bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Measures of the Core Microbiome
Authors: Bewick Sharon Anne , Camper Benjamin Thomas 
Published: October 2024

AbstractBackgroundA fundamental concept in microbial ecology is the ‘core microbiome.’ Typically, core microbiomes are defined as the microbial taxa, genes, or functions shared by a threshold number of microbiome samples from a particular type of habitat (e.g., a particular type of host or a particular type of environment/ecosystem). In defining the core microbiome, the goal is to capture the portion of the microbial community that is conserved across samples from the focal habitat. Recently, there has been growing interest in developing methods to better characterize core microbiomes. As a result, numerous occurrence- and abundance-based measures have been defined. However, none have included phylogenetically aware metrics for analyzing core microbiomes.ResultsIn this paper, we develop the concept of the ‘core community phylogeny’ – a phylogeny where branches are selected based on their presence in multiple samples from a single type of habitat. We then use the core community phylogeny to define phylogenetic metrics for the diversity of core microbiomes from a single type of habitat, for turnover between core microbiomes from two different types of habitat, and for shared diversity across core microbiomes from two or more different types of habitat. As compared to non-phylogenetic metrics, our phylogenetic metrics show greater consistency across taxonomic rank and less sensitivity to strain variation across microbiome samples. Thus, our metrics address key challenges in the interpretation of core microbiomes.ConclusionsWe provide a phylogenetic framework for characterizing and comparing core microbiomes. Importantly, the methods that we propose allows integration of microbiome properties across taxonomic rank. Ultimately, this will provide both a more consistent picture of the core microbiome, as well as novel biological insight into the conserved components of microbial communities.
Double-stranded DNA reduces dsRNA degradation in the saliva and significantly enhanced RNAi-mediated gene silencing inHalyomorpha halys
Authors: Amineni Venkata Partha Sarathi , Petschenka Georg , Koch Aline 
Published: October 2024

AbstractThe invasive pestHalyomorpha halys(Hemiptera: Pentatomidae) poses a significant threat to agriculture, necessitating effective control methods beyond chemical pesticides. Our research explores RNA interference (RNAi) as a targeted gene silencing approach forH. halyspopulation management. However, the variable efficacy of RNAi across insect orders, particularly in hemipteran insects likeH. halys, poses challenges. Ex vivo degradation assays revealed rapid degradation of double-stranded RNA (dsRNA) inH. halys(Hh) saliva and extracts of salivary glands across several growth stages, attributed to the high expression of the DNA/RNA non-specific nuclease (HhNSE). A key discovery from our research was that double-stranded DNA (dsDNA) can act as a protective agent, increasing the stability of dsRNA in saliva probably by competitive inhibition ofHhNSE. Based on the well-established lethality of silencing the gene encoding the heavy chain of clathrin (HhCHC) in insects, this gene was chosen as a target to test the functionality of our dsDNA-based formulation for enhancing dsRNA-mediated gene silencing. Our in-vivo experiments showed increasedHhCHCsilencing after 72 hours of feeding initiation with a mixture of dsRNA-CHC and dsDNA, as opposed to dsRNA alone. This discovery indicates potential for enhancing the efficiency of orally delivered dsRNA through formulations based on dsDNA. Although the injection of dsRNA-CHC resulted in near-total mortality, the dsDNA formulation did not significantly enhance mortality rates when fed together with dsRNA-CHC. This emphasises the necessity for further investigation into additional factors beyond nuclease activity, such as the understanding of dsRNA uptake and release mechanisms within the gut epithelial cells ofH. halys. Nevertheless, our study opens avenues for developing cost-effective formulations to enhance RNAi efficacy inH. halysand perhaps other insects where nucleases hinder dsRNA delivery, representing a promising solution for sustainable pest control.Graphical Abstract
Assessment of a high-throughput mass spectrometry method to accelerate biomarker discovery in clinical cancer cohorts using volumetric absorptive microsampling (VAMS) devices
Authors: Lucas N. , Hill C. , Pascovici D. , McMahon R. , Herbert B. , Karsten E. 
Published: October 2024

AbstractIdentification of biomarkers of early-stage disease typically requires analysis of very large cohorts which can only be reasonably achieved using high-throughput methods. We have developed and optimised novel methods for whole blood analysis using volumetric absorptive microsampling devices to produce over 3000 protein identifications by LCMS on a Q Exactive HF-X Orbitrap. These methods were tested using a set of whole blood samples from lung cancer patients and matching healthy controls finding 455 differentially expressed proteins, using a mid-throughput method enabling analysis of 18 samples per day. To increase throughput for larger clinical cohorts, a 60-sample per day method was tested on a Sciex ZenoTOF 7600. The high-throughput method produced 1.5-fold fewer protein identifications and a higher overall % CV compared to the mid-throughput method. Despite the lower numbers, it produced a set of 36 disease-relevant and discriminatory differentially expressed proteins that, using a machine learning model, could differentiate between the disease and control samples with an area under the ROC curve (AUC) of 88.9% using random forest algorithms. These data support the use of high-throughput mass spectrometry methods to screen large cohorts for diagnostic biomarkers that can then be followed up with more targeted analyses.
2022 Sudan Ebolavirus Outbreak in Uganda: Modelling Case Burden and Outbreak Duration
Authors: Bisanzio Donal , Bosa Henry Kyobe , Bakamutumaho Barnabas , Nasimiyu Carolyne , Atwine Diana , Kyabayinze Daniel , Olaro Charles , Breiman Robert F. , Njenga M. Kariuki , Mwebesa Henry , Aceng Jane Ruth , Reithinger Richard 
Published: October 2024

ABSTRACTIn September 2022, an outbreak of Sudan virus (SUDV) was confirmed in Uganda. Following the first case report, we developed an individual based modelling platform (IBM-SUDV) to estimate the burden of cases and deaths, as well as the duration of the unfolding SUDV outbreak, using different scenarios. Modelled projections were within the range of cases and deaths ultimately observed.
The impact of non-pharmaceutical interventions on early-stage COVID-19 epidemic dynamics in rural communities in the United States
Authors: Alahakoon Punya , Taylor Peter G. , McCaw James M. 
Published: October 2024

AbstractCOVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected millions of people around the globe. We study the spread of SARS-CoV-2 across six rural counties in North and South Dakota in the United States. The study period is from early March 2020 to mid-June 2021, from near the onset of the pandemic to just before the arrival of theDeltavariant in the United States. We model the transmission dynamics in each county using a stochastic compartmental model and analyse the data within a Bayesian hierarchical statistical framework. We estimate the model parameters and characterise the effects of non-pharmaceutical interventions (NPIs) implemented at the time. Counterfactual analyses in which NPIs were lifted earlier indicate that notified cases may have increased by up to 51% in the case of low NPI stringency levels with potential additional deaths. Our study underscores the importance of timely public health measures and compliance with them. From a methodological perspective, our study demonstrates that despite the inherent high variability in epidemic behaviour in small rural communities, the combination of stochastic modelling and application of Bayesian hierarchical analyses can support the quantitative evaluation of the impact of public health measures in small low population density communities.
Knowledge and representations of the placenta in a French population of womenpost-partum
Authors: Riquet Sébastien , Busca Jade , Zakarian Carole , Le Coz Pierre , Mege Jean-Louis , Mezouar Soraya 
Published: October 2024

AbstractIn many cultures, the placenta is considered to be the twin brother, counselor or guardian angel of the baby throughout pregnancy and is the subject of many beliefs and practices. In France, it is better known from a biomedical point of view including the protocols related to its disposal as biomedical waste in the hospital environment. Our study aims to evaluate the knowledge and representations of the placenta before being discarded by health personnel who assisted the parturient at birth. Our results show a lack of knowledge and misconceptions about the placenta and its different functions. Nevertheless, mothers consider it essential to their children’s development and are ready to give it to science "if it can help" once the birth is complete. Information and documentation on the placenta among pregnant women are necessary for better management of childbirth and practices, especially for mothers who wish to give birth at home or in a delivery center.
Fast and accurate algorithm for calculating long-baseline neutrino oscillation probabilities with matter effects
Authors: Denton Peter B. , Parke Stephen J. 
Published: October 2024

Neutrino oscillation experiments will be entering the precision era in the next decade with the advent of high statistics experiments like DUNE, HK, and JUNO. Correctly estimating the confidence intervals from data for the oscillation parameters requires very large Monte Carlo datasets involving calculating the oscillation probabilities in matter many, many times. In this paper, we leverage past work to present a new, fast, precise technique for calculating neutrino oscillation probabilities in matter optimized for long-baseline neutrino oscillations in the Earth’s crust including both accelerator and reactor experiments. For ease of use by theorists and experimentalists, we provide fast ++ and codes .

Published by the American Physical Society
2024
First lattice QCD calculation of
J/ψ
semileptonic decay containing
D
and
Ds
particles
Authors: Meng Yu , Dang Jin-Long , Liu Chuan , Tuo Xin-Yu , Yan Haobo , Yang Yi-Bo , Zhang Ke-Long 
Published: October 2024

We perform the first lattice calculation on the semileptonic decay of J/ψ using the (2+1)-flavor Wilson-clover gauge ensembles generated by CLQCD collaboration. Three gauge ensembles with different lattice spacings, from 0.0519 to 0.1053 fm, and pion masses, mπ∼300  MeV, are utilized. After a naive continuum extrapolation using three lattice spacings, we obtain Br(J/ψ→Dseνe)=1.90(6)(5)Vcs×10−10 and Br(J/ψ→Deνe)=1.21(6)(9)Vcd×10−11, where the first errors are statistical, and the second come from the uncertainties of Cabibbo-Kobayashi-Maskawa matrix element Vcs(d). The ratios of the branching fractions between lepton μ and e are also calculated as RJ/ψ(Ds)=0.97002(8) and RJ/ψ(D)=0.97423(15) after performing a continuum limit including only a2 term. The ratios provide necessary theoretical support for the future experimental test of lepton flavor universality.

Published by the American Physical Society
2024
Inferring geometrical dynamics of cell nucleus translocation
Authors: Amiri Sirine , Zhang Yirui , Gerardos Andonis , Sykes Cécile , Ronceray Pierre 
Published: October 2024

The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller than their nucleus, a mechanism that is not yet understood. Here, we propose a methodological framework to observe, quantify, and model this phenomenon through a data-driven approach using microfluidic devices where cells migrate through controlled narrow spaces of sizes comparable to the ones encountered in physiological situations. Stochastic force inference is applied to experimental nuclear trajectories and nuclear shape descriptors, resulting in equations that effectively describe the kinematics of this phenomenon. By employing a model where the channel geometry is an explicit parameter and by training it over experimental data with different sizes of constrictions, we ensure that the resulting equations are predictive. Altogether, the approach developed here paves the way for a mechanistic and quantitative description of dynamical cell complexity during its motility.

Published by the American Physical Society
2024
Quantum algorithm for dynamic mode decomposition integrated with a quantum differential equation solver
Authors: Mizuno Yuta , Komatsuzaki Tamiki 
Published: October 2024

We present a quantum algorithm that analyzes time series data simulated by a quantum differential equation solver. The proposed algorithm is a quantum version of a dynamic mode decomposition algorithm used in diverse fields such as fluid dynamics, molecular dynamics, and epidemiology. Our quantum algorithm can also compute matrix eigenvalues and eigenvectors by analyzing the corresponding linear dynamical system. Our algorithm handles a broad range of matrices, particularly those with complex eigenvalues. The complexity of our quantum algorithm is O(polylogN) for an N-dimensional system. This is an exponential speedup over known classical algorithms with at least O(N) complexity. Thus, our quantum algorithm is expected to enable high-dimensional dynamical systems analysis and large matrix eigenvalue decomposition, intractable for classical computers.

Published by the American Physical Society
2024
Interfacial Exciton-Polaron Quenching in Organic Light-Emitting Diodes
Authors: Yang Kwangmo , Kwon Doyoun , Nam Sungho , Kim Joonghyuk , Chung Yeon Sook , Yoo Hyunjoon , Park Insung , Park Yongsup , Kim Ji Whan , Lee Jaesang 
Published: October 2024

In organic light-emitting diodes (OLEDs), understanding the efficiency loss mechanism known as exciton-polaron quenching (EPQ) has been a longstanding challenge. Traditionally, EPQ was believed to occur mainly the bulk of the OLED emission layer (EML) due to the coexistence of polarons and excitons, limiting our understanding of its full impact. Here, we report a previously overlooked phenomenon termed “interfacial EPQ (Inf. EPQ),” which occurs at the heterointerface between the EML and the adjacent charge transport layer (CTL). We observe the transfer of EML excitons to CTL polarons across this interface, spanning distances of up to 4 nm. Notably, Inf. EPQ exceeds EPQ within the EML bulk, even in devices with a interfacial energy barrier (>0.2  eV). We propose a methodology that enables independent probing of Inf. EPQ, systematic validation of its essential parameters, and the identification of Dexter energy transfer as its governing mechanism. Importantly, our findings highlight Inf. EPQ as a phenomenon across devices with various luminescent mechanisms, wavelengths, and injection levels. By effectively addressing Inf. EPQ, we achieve efficiency enhancements in red, green, and blue phosphorescent OLEDs, by 70%±8%, 47%±5%, and 66%±6%, respectively. Our work advances the physical understanding of exciton and polaron dynamics at organic heterointerfaces, providing applicable solutions to Inf. EPQ-related issues in practical devices.

Published by the American Physical Society
2024
Nanometer-Scale Acoustic Wave Packets Generated by Stochastic Core-Level Photoionization Events
Authors: Huang Yijing , Sun Peihao , Teitelbaum Samuel W. , Li Haoyuan , Sun Yanwen , Wang Nan , Song Sanghoon , Sato Takahiro , Chollet Matthieu , Osaka Taito , Inoue Ichiro , Duncan Ryan A. , Shin Hyun D. , Haber Johann , Zhou Jinjian , Bernardi Marco , Gu Mingqiang , Rondinelli James M. , Trigo Mariano , Yabashi Makina , Maznev Alexei A. , Nelson Keith A. , Zhu Diling , Reis David A. 
Published: October 2024

We demonstrate that the absorption of femtosecond hard x-ray pulses excites quasispherical, high-amplitude, and high-wave-vector coherent acoustic phonon wave packets using an all hard-x-ray pump-probe scattering experiment. The time- and momentum-resolved diffuse scattering signal is consistent with an ensemble of 3D strain wave packets induced by the rapid electron cascade dynamics following photoionization at uncorrelated excitation centers. We quantify key parameters of this process, including the localization size of the stress field and the photon energy conversion efficiency into elastic energy. The parameters are determined by the photoelectron and Auger electron cascade dynamics, as well as the electron-phonon interaction. In particular, we obtain the localization size of the observed strain wave packet to be 1.5 and 2.5 nm for bulk SrTiO3 and KTaO3 single crystals, respectively. The results provide crucial information on the mechanism of x-ray energy deposition into matter and shed light on the shortest collective length scales accessible to coherent acoustic phonon generation using x-ray excitation.

Published by the American Physical Society
2024
Examining the green sourcing behavior from the cross-national perspective
Authors: Min Hokey 
Published: October 2024

PurposeRecognizing the growing role of green sourcing in a supply chain ecosystem, this paper identifies the most common business practices that make green sourcing more successful and then examines the ramifications of green sourcing practices from cost, ecological and cultural perspectives based on cross-national surveys of both Korean and US firms.Design/methodology/approachAfter conducting the questionnaire surveys in Korea and the US, we analyzed the results by running a series of binary logistics regression, ordinal regression, canonical correlation, discriminant analyses and chi-square tests of independence and cross-tabulation. These statistical data analyses were also used to test a number of hypotheses and validate the proposed theories.FindingsAnalyses of these results revealed significant differences in green sourcing practices between Korean and US firms in that US firms tended to make more substantial commitments to green sourcing than Korean firms. For instance, Korean firms viewed the supplier’s advances in providing eco-friendly packages and goods as the most important attribute for their green supplier selection. In contrast, the US firms prioritized the supplier’s capability to handle hazardous waste disposal and compliance with federal and state environmental regulations in their green supplier selection.Originality/valueThis paper is one of a few studies that expanded the research scope from cross-national and/or cultural perspectives and empirically identified idiosyncrasies unique to the national origin of buying firms that explored green-sourcing initiatives, which aim to reduce the carbon footprints of supply chain activities and minimize unnecessary waste. This paper is also one of the first studies to build a theoretical foundation for worldwide green sourcing practices predicated on institutional and Edgar Schein theories.
Tohoku resilient schools and youth engagement in memory after 2011 tsunami
Authors: Grau Vila Carmen 
Published: October 2024

PurposeIn 2011, a disaster devastated the Tohoku region in Japan and left more than 15,000 victims. However, there could have been more. School buildings became a center of response and evacuation during the emergency, playing a central role in each disaster phase. How did the schools manage the situation in small Japanese communities and what lessons can be drawn? Disaster prevention education and training, rapid evacuation, survival in shelters and transmission of experiences to future generations are the key to disaster management in Japan. In the Tohoku area, these lessons are also connected with the history and memory of previous tsunamis.Design/methodology/approachFrom a local approach and socio-historical methodology, research is based on ethnographic fieldwork in disaster-affected communities, archival data collection and oral testimonies. Between November 2020 and March 2023, in-depth interviews were conducted with tsunami survivors, children and community leaders involved in disaster response during the months and years following the tsunami. The analysis focuses on disaster response in schools, survival and building capacities of youth during reconstruction through six case studies.FindingsThis research determines the importance of local history in tsunami management in Tohoku. It offers practical examples from each disaster phase for individuals and communities to face disasters and foster resilience. It reveals, on the other hand, how during the reconstruction process, a young generation embraced memory to reinforce disaster prevention for the future of the region.Originality/valueHighlighting the importance of including children and youth in disaster response, reconstruction and memory through applicable cases, this study provides a guide of school experiences in Japan that can become global lessons for disaster risk reduction (DRR).