bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-world clinical impact of plasma cell-free DNA metagenomic next-generation sequencing assay
Authors: Kaur Ishminder , Shaw Bennett , Multani Ashrit , Pham Christine , Malhotra Sanchi , Smith Ethan , Adachi Kristina , Allyn Paul , Bango Zackary , Beaird Omer Eugene , Caldera JR , Chandrasekaran Sukantha , Chan Lynn , Cheema Rabia , Daouk Sarah , Deville Jaime , Dong Huan Vinh , Fan Austin , Garner Omai , Gaynor Pryce , Gray Hannah , Gorin Aleksandr , Kalava Sowmya , Kanatani Meganne , Karnaze Andrew , Saleh Tawny , Sharma Yamini , Stauber Stacey , Vargas Moises , Veral Monette , Winston Drew , Yanagimoto-Ogawa Lauren , Aldrovandi Grace , Nielsen-Saines Karin , Fuller Trevon , Jackson Nicholas , Uslan Daniel , Schaenman Joanna , Vijayan Tara , Sakona Ashlyn , Yang Shangxin 
Published: January 2025

Abstract

Objective:
To describe the real-world clinical impact of a commercially available plasma cell-free DNA metagenomic next-generation sequencing assay, the Karius test (KT).

Methods:
We retrospectively evaluated the clinical impact of KT by clinical panel adjudication. Descriptive statistics were used to study associations of diagnostic indications, host characteristics, and KT-generated microbiologic patterns with the clinical impact of KT. Multivariable logistic regression modeling was used to further characterize predictors of higher positive clinical impact.

Results:
We evaluated 1000 unique clinical cases of KT from 941 patients between January 1, 2017–August 31, 2023. The cohort included adult (70%) and pediatric (30%) patients. The overall clinical impact of KT was positive in 16%, negative in 2%, and no clinical impact in 82% of the cases. Among adult patients, multivariable logistic regression modeling showed that culture-negative endocarditis (OR 2.3; 95% CI, 1.11–4.53; P .022) and concern for fastidious/zoonotic/vector-borne pathogens (OR 2.1; 95% CI, 1.11–3.76; P .019) were associated with positive clinical impact of KT. Host immunocompromised status was not reliably associated with a positive clinical impact of KT (OR 1.03; 95% CI, 0.83–1.29; P .7806). No significant predictors of KT clinical impact were found in pediatric patients. Microbiologic result pattern was also a significant predictor of impact.

Conclusions:
Our study highlights that despite the positive clinical impact of KT in select situations, most testing results had no clinical impact. We also confirm diagnostic indications where KT may have the highest yield, thereby generating tools for diagnostic stewardship.
Demystifying China's Critical Minerals Strategies: Rethinking ‘De-risking’ Supply Chains
Authors: Zhou Weihuan , Crochet Victor , Wang Haoxue 
Published: January 2025

Abstract
‘De-risking’ is the latest buzzword in the China strategy of the United States and its allies. It means limiting dependence on and engagement with China in select strategic sectors. One of such sectors concerns critical minerals (CMs) which are essential for the ongoing green economic transition. To secure access to CMs and reduce reliance on China, the US and its allies have been developing networks for ally-shoring supply chains. A major problem with the ‘de-risking’ strategy in this regard is that it treats China as the risk and hence excludes China from the discussions and collaboration on global supply chain issues. In this paper, we argue that this strategy fails to consider China's strategies and policies regarding CMs. We therefore offer a detailed analysis of China's policies which shows that they have been primarily aimed at addressing internal challenges and policy priorities in China rather than dominating, weaponizing, or causing disruptions in global supply chains. To address supply chain risks most effectively, international collaborative frameworks should engage with, rather than exclude, China. Confrontational strategies with ‘China being the risk’ at the core might themselves be a risk by undermining rational policymaking and leading to disruptive policies.
Free Trade Agreements as Sites of Economic Diplomacy: Agreeing Common Standards for Sustainable Development
Authors: Messenger Gregory 
Published: January 2025

Abstract
In the face of ongoing disruptions to the multilateral trade regime, from deadlock at the WTO to the rise in unilateralism, this contribution examines the role that free trade agreements (FTAs) can play in supporting the adoption of common standards for sustainable development. It does this in three moves: first, it reframes the role of FTAs from sources of obligation and mechanisms of compliance to sites of economic diplomacy where governments can shape international standards through FTA structures; second, it unpacks the relationship between regulation and standards through three case studies (dolphin-safe labelling, automotive standards, and nutrient profiling), identifying means through which FTAs can be leveraged by trade policy actors; third, it draws on these lessons to examine how FTAs can support the uptake of key new standards and quasi-standards for sustainability, in this case, the ISO Net Zero Guidelines. Finally, this contribution reflects on the implications of reappraising the development of world trade law as part of the practice of economic diplomacy.
Regional Patterns of Organic Matter Export Rates Along the GEOTRACES Pacific Meridional Transect GP15
Authors: Quay Paul , Stephens Mark 
Published: January 2025

AbstractExport rates of organic matter (OM) were determined based on PO43−, NO3− and O2 budgets during GEOTRACES cruise GP15 in the Pacific Ocean that crossed subpolar, subtropical and equatorial regimes. Lowest OM export rates at 3–5 mmol C/m2/yr were found in the subtropical regions and highest rates at 9–12 mmol C/m2/yr were found in the equatorial and subpolar regions. Satellite based OM export rates showed similar regional trends but with a significantly larger range. The budget and satellite‐based OM export rates were 3–15× higher than estimates of particle loss rates based on 234Th and sediment trap collections, with the differences primarily due to non‐particle forms of OM export and different integration times of methods. The efficiency of export varied from 0.1 to 0.3, with the lowest efficiencies in the subtropics and highest efficiencies in the subpolar and equatorial regions.
Seasonal and Geomagnetic Activity Dependence of Auroral E‐Region Neutral Winds at Poker Flat
Authors: Zhan Weijia , Kaeppler Stephen R. 
Published: January 2025

AbstractIn this paper, we investigated the seasonal and geomagnetic dependence of the auroral ‐region neutral winds and the tidal components between 90 and 125 km using nearly continuously sampled measurements from the Poker Flat Incoherent Scatter Radar (PFISR) from 2010 to 2019. The average winds show consistent semidiurnal oscillations between 100 and 115 km and diurnal oscillations above 115 km in all seasons with some seasonal and geomagnetic activity dependencies. In general, the semidiurnal oscillation in zonal and meridional directions is strongest in summer and weakest in winter. The diurnal oscillation is strongest in winter and weakest in spring. More details on the seasonal and geomagnetic activity dependencies are revealed in the tidal decomposition results. Tidal decomposition results show eastward mean wind below 115 km in summer, fall, and winter and westward mean wind above 115 km in all seasons. The meridional mean is northward below 115 km and southward above in all seasons. The diurnal amplitudes are small below 110 km and increase with altitude above 110 km in all seasons with larger enhancements in the meridional direction. The semidiurnal amplitudes increase with altitude below 110 km and reach a maximum at around 110 km, then decrease or keep stable (depending on the geomagnetic activity) above 110 km in both directions and all seasons. The diurnal phases shift to earlier times with the increase of geomagnetic activity but show different variations with altitudes in zonal and meridional directions. The semidiurnal phases show a downward progressing trend in both directions and in all seasons.
Loss of ARID1A accelerates prostate tumourigenesis with a proliferative collagen-poor phenotype through co-operation with AP1 subunit cFos
Authors: Hartley Andrew , Galbraith Laura C. A. , Shaw Robin , Tibbo Amy , Veeratterapillay Rajan , Wilson Laura , Heer Rakesh , Blyth Karen , Leung Hing , Ahmad Imran 
Published: January 2025

Abstract

Background
Prostate cancer (PC) is the commonest male visceral cancer, and second leading cause of cancer mortality in men in the Western world.

Methods
Using a forward-mutagenesis Sleeping Beauty (SB) transposon-based screen in a Probasin Cre-Recombinase (Pb-Cre) Pten-deficient mouse model of PC, we identified Arid1a loss as a driver in the development of metastatic disease.

Results
The insertion of transposon in the Arid1a gene resulted in a 60% reduction of Arid1a expression, and reduced tumour free survival (SB:Pten

fl/fl

Arid1a

INT
median 226 days vs SB:Pten

fl/fl

Arid1a

WT
293 days, p = 0.02),with elevated rates of metastasis (SB:Pten

fl/fl

Arid1a

INT
75% lung metastasis rate vs 17% SB:Pten

fl/fl

Arid1a

WT
, p < 0.001). We further generated a Pb-Cre Pten- and Arid1a-deficient mouse model, in which loss of Arid1a demonstrated a profound acceleration in tumorigenesis in Pten

fl/fl
mice compared to Pten loss alone (Pb-Cre Pten

fl/fl

Arid1a

+/+
median survival of 267 days vs Pb-Cre Pten

fl/fl

Arid1a

fl/fl
103 days, p < 0.0001).

Conclusion
Our data revealed homozygous Arid1a loss is required to dramatically accelerate prostate tumourigenesis. Analysis of RNA and ChIP -Sequencing data suggests Arid1a loss enhanced the function of AP-1 subunit cFos. In clinical PC cohort, ARID1A and cFos levels stratified an aggressive subset of PC with a poor survival outcome with a median of only 30 months.
Mitochondrial KMT9 methylates DLAT to control pyruvate dehydrogenase activity and prostate cancer growth
Authors: Jia Yanhan , Wang Sheng , Urban Sylvia , Müller Judith M. , Sum Manuela , Wang Qing , Bauer Helena , Schulte Uwe , Rampelt Heike , Pfanner Nikolaus , Schüle Katrin M. , Imhof Axel , Forné Ignasi , Berlin Christopher , Sigle August , Gratzke Christian , Greschik Holger , Metzger Eric , Schüle Roland 
Published: January 2025

Abstract
Prostate cancer (PCa) growth depends on de novo lipogenesis controlled by the mitochondrial pyruvate dehydrogenase complex (PDC). In this study, we identify lysine methyltransferase (KMT)9 as a regulator of PDC activity. KMT9 is localized in mitochondria of PCa cells, but not in mitochondria of other tumor cell types. Mitochondrial KMT9 regulates PDC activity by monomethylation of its subunit dihydrolipoamide transacetylase (DLAT) at lysine 596. Depletion of KMT9 compromises PDC activity, de novo lipogenesis, and PCa cell proliferation, both in vitro and in a PCa mouse model. Finally, in human patients, levels of mitochondrial KMT9 and DLAT K596me1 correlate with Gleason grade. Together, we present a mechanism of PDC regulation and an example of a histone methyltransferase with nuclear and mitochondrial functions. The dependency of PCa cells on mitochondrial KMT9 allows to develop therapeutic strategies to selectively fight PCa.
Plasma proteomic evidence for increased β-amyloid pathology after SARS-CoV-2 infection
Authors: Duff Eugene P. , Zetterberg Henrik , Heslegrave Amanda , Dehghan Abbas , Elliott Paul , Allen Naomi , Runz Heiko , Laban Rhiannon , Veleva Elena , Whelan Christopher D. , Sun Benjamin B. , Matthews Paul M. 
Published: January 2025

Abstract
Previous studies have suggested that systemic viral infections may increase risks of dementia. Whether this holds true for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections is unknown. Determining this is important for anticipating the potential future incidence of dementia. To begin to do this, we measured plasma biomarkers linked to Alzheimer’s disease pathology in the UK Biobank before and after serology-confirmed SARS-CoV-2 infections. SARS-CoV-2 infection was associated with biomarkers associated with β-amyloid pathology: reduced plasma Aβ42:Aβ40 ratio and, in more vulnerable participants, lower plasma Aβ42 and higher plasma pTau-181. The plasma biomarker changes were greater in participants who had been hospitalized with COVID-19 or had reported hypertension previously. We showed that the changes in biomarkers were linked to brain structural imaging patterns associated with Alzheimer’s disease, lower cognitive test scores and poorer overall health evaluations. Our data from this post hoc case–control matched study thus provide observational biomarker evidence that SARS-CoV-2 infection can be associated with greater brain β-amyloid pathology in older adults. While these results do not establish causality, they suggest that SARS-CoV-2 (and possibly other systemic inflammatory diseases) may increase the risk of future Alzheimer’s disease.
Optimizing multiprocessor performance in real-time systems using an innovative genetic algorithm approach
Authors: Hassan Heba E. , Ibrahiem Khaled Hosny , Madian Ahmed H. 
Published: January 2025

Abstract
Due to its enormous influence on system functionality, researchers are presently looking into the issue of task scheduling on multiprocessors. Establishing the most advantageous schedules is often regarded as a difficult-to-compute issue. Genetic Algorithm is a recent tool employed by researchers to optimize scheduling tasks and boost performance, although this field of research is yet mostly unexplored. In this article, a novel approach for generating task schedules for real-time systems utilizing a Genetic Algorithm is proposed. The approach seeks to design task schedules for multiprocessor systems with optimal or suboptimal lengths, with the ultimate goal of achieving high performance. This research project focuses on non-preemptive independent tasks in a multiprocessor environment. All processors are assumed to be identical. We conducted a thorough analysis of the proposed approach and pitted it against three frequently utilized scheduling methodologies: the “Evolutionary Fuzzy Based Scheduling Algorithm”, the “Least Laxity First Algorithm”, and the “Earliest Deadline First Algorithm”. The Proposed Algorithm demonstrated superior efficiency and reliability compared to Earliest Deadline First, Least Laxity First, and Evolutionary Fuzzy-based Scheduling Algorithm. It consistently achieved zero missed deadlines and the lowest average response and turnaround times across all scenarios, maintaining optimal performance even under high load conditions.
Cross-talk-free, high extinction ratio, and ultra-compact all‑optical 4 × 2 encoder using graphene-based plasmonic waveguides
Authors: Kanwal Saima , Saeed Mohammed R. , AL-Shammri Faris K. , Rezaei Mir Hamid 
Published: January 2025

Abstract
This paper presents an all-optical 4 × 2 encoder based on graphene-plasmonic waveguides for operation in the wavelength range of 8–12 μm. The basic plasmonic waveguide consists of a silicon (Si) strip and a graphene sheet supported by two dielectric ridges. Surface plasmon polaritons (SPPs) are stimulated in the spatial gap between the graphene sheet and the Si strip. The effect of geometric parameters and chemical potential of the graphene sheet changes on the suggested waveguide’s waveguiding behavior is meticulously investigated using the three-dimensional finite-difference time-domain (3D-FDTD) method. The encoder comprises a straight waveguide to detect the state of the In0 input and two Y-combiners with outputs Out0 and Out1 to detect the state of the In1, In2, and In3 inputs. The encoder exhibits a minimum extinction ratio (ER

min
) of 19 dB at a wavelength of 10 μm. In addition, the cross-talk (CT) and insertion loss (IL) values are −21.3 and −1.31 dB, respectively. The encoder offers an ultra-compact structure with a total footprint of 4.25 μm2. Due to its exceptional waveguiding features, low CT and IL values, and high ER

min
, the proposed encoder holds promise for various communication and signal processing applications.
Adaptive hybrid virtual inertia controller for PMSG-based wind turbine based on fuzzy logic control
Authors: Hosny Mohamed , Marei Mostafa I. , Mohamad Ahmed M.I. 
Published: January 2025

Abstract
The integration of renewable energy sources into microgrids presents some challenges due to the decreased system overall inertia associated with the presence of converter -based sources. To overcome this issue and to enhance the system inertia, various concepts for virtual inertial control have been proposed in the literature. However, the concept of improving the system frequency through wind turbines has gained widespread acceptance. Several frequency support techniques have been proposed recently. However, conventional virtual inertia controllers may not satisfy the performance requirements in terms of frequency nadir and rate of change of frequency (ROCOF) over a wide range of microgrid operating conditions. This paper proposes a hybrid adaptive virtual inertia control strategy based on Fuzzy logic. The hybrid strategy integrates kinetic energy based virtual inertia control and virtual capacitance control schemes. The gains of both KE based virtual inertia control loop and virtual capacitance control loop are adapted simultaneously to enhance frequency support of low inertia microgrid under wide range of renewable energy sources (RES) disturbances and load changes. Different case studies are simulated on MATLAB/ Simulink to evaluate the dynamic performance of the proposed adaptive hybrid virtual inertia strategy under different conditions.
Radial X-ray profiles of simulated galaxies
Authors: Vladutescu-Zopp S. , Biffi V. , Dolag K. 
Published: January 2025

Context. Theoretical models of structure formation predict the presence of a hot gaseous atmosphere around galaxies. While this hot circumgalactic medium (CGM) has been observationally confirmed through UV absorption lines, the detection of its direct X-ray emission remains scarce. Recent results from the eROSITA collaboration have claimed the detection of the CGM out to the virial radius for a stacked sample of Milky Way-mass galaxies.
Aims. We investigate theoretical predictions of the intrinsic CGM X-ray surface brightness (SB) using simulated galaxies and connect them to their global properties, such as the gas temperature, hot gas fraction, and stellar mass.
Methods. We selected a sample of central galaxies from the ultra-high-resolution cosmological volume (48 cMpc h−1) of the Magneticum Pathfinder set of hydrodynamical cosmological simulations. We classified them as star-forming (SF) or quiescent (QU) based on their specific star formation rate (SFR). For each galaxy, we generated X-ray mock data using the X-ray photon simulator PHOX, from which we obtained SB profiles out to the virial radius for different X-ray emitting components; namely, gas, active galactic nuclei (AGNs), and X-ray binaries (XRBs). We fit a β-profile to the gas component of each galaxy and observed trends between its slope and global quantities of the simulated galaxy.
Results. We found marginal differences among the average total SB profile in SF and QU galaxies beyond r > 0.05 Rvir. The relative contribution from hot gas exceeds 70% and is non-zero (≲10%) for XRBs in both galaxy types. At small radii (r < 0.05 Rvir), XRBs dominate the SB profile over the hot gas for QU galaxies. We found positive correlations between the galaxies’ global properties and the normalization of their SB profiles. The fitted β-profile slope is correlated with the total gas luminosity, which, in turn, shows strong connections to the current accretion rate of the central supermassive black hole (SMBH). We found the halo scaling relations to be consistent with the literature.
COmoving Computer Acceleration (COCA): N-body simulations in an emulated frame of reference
Authors: Bartlett Deaglan J. , Chiarenza Marco , Doeser Ludvig , Leclercq Florent 
Published: January 2025

Context.N-body simulations are computationally expensive and machine learning (ML) based emulation techniques have thus emerged as a way to increase their speed. Surrogate models are indeed fast, however, they are limited in terms of their trustworthiness due to potentially substantial emulation errors that current approaches are not equipped to correct.
Aims. To alleviate this problem, we have introduced COmoving Computer Acceleration (COCA), a hybrid framework interfacing ML algorithm with an N-body simulator. The correct physical equations of motion are solved in an emulated frame of reference, so that any emulation error is corrected by design. Thus, we are able to find a solution for the perturbation of particle trajectories around the ML solution. This approach is computationally cheaper than obtaining the full solution and it is guaranteed to converge to the truth as the number of force evaluations is increased.
Methods. Even though it is applicable to any ML algorithm and N-body simulator, we assessed this approach in the particular case of particle-mesh (PM) cosmological simulations in a frame of reference predicted by a convolutional neural network. In such cases, the time dependence is encoded as an additional input parameter to the network.
Results. We find that COCA efficiently reduces emulation errors in particle trajectories, requiring far fewer force evaluations than running the corresponding simulation without ML. As a consequence, we were able to obtain accurate final density and velocity fields for a reduced computational budget. We demonstrate that this method exhibits robustness when applied to examples outside the range of the training data. When compared to the direct emulation of the Lagrangian displacement field using the same training resources, COCA’s ability to correct emulation errors results in more accurate predictions.
Conclusions. Therefore, COCA makes N-body simulations cheaper by skipping unnecessary force evaluations, while still solving the correct equations of motion and correcting for emulation errors made by ML.