulnerable areas, allowing for the development of targeted strategies and interventions to mitigate the impacts, ensure resilience, and protect the population living in the most affected areas. Secondly, we assess differentials in the vulnerability of local populations, showing how African regions would become among one of the most exposed to climate change by the end of the century. The findings support the targeting of policy measures to prevent increased vulnerability among already disadvantaged populations.
Cauchy robust principal component analysis with applications to high-dimensional data sets
Authors: Fayomi Aisha , Pantazis Yannis , Tsagris Michail , Wood Andrew T. A.
Published: November 2023

Principal component analysis (PCA) is a standard dimensionality reduction technique used in various research and applied fields. From an algorithmic point of view, classical PCA can be formulated in terms of operations on a multivariate Gaussian likelihood. As a consequence of the implied Gaussian formulation, the principal components are not robust to outliers. In this paper, we propose a modified formulation, based on the use of a multivariate Cauchy likelihood instead of the Gaussian likelihood, which has the effect of robustifying the principal components. We present an algorithm to compute these robustified principal components. We additionally derive the relevant influence function of the first component and examine its theoretical properties. Simulation experiments on high-dimensional datasets demonstrate that the estimated principal components based on the Cauchy likelihood typically outperform, or are on a par with, existing robust PCA techniques. Moreover, the Cauchy PCA algorithm we have used has much lower computational cost in very high dimensional settings than the other public domain robust PCA methods we consider.
A problem with the fixed past fixed
Authors: Wawer Jacek
Published: November 2023

A novel fatalistic argument that combines elements of modal, temporal, and epistemic logic to prove that the fixed past is not compatible with the open future has recently been presented by Lampert (Analysis 82(3):426–434, 2022). By the construction of a countermodel, it is shown that his line of reasoning is defective. However, it is also explained how Lampert’s argument could be corrected if it were supported with an extra premise regarding the temporal status of a priori knowledge. This additional assumption—which was tacit in the original presentation—is shown to be the weakest link, and it is argued that, despite Lampert’s assurance, it can be plausibly rejected in a roughly Ockhamist framework. Thus, it is concluded that the fixed past poses no threat to the open future; however, a few different lessons about knowledge, necessity, and time are drawn from careful reflection on this novel argument.
Why reasons and reasoning don’t come apart
Authors: Kietzmann Christian
Published: November 2023

In recent years several philosophers have proposed what has come to be called the Reasoning View of normative reasons, according to which normative reasons are premises of sound reasoning. The reasoning view has come under some criticism, which chiefly consists in counterexamples that purport to show that something can be a premise of sound reasoning without intuitively being a normative reason, or can be a normative reason without being a premise of sound reasoning. I here consider and reject three examples that were recently put forward. Discussing them will allow me to clarify the Reasoning View in important respects.
Leveraging response times in learning environments: opportunities and challenges
Authors: Pelánek Radek
Published: November 2023

Computer-based learning environments can easily collect student response times. These can be used for multiple purposes, such as modeling student knowledge and affect, domain modeling, and cheating detection. However, to fully leverage them, it is essential to understand the properties of response times and associated caveats. In this study, we delve into the properties of response time distributions, including the influence of aberrant student behavior on response times. We then provide an overview of modeling approaches that use response times and discuss potential applications of response times for guiding the adaptive behavior of learning environments.
FGF2 Functions in H2S’s Attenuating Effect on Brain Injury Induced by Deep Hypothermic Circulatory Arrest in Rats
Authors: Zhu Yu-Xiang , Yang Qin , Zhang You-Peng , Liu Zhi-Gang
Published: November 2023

Deep hypothermic circulatory arrest (DHCA) can protect the brain during cardiac and aortic surgery by cooling the body, but meanwhile, temporary or permanent brain injury may arise. H2S protects neurons and the central nervous system, especially from secondary neuronal injury. We aim to unveil part of the mechanism of H2S’s attenuating effect on brain injury induced by DHCA by exploring crucial target genes, and further promote the clinical application of H2S in DHCA. Nine SD rats were utilized to provide histological and microarray samples, and further the differential expression analysis. Then we conducted GO and KEGG pathway enrichment analyses on candidate genes. The protein-protein interaction (PPI) networks were performed by STRING and GeneMANIA. Crucial target genes’ expression was validated by qRT-PCR and western blot. Histological study proved DHCA’s damaging effect and H2S’s repairing effect on brain. Next, we got 477 candidate genes by analyzing differentially expressed genes. The candidate genes were enriched in 303 GO terms and 28 KEGG pathways. Then nine genes were selected as crucial target genes. The function prediction by GeneMANIA suggested their close relation to immunity. FGF2 was identified as the crucial gene. FGF2 plays a vital role in the pathway when H2S attenuates brain injury after DHCA. Our research provides more information for understanding the mechanism of H2S attenuating brain injury after DHCA. We infer the process might probably be closely associated with immunity.
Development of Liquid Chromatography-Mass Spectrometry (LC-MS) Method for Quantification of Broccoli Sulforaphane
Authors: Ali Redha Ali , Hong Hung T. , Torquati Luciana , Nash Geoffrey R. , Gidley Michael J. , Cozzolino Daniel
Published: November 2023

Sulforaphane (SFN) is an isothiocyanate and the product of the hydrolysis of glucoraphanin (GRA) by myrosinase. Broccoli is one of the rich sources of GRA and thus SFN. SFN possess a wide range of bioactivities and is considered an anti-cancer phytochemical. Most of the current common methods used to quantify SFN are based on high-pressure liquid chromatography (HPLC) with diode array detection (DAD) — also known as HPLC-DAD. Although this technique has shown encouraging results, the detection of SFN by DAD is relatively weak and affected by high interference of sample matrices. Therefore, the aim of this study was to develop a liquid chromatography-mass spectrometry (LC-MS) method in which SFN is identified by molecular mass to give more accurate results. The developed method demonstrated a highly reproducible retention time (7.204 ± 0.008 min), producing a sharp, symmetrical and well-defined sulforaphane peak in standard and test samples. The most dominant ion of sulforaphane in the pure and test samples was 178 m/z ([M + H]+). In terms of linearity, the calibration curve had a coefficient of determination (R2) of 0.9963. The limit of detection of this method is 1.3 ng/mL, and the limit of quantification is 3.9 ng/mL, indicating high sensitivity. The uniformity of peak shape and retention time in both pure and test samples were the same suggesting excellent selectivity. Overall, the developed method showed promising results in identifying and quantifying broccoli SFN.
“It Brings the Good Vibes”: Exploring Biomorphic Aesthetics in the Design of Soft Personal Robots
Authors: Christiansen Mads Bering , Rafsanjani Ahmad , Jørgensen Jonas
Published: November 2023

The flexible bodies of soft robots provide exciting new possibilities for interaction with humans. In this paper, we propose a novel design paradigm, Soft Biomorphism, for soft robots centered on the idea of amplifying their inherent biomorphic aesthetic qualities and activating these as affordances for human interaction. Following this approach, we developed a set of biomorphic soft robotic prototypes and conducted two studies to understand the effects of biomorphic design aesthetics on people’s impressions of these prototypes. Based on qualitative data collected through five workshop sessions, the first exploratory study (n = 10) sought to investigate the envisioned uses and types of interactions that prototypes elicited within the context of personal robots. We found that various uses were considered and that most participants associated the biomorphic aesthetic design with soft robots contributing to emotional and physical well-being. Building on these results, we conducted a second study (n = 32) to investigate if soft robots with enhanced biomorphic qualities are perceived as more appealing and appropriate for physical human–robot interaction aimed at supporting well-being. We did not find any statistically significant preference for biomorphic soft robots. However, we found statistically significant differences in appeal ratings post-interaction for some prototypes, suggesting that physical interaction with soft robots can impact the perceived appeal. Based on our findings, we highlight key issues to bear in mind when considering biomorphic aesthetics in soft personal robot designs and provide tentative design recommendations to combine biomorphic and geometric elements and align visual appearance, tactility, and movement in future robot designs.
Experimental investigation on the turbulent wake flow in fully established transonic buffet conditions
Authors: Schauerte Christopher Julian , Schreyer Anne-Marie
Published: November 2023

The transonic flight regime is often dominated by transonic buffet, a highly unsteady and complex shock-wave/boundary-layer interaction involving major parts of the flow field. The phenomenon is associated with a large-amplitude periodic motion of the compression shock coupled with large-scale flow separation and intermittent re-attachment. Due to the resulting large-scale variation of the global flow topology, also the turbulent wake of the airfoil or wing is severely affected, and so are any aerodynamic devices downstream on which the wake impinges. To analyze and understand the turbulent structures and dynamics of the wake, we performed a comprehensive experimental study of the near wake of the supercritical OAT15A airfoil in transonic buffet conditions at a chord Reynolds number of$$2\times 10^{6}$$2×106. Velocity field measurements reveal severe global influences of the buffet mode on both the surface-bound flow field on the suction side of the airfoil and the wake. The flow is intermittently strongly separated, with a significant momentum deficit that extends far into the wake. The buffet motion induces severe disturbances and variations of the turbulent flow, as shown on the basis of phase-averaged turbulent quantities in terms of Reynolds shear stress and RMS-values. The spectral nature of downstream-convecting fluctuations and turbulent structures are analyzed using high-speed focusing schlieren sequences. Analyses of the power spectral density pertaining to the vortex shedding in the direct vicinity of the trailing edge indicate dominant frequencies one order of magnitude higher than those associated with shock buffet ($$St_c=\mathcal {O}({1})$$Stc=O(1)) vs.$$St_c=\mathcal {O}({0.1})$$Stc=O(0.1)). It is shown that the flapping motion of the shear layer is accompanied by the formation of a von Kármán-type vortex street of fluctuating strength. These wake structures and dynamics will impact any downstream aerodynamic devices affected by the wake. Our study, therefore, allows conclusions regarding the incoming flow of devices such as the tail plane.
Rock Typing and Reservoir Quality Analysis of the Abu Madi Reservoir: Distribution Prediction Using Artificial Neural Networks in the West El Manzala Area, Onshore Nile Delta, Egypt
Authors: Elmaadawy Khaled Gamal , El Hassan Mohamed Mahmoud Abu , Sallam Ahmed Mashhout
Published: November 2023

In the Nile Delta gas province of Egypt, the Abu Madi Formation is the most promising sandstone gas reservoir. This study aimed to investigate reservoir rock typing and quality by integrating petrophysical and petrographical data, including well logs, image logs, and cores. Furthermore, it sought to predict the permeability and reservoir quality of uncored wells by integrating artificial neural network technique with core analysis data and evaluate the effectiveness of this approach as an exploration tool in the West El Manzala area. The core petrography revealed the presence of microfacies consisting of arenites and wackes. The measured porosity, permeability, and pore sizes obtained from the cores, along with the parameters of the reservoir quality index, normalized porosity, and flow zone indicator, indicated that the Abu Madi reservoirs could be subdivided into three categories based on reservoir quality. High reservoir quality (RT-I) is characterized by megapores within the hydraulic flow unit (HFU-1) associated with bioturbated coarse to gravelly sandstone facies. Moderate reservoir quality (RT-II) is characterized by macropores within the hydraulic flow unit (HFU)-II associated with massive coarse to gravelly sandstone facies. Poor reservoir quality (RT-III) was characterized by mesopores within the HFU-III hydraulic flow unit related to laminated silty mudstone facies. The findings of this study demonstrate that the combination of reservoir rock typing and artificial neural networks is an extremely successful method for petroleum exploration in the West El Manzala region.
A note on 1-parameter stable unfoldings
Authors: Breva Ribes I. , Oset Sinha R.
Published: November 2023

We give two characterisations of when a map-germ admits a 1-parameter stable unfolding, one related to the $${\mathscr {K}}_e$$

K
e

-codimension and another related to the normal form of a versal unfolding. We then prove that there are infinitely many finitely determined map-germs of multiplicity 4 from $${\mathbb {K}}^3$$

K

3

to $${\mathbb {K}}^3$$

K

3

which do not admit a 1-parameter stable unfolding.
Post-truth and scientific authority
Authors: Benetka Gerhard , Schor-Tschudnowskaja Anna
Published: November 2023

Post-truth refers to a social situation in which trust in clear and solid knowledge has been shaken, even though the ‘demand’ or ‘need’ for such solid knowledge has not diminished. This contradictory situation is particularly evident in the way in which science appears in public: on the one hand, expertise is transformed into a set of opinions that can be shared or not shared, as political decision-making seeks to legitimise itself more and more through ‘experts’. On the other hand, in times of crisis or rapid social change in general, the call for the replacement of politics by science grows louder: to bring the pandemic under control, virologists are supposed to say what measures should be taken to restrict individual freedoms. Such scientification of politics ultimately affects both fields, so that the fact that politics and science follow different functional principles is no longer recognised on either side: ‘evidence-based’ politics forgets that the political field is about balancing interests and setting values. In our article, however, we ask about the connection of this paradoxical situation with ‘the’ scientific practice itself: to what extent has science itself contributed to this strangely contradictory social role of its production of knowledge? And how does it seek to address the crisis of post-truth?
Global Distribution of Relativistic Electron Precipitation and the Dependences on Substorm Injection and Solar Wind Ram Pressure: Long‐Term POES Observations
Authors: Chen Huayue , Gao Xinliang , Lu Quanming , Tsurutani Bruce T.
Published: November 2023

Relativistic electron precipitation (REP) into the Earth's atmosphere is one of the fundamental mechanisms causing radiation belt electron flux dropout. It is important to know the preferred regions of REP events and the interplanetary and magnetospheric conditions under which the events take place. In this study of the POES relativistic electron data during 1998–2017, we have examined all REP events from L = 3–10 using an automatic algorithm. The REP events preferentially occur in MLT = 17–03 at L = 4–6.5, where the precipitation fluxes also peak. The monthly average REP event number is correlated with both monthly average AE (auroral electrojet index) and Pd (solar wind ram pressure) indices, so we separately investigate the spatial dependences of the events on one index by restricting the other one to a low level. The occurrence rate of REP events increases with both the AE* and the indices (where AE* and are time‐modified from the AE and Pd indices). During large AE* but low , the events occur mainly in the dusk sector (MLT = 17–22) near the plasmapause. For large but low AE* intervals, most of the events occur outside the plasmapause in the midnight sector (MLT = 23–03). Possible REP loss mechanisms are discussed based on our findings. Our study provides new insights into the distribution and dependences of REP in the Earth's magnetosphere.
Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes’ repertoires
Authors: Meier Caroline S. , Pagni Marco , Richard Sophie , Mühlethaler Konrad , Almeida João M. G. C. F. , Nevez Gilles , Cushion Melanie T. , Calderón Enrique J. , Hauser Philippe M.
Published: November 2023

Surface antigenic variation is crucial for major pathogens that infect humans. To escape the immune system, they exploit various mechanisms. Understanding these mechanisms is important to better prevent and fight the deadly diseases caused. Those used by the fungus Pneumocystis jirovecii that causes life-threatening pneumonia in immunocompromised individuals remain poorly understood. Here, though this fungus is currently not cultivable, our detailed analysis of the subtelomeric sequence motifs and genes encoding surface proteins suggests that the system involves the reassortment of the repertoire of ca. 80 non-expressed genes present in each strain, from which single genes are retrieved for mutually exclusive expression. Dispersion of the new repertoires, supposedly by healthy carrier individuals, appears very efficient because identical alleles are observed in patients from different countries. Our observations reveal a unique strategy of antigenic variation. They also highlight the possible role in genome rearrangements of small imperfect mirror sequences forming DNA triplexes.
Deep brain stimulation of thalamic nucleus reuniens promotes neuronal and cognitive resilience in an Alzheimer’s disease mouse model
Authors: Shoob Shiri , Buchbinder Nadav , Shinikamin Ortal , Gold Or , Baeloha Halit , Langberg Tomer , Zarhin Daniel , Shapira Ilana , Braun Gabriella , Habib Naomi , Slutsky Inna
Published: November 2023

The mechanisms that confer cognitive resilience to Alzheimer’s Disease (AD) are not fully understood. Here, we describe a neural circuit mechanism underlying this resilience in a familial AD mouse model. In the prodromal disease stage, interictal epileptiform spikes (IESs) emerge during anesthesia in the CA1 and mPFC regions, leading to working memory disruptions. These IESs are driven by inputs from the thalamic nucleus reuniens (nRE). Indeed, tonic deep brain stimulation of the nRE (tDBS-nRE) effectively suppresses IESs and restores firing rate homeostasis under anesthesia, preventing further impairments in nRE-CA1 synaptic facilitation and working memory. Notably, applying tDBS-nRE during the prodromal phase in young APP/PS1 mice mitigates age-dependent memory decline. The IES rate during anesthesia in young APP/PS1 mice correlates with later working memory impairments. These findings highlight the nRE as a central hub of functional resilience and underscore the clinical promise of DBS in conferring resilience to AD pathology by restoring circuit-level homeostasis.
Evidence for ground state coherence in a two-dimensional Kondo lattice
Authors: Wan Wen , Harsh Rishav , Meninno Antonella , Dreher Paul , Sajan Sandra , Guo Haojie , Errea Ion , de Juan Fernando , Ugeda Miguel M.
Published: November 2023

Kondo lattices are ideal testbeds for the exploration of heavy-fermion quantum phases of matter. While our understanding of Kondo lattices has traditionally relied on complex bulk f-electron systems, transition metal dichalcogenide heterobilayers have recently emerged as simple, accessible and tunable 2D Kondo lattice platforms where, however, their ground state remains to be established. Here we present evidence of a coherent ground state in the 1T/1H-TaSe2 heterobilayer by means of scanning tunneling microscopy/spectroscopy at 340 mK. Our measurements reveal the existence of two symmetric electronic resonances around the Fermi energy, a hallmark of coherence in the spin lattice. Spectroscopic imaging locates both resonances at the central Ta atom of the charge density wave of the 1T phase, where the localized magnetic moment is held. Furthermore, the evolution of the electronic structure with the magnetic field reveals a non-linear increase of the energy separation between the electronic resonances. Aided by ab initio and auxiliary-fermion mean-field calculations, we demonstrate that this behavior is inconsistent with a fully screened Kondo lattice, and suggests a ground state with magnetic order mediated by conduction electrons. The manifestation of magnetic coherence in TMD-based 2D Kondo lattices enables the exploration of magnetic quantum criticality, Kondo breakdown transitions and unconventional superconductivity in the strict two-dimensional limit.
Structural basis for stabilisation of the RAD51 nucleoprotein filament by BRCA2
Authors: Appleby Robert , Joudeh Luay , Cobbett Katie , Pellegrini Luca
Published: November 2023

The BRCA2 tumour suppressor protein preserves genomic integrity via interactions with the DNA-strand exchange RAD51 protein in homology-directed repair. The RAD51-binding TR2 motif at the BRCA2 C-terminus is essential for protection and restart of stalled replication forks. Biochemical evidence shows that TR2 recognises filamentous RAD51, but existing models of TR2 binding to RAD51 lack a structural basis. Here we used cryo-electron microscopy and structure-guided mutagenesis to elucidate the mechanism of TR2 binding to nucleoprotein filaments of human RAD51. We find that TR2 binds across the protomer interface in the filament, acting as a brace for adjacent RAD51 molecules. TR2 targets an acidic-patch motif on human RAD51 that serves as a recruitment hub in fission yeast Rad51 for recombination mediators Rad52 and Rad55-Rad57. Our findings provide a structural rationale for RAD51 filament stabilisation by BRCA2 and reveal a common recruitment mechanism of recombination mediators to the RAD51 filament.
Subjective data models in bioinformatics and how wet lab and computational biologists conceptualise data
Authors: Yehudi Yo , Hughes-Noehrer Lukas , Goble Carole , Jay Caroline
Published: November 2023

Biological science produces “big data” in varied formats, which necessitates using computational tools to process, integrate, and analyse data. Researchers using computational biology tools range from those using computers for communication, to those writing analysis code. We examine differences in how researchers conceptualise the same data, which we call “subjective data models”. We interviewed 22 people with biological experience and varied levels of computational experience, and found that many had fluid subjective data models that changed depending on circumstance. Surprisingly, results did not cluster around participants’ computational experience levels. People did not consistently map entities from abstract data models to the real-world entities in files, and certain data identifier formats were easier to infer meaning from than others. Real-world implications: 1) software engineers should design interfaces for task performance, emulating popular user interfaces, rather than targeting professional backgrounds; 2) when insufficient context is provided, people may guess what data means, whether or not they are correct, emphasising the importance of contextual metadata to remove the need for erroneous guesswork.
Multi-class glioma segmentation on real-world data with missing MRI sequences: comparison of three deep learning algorithms
Authors: Pemberton Hugh G. , Wu Jiaming , Kommers Ivar , Müller Domenique M. J. , Hu Yipeng , Goodkin Olivia , Vos Sjoerd B. , Bisdas Sotirios , Robe Pierre A. , Ardon Hilko , Bello Lorenzo , Rossi Marco , Sciortino Tommaso , Nibali Marco Conti , Berger Mitchel S. , Hervey-Jumper Shawn L. , Bouwknegt Wim , Van den Brink Wimar A. , Furtner Julia , Han Seunggu J. , Idema Albert J. S. , Kiesel Barbara , Widhalm Georg , Kloet Alfred , Wagemakers Michiel , Zwinderman Aeilko H. , Krieg Sandro M. , Mandonnet Emmanuel , Prados Ferran , de Witt Hamer Philip , Barkhof Frederik , Eijgelaar Roelant S.
Published: November 2023

This study tests the generalisability of three Brain Tumor Segmentation (BraTS) challenge models using a multi-center dataset of varying image quality and incomplete MRI datasets. In this retrospective study, DeepMedic, no-new-Unet (nn-Unet), and NVIDIA-net (nv-Net) were trained and tested using manual segmentations from preoperative MRI of glioblastoma (GBM) and low-grade gliomas (LGG) from the BraTS 2021 dataset (1251 in total), in addition to 275 GBM and 205 LGG acquired clinically across 12 hospitals worldwide. Data was split into 80% training, 5% validation, and 15% internal test data. An additional external test-set of 158 GBM and 69 LGG was used to assess generalisability to other hospitals’ data. All models’ median Dice similarity coefficient (DSC) for both test sets were within, or higher than, previously reported human inter-rater agreement (range of 0.74–0.85). For both test sets, nn-Unet achieved the highest DSC (internal = 0.86, external = 0.93) and the lowest Hausdorff distances (10.07, 13.87 mm, respectively) for all tumor classes (p < 0.001). By applying Sparsified training, missing MRI sequences did not statistically affect the performance. nn-Unet achieves accurate segmentations in clinical settings even in the presence of incomplete MRI datasets. This facilitates future clinical adoption of automated glioma segmentation, which could help inform treatment planning and glioma monitoring.
Incidence and risk of pancreatic cancer in patients with acute or chronic pancreatitis: a population-based cohort study
Authors: Park Seon Mee , Kim Ki Bae , Han Joung-Ho , Kim Nayoung , Kang Tae Uk , Swan Heather , Kim Hyun Jung
Published: November 2023

We aimed to evaluate the incidence and risk of pancreatic cancer (PC) in pancreatitis. We identified patients with acute pancreatitis (AP) (n = 225,811, 50.0%) and chronic pancreatitis (CP) (n = 225,685, 50.0%) from Korean population-based data and matched them with age- and sex-matched controls (n = 4,514,960). We analyzed the incidence and adjusted hazard ratios (aHRs) of PC among patients followed for more than 2 years or 5 years, and assessed risk changes over time in single episode of AP (SAP), recurrent AP (RAP), CP with AP, and CP without AP groups. We also performed subgroup analysis for both sexes. The incidences (per 104 person-years) and risks (aHR) of PC were higher in the RAP (12.69, 5.00) or CP with AP (12.12, 5.74) groups compared to the SAP (2.31, 1.32) or CP without AP (2.28, 1.57) groups. The risks of PC decreased over time, however, the risk of PC remained elevated in the RAP and CP with AP groups for more than 8 years. Females with RAP, SAP, and CP with AP had higher risks of PC than males. The risk of PC is higher and persists for longer duration in patients with RAP and CP with AP compared to those with SAP or CP without AP.
Segmentation of glioblastomas in early post-operative multi-modal MRI with deep neural networks
Authors: Helland Ragnhild Holden , Ferles Alexandros , Pedersen André , Kommers Ivar , Ardon Hilko , Barkhof Frederik , Bello Lorenzo , Berger Mitchel S. , Dunås Tora , Nibali Marco Conti , Furtner Julia , Hervey-Jumper Shawn , Idema Albert J. S. , Kiesel Barbara , Tewari Rishi Nandoe , Mandonnet Emmanuel , Müller Domenique M. J. , Robe Pierre A. , Rossi Marco , Sagberg Lisa M. , Sciortino Tommaso , Aalders Tom , Wagemakers Michiel , Widhalm Georg , Witte Marnix G. , Zwinderman Aeilko H. , Majewska Paulina L. , Jakola Asgeir S. , Solheim Ole , Hamer Philip C. De Witt , Reinertsen Ingerid , Eijgelaar Roelant S. , Bouget David
Published: November 2023

Extent of resection after surgery is one of the main prognostic factors for patients diagnosed with glioblastoma. To achieve this, accurate segmentation and classification of residual tumor from post-operative MR images is essential. The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection. In this study, two state-of-the-art neural network architectures for pre-operative segmentation were trained for the task. The models were extensively validated on a multicenter dataset with nearly 1000 patients, from 12 hospitals in Europe and the United States. The best performance achieved was a 61% Dice score, and the best classification performance was about 80% balanced accuracy, with a demonstrated ability to generalize across hospitals. In addition, the segmentation performance of the best models was on par with human expert raters. The predicted segmentations can be used to accurately classify the patients into those with residual tumor, and those with gross total resection.
Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple
Authors: Yow Ashley G. , Laosuntisuk Kanjana , Young Roberto A. , Doherty Colleen J. , Gillitt Nicholas , Perkins-Veazie Penelope , Jenny Xiang Qiu-Yun , Iorizzo Massimo
Published: November 2023

Pineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.
Two-stage multi-objective optimization for ICU bed allocation under multiple sources of uncertainty
Authors: Wan Fang , Fondrevelle Julien , Wang Tao , Duclos Antoine
Published: November 2023

Due to the impact of COVID-19, a significant influx of emergency patients inundated the intensive care unit (ICU), and as a result, the treatment of elective patients was postponed or even cancelled. This paper studies ICU bed allocation for three categories of patients (emergency, elective, and current ICU patients). A two-stage model and an improved Non-dominated Sorting Genetic Algorithm II (NSGA-II) are used to obtain ICU bed allocation. In the first stage, bed allocation is examined under uncertainties regarding the number of emergency patients and their length of stay (LOS). In the second stage, in addition to including the emergency patients with uncertainties in the first stage, it also considers uncertainty in the LOS of elective and current ICU patients. The two-stage model aims to minimize the number of required ICU beds and maximize resource utilization while ensuring the admission of the maximum number of patients. To evaluate the effectiveness of the model and algorithm, the improved NSGA-II was compared with two other methods: multi-objective simulated annealing (MOSA) and multi-objective Tabu search (MOTS). Drawing on data from real cases at a hospital in Lyon, France, the NSGA-II, while catering to patient requirements, saves 9.8% and 5.1% of ICU beds compared to MOSA and MOTS. In five different scenarios, comparing these two algorithms, NSGA-II achieved average improvements of 0%, 49%, 11.4%, 9.5%, and 17.1% across the five objectives.
Hydroclimate variability in the central Mediterranean during MIS 17 interglacial (Middle Pleistocene) highlights timing offset with monsoon activity
Authors: Capraro Luca , Incarbona Alessandro , Fornaciari Eliana , Sabatino Nadia , Scaillet Stéphane , Sprovieri Rodolfo , Sprovieri Mario
Published: November 2023

Mediterranean climates are characterized by warm, dry summers and mild, rainy winters. Previous studies suggest that over the last 1.36 Myr, Mediterranean winter rainfalls were in phase with the African monsoon. Here we present a high-resolution terrestrial and marine dataset for the Marine Isotope Stage 17 interglacial (Middle Pleistocene) from Southern Italy, showing that precipitation rates and regimes in the central Mediterranean varied independently of the monsoon system. Specifically, events of extreme summer precipitation were promoted by increased regional insolation rates and/or extratropical cyclones, and their magnitude was further enhanced by the advection of cool and humid North Atlantic air during stadials. Our findings provide new information on the short- to mid-term natural hydroclimatic variability of the Mediterranean basin, and offer new critical insights on land–ocean interactions at the regional scale by complementing previous analyses on the displacement of storm tracks toward southern Europe.
Detection of cracks in concrete using near-IR fluorescence imaging
Authors: Karpf Andreas , Selig Michael , Alchaar Aktham , Iskander Magued
Published: November 2023

Structural health monitoring of civil infrastructure is a crucial component of assuring the serviceability and integrity of the built environment. A primary material used in the construction of civil infrastructure is concrete, a material that is susceptible to cracking due to a variety of causes, such as shrinkage, creep, overloading, and temperature change. Cracking reduces the durability of concrete structures, as it allows deleterious environmental agents to penetrate the surface, causing such damage as corrosion of steel reinforcement and delamination of the concrete itself. Conventional crack detection techniques are limited in scope due to issues relating to pre-planning, accessibility, and the need for close proximity to the test surface. Contactless optical image monitoring techniques offer the opportunity to overcome these limitations and have the potential to detect cracks at a distance. Concrete has been reported to have a near-infrared (Near-IR) fluorescence line at a wavelength of 1140 nm when excited with red light. This work investigates the use of fluorescence imaging for the detection of cracks in cementitious surfaces using shallow angle incidence excitation red light. Light oriented at a shallow angle does not excite interior surfaces of cracks, which appear as darker features in images of fluorescing concrete. Artificial cracks with widths of 0.2–1.5 mm were readily imaged using a near-IR camera at distances of 0.5 and 1.3 m. An additional concrete sample with a 0.08 mm wide crack was produced using a flexure apparatus and was also imaged. It is worth noting that the 0.08 mm crack was detected despite its width being below the 0.1 mm pixel resolution of the camera, with the aid of digital image enhancement algorithms.
Charge stripes in the graphene-based materials
Authors: Grozić Petra , Keran Barbara , Kadigrobov Anatoly M. , Radić Danko
Published: November 2023

We present an analytical model of the charge density wave instability in graphene sheets within the intercalated graphite CaC6 compound. The instability yields the experimentally observed uniaxial charge stripes of periodically modulated electron density, coupled to the softest phonon mode of the superlattice consisting of the Ca atoms intercalated between graphene planes. The Fermi surface of the chemically doped graphene undergoes the novel type of instability driven by the mechanism that gains the condensation energy of the stripe state by the topological reconstruction of the Fermi surface. This mechanism appears to be entirely different from the one based on the Fermi surface nesting, which has been considered a paradigm in the present literature concerning the onset of charge density waves.
Multimodal teaching analytics: the application of SCORM courseware technology integrating 360-degree panoramic VR in historical courses
Authors: Zhang Yanxiang , Wang Ya , Fan Guimin , Song Yi , Hu Yunfeng
Published: November 2023

History courses are an essential part of a national education. The application of traditional courseware's media forms in education still requires further development and refinement. Herein, we report on a history courseware mode that integrates various historical teaching media, including 360-degree VR, paintings, maps, infographics, text, audio, and videos, based on the SCORM standard. These media elements are used to provide learners with a multimodal learning experience in history courses. We monitor the learning effects using EEG and questionnaires. The results show a significant improvement in our multimodal courseware technology compared to traditional courseware.