bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Depth Measurements From Gaging Stations With Image Archives for Spectrally Based Remote Sensing of River Bathymetry
Authors: Legleiter Carl J. , Overstreet Brandon T. , Kinzel Paul J. 
Published: July 2024

AbstractRemote sensing can be an effective tool for mapping river bathymetry, but the need for direct measurements to calibrate image‐derived depth estimates impedes broader application of this approach. One way to circumvent the need for field campaigns dedicated to calibration is to capitalize upon existing data. In this study, we introduce a framework for Bathymetric Mapping using Gage Records and Image Databases (BaMGRID). This workflow involves retrieving depth measurements made during gaging station site visits, downloading archived multispectral images, and then combining these two data sets to establish a relationship between depth and reflectance. We developed a processing chain that involves using application programming interfaces to obtain both depth measurements made during site visits and images centered on the gage and then linking depth to reflectance via an optimal band ratio analysis (OBRA) algorithm modified for small sample sizes. Applying this workflow to selected gages within two river basins indicated that depth retrieval from multispectral satellite images could be highly accurate, but with variable results from one image to the next at a given site. High resolution aerial photography was less conducive to bathymetric mapping in one of the basin considered. Of the four predictors of depth retrieval performance we evaluated (mean and standard deviation of depth, width, and an index of water clarity), only width was consistently significantly correlated with OBRA R2 (p < 0.026). Currently, BaMGRID is best‐suited for site‐by‐site analysis to support practical applications at the reach scale; continuous, basin‐wide mapping of river bathymetry will require additional research.
Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity
Authors: Visuthranukul Chonnikant , Sriswasdi Sira , Tepaamorndech Surapun , Chamni Supakarn , Leelahavanichkul Asada , Joyjinda Yutthana , Aksornkitti Vitavat , Chomtho Sirinuch 
Published: July 2024

Abstract
Background and objectives
Gut dysbiosis that resulted from the alteration between host-microbe interaction might worsen obesity-induced systemic inflammation. Gut microbiota manipulation by supplementation of prebiotic inulin may reverse metabolic abnormalities and improve obesity. This study aimed to determine whether inulin supplementation improved intestinal microbiota and microbial functional pathways in children with obesity.

Methods
Children with obesity whose BMI above median + 2SDs were recruited to a randomized, double-blinded placebo-controlled study. The participants aged 7–15 years were assigned to inulin supplement extracted from Thai Jerusalem artichoke (intervention), maltodextrin (placebo), and dietary fiber advice groups. All participants received similar monthly conventional advice and follow-up for 6 months. Fecal samples were collected for gut microbiome analysis using 16S rRNA sequencing. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was performed to infer microbial functional pathways.

Results
One hundred and forty-three children with available taxonomic and functional pathway abundance profiles were evaluated. A significant increase in alpha-diversity was observed in the inulin group. Inulin supplementation substantially enhanced Bifidobacterium, Blautia, Megasphaera, and several butyrate-producing bacteria, including Agathobacter, Eubacterium coprostanoligenes, and Subdoligranulum, compared to the other groups. The inulin group showed a significant difference in functional pathways of proteasome and riboflavin metabolism. These changes correlated with clinical and metabolic outcomes exclusively in the inulin group.

Conclusions
Inulin supplementation significantly promoted gut bacterial diversity and improved gut microbiota dysbiosis in children with obesity. The modulation of functional pathways by inulin suggests its potential to establish beneficial interactions between the gut microbiota and host physiology. Inulin supplementation could be a strategic treatment to restore the balance of intestinal microbiota and regulate their functions in childhood obesity.
Electrothermal mineralization of per- and polyfluoroalkyl substances for soil remediation
Authors: Cheng Yi , Deng Bing , Scotland Phelecia , Eddy Lucas , Hassan Arman , Wang Bo , Silva Karla J. , Li Bowen , Wyss Kevin M. , Ucak-Astarlioglu Mine G. , Chen Jinhang , Liu Qiming , Si Tengda , Xu Shichen , Gao Xiaodong , JeBailey Khalil , Jana Debadrita , Torres Mark Albert , Wong Michael S. , Yakobson Boris I. , Griggs Christopher , McCary Matthew A. , Zhao Yufeng , Tour James M. 
Published: July 2024

AbstractPer- and polyfluoroalkyl substances (PFAS) are persistent and bioaccumulative pollutants that can easily accumulate in soil, posing a threat to environment and human health. Current PFAS degradation processes often suffer from low efficiency, high energy and water consumption, or lack of generality. Here, we develop a rapid electrothermal mineralization (REM) process to remediate PFAS-contaminated soil. With environmentally compatible biochar as the conductive additive, the soil temperature increases to >1000 °C within seconds by current pulse input, converting PFAS to calcium fluoride with inherent calcium compounds in soil. This process is applicable for remediating various PFAS contaminants in soil, with high removal efficiencies ( >99%) and mineralization ratios ( >90%). While retaining soil particle size, composition, water infiltration rate, and cation exchange capacity, REM facilitates an increase of exchangeable nutrient supply and arthropod survival in soil, rendering it superior to the time-consuming calcination approach that severely degrades soil properties. REM is scaled up to remediate soil at two kilograms per batch and promising for large-scale, on-site soil remediation. Life-cycle assessment and techno-economic analysis demonstrate REM as an environmentally friendly and economic process, with a significant reduction of energy consumption, greenhouse gas emission, water consumption, and operation cost, when compared to existing soil remediation practices.
Anomalous friction of supercooled glycerol on mica
Authors: Lizée Mathieu , Coquinot Baptiste , Mariette Guilhem , Siria Alessandro , Bocquet Lydéric 
Published: July 2024

AbstractAlthough friction of liquids on solid surfaces is traditionally linked to wettability, recent works have unveiled the role of the solid’s internal excitations on interfacial dissipation. In order to directly evidence such couplings, we take advantage of the considerable variation of the molecular timescales of supercooled glycerol under mild change of temperature to explore how friction depends on the liquid’s molecular dynamics. Using a dedicated tuning-fork AFM, we measure the slippage of glycerol on mica. We report a 100 fold increase of slip length upon cooling, while liquid-solid friction exhibits a linear scaling with molecular relaxation rate at high temperature. This scaling can be explained by a contribution of mica’s phonons which resonate with density fluctuations in the liquid, allowing efficient momentum transfer to mica. These results suggest that engineering phononic spectra of materials could enhance flow performance in nanofluidic channels and industrially relevant membranes.
Reversible metal cluster formation on Nitrogen-doped carbon controlling electrocatalyst particle size with subnanometer accuracy
Authors: Timoshenko Janis , Rettenmaier Clara , Hursán Dorottya , Rüscher Martina , Ortega Eduardo , Herzog Antonia , Wagner Timon , Bergmann Arno , Hejral Uta , Yoon Aram , Martini Andrea , Liberra Eric , Monteiro Mariana Cecilio de Oliveira , Cuenya Beatriz Roldan 
Published: July 2024

AbstractCopper and nitrogen co-doped carbon catalysts exhibit a remarkable behavior during the electrocatalytic CO2 reduction (CO2RR), namely, the formation of metal nanoparticles from Cu single atoms, and their subsequent reversible redispersion. Here we show that the switchable nature of these species holds the key for the on-demand control over the distribution of CO2RR products, a lack of which has thus far hindered the wide-spread practical adoption of CO2RR. By intermitting pulses of a working cathodic potential with pulses of anodic potential, we were able to achieve a controlled fragmentation of the Cu particles and partial regeneration of single atom sites. By tuning the pulse durations, and by tracking the catalyst’s evolution using operando quick X-ray absorption spectroscopy, the speciation of the catalyst can be steered toward single atom sites, ultrasmall metal clusters or large metal nanoparticles, each exhibiting unique CO2RR functionalities.
Modelling of negative equivalent magnetic reluctance structure and its application in weak-coupling wireless power transmission
Authors: Chen Yuanxi , Niu Shuangxia , Fu Weinong , Lin Hongjian 
Published: July 2024

AbstractIn weak-coupling wireless power transmission, increasing operating frequency, and incorporating metamaterials, resonance structures or ferrite cores have been explored as effective solutions to enhance power efficiency. However, these solutions present significant challenges that need to be addressed. The increased operating frequency boosts ferrite core losses when it exceeds the working frequency range of the material. Existing metamaterial-based solutions present challenges in terms of requiring additional space for slab installation, resulting in increased overall size. In addition, limitations are faced in using Snell’s law for explaining the effects of metamaterial-based solutions outside the transmission path, where the magnetic field can not be reflected or refracted. To address these issues, in this work, the concept of a negative equivalent magnetic reluctance structure is proposed and the metamaterial theory is extended with the proposed magnetic reluctance modelling method. Especially, the negative equivalent magnetic reluctance structure is effectively employed in the weak-coupling wireless power transfer system. The proposed negative equivalent magnetic reluctance structure is verified by the stacked negative equivalent magnetic reluctance structure-based transformer experiments and two-coil mutual inductance experiments. Besides, the transmission gain, power experiments and loss analysis experiments verify the effectiveness of the proposed structure in the weak-coupling wireless power transfer system.
An 8000 years old genome reveals the Neolithic origin of the zoonosis Brucella melitensis
Authors: L’Hôte Louis , Light Ian , Mattiangeli Valeria , Teasdale Matthew D. , Halpin Áine , Gourichon Lionel , Key Felix M. , Daly Kevin G. 
Published: July 2024

AbstractBrucella melitensis is a major livestock bacterial pathogen and zoonosis, causing disease and infection-related abortions in small ruminants and humans. A considerable burden to animal-based economies today, the presence of Brucella in Neolithic pastoral communities has been hypothesised but we lack direct genomic evidence thus far. We report a 3.45X B. melitensis genome preserved in an ~8000 year old sheep specimen from Menteşe Höyük, Northwest Türkiye, demonstrating that the pathogen had evolved and was circulating in Neolithic livestock. The genome is basal with respect to all known B. melitensis and allows the calibration of the B. melitensis speciation time from the primarily cattle-infecting B. abortus to approximately 9800 years Before Present (BP), coinciding with a period of consolidation and dispersal of livestock economies. We use the basal genome to timestamp evolutionary events in B. melitensis, including pseudogenization events linked to erythritol response, the supposed determinant of the pathogen’s placental tropism in goats and sheep. Our data suggest that the development of herd management and multi-species livestock economies in the 11th–9th millennium BP drove speciation and host adaptation of this zoonotic pathogen.
Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations
Authors: Besedina Elizaveta , Supek Fran 
Published: July 2024

AbstractCancer driver genes can undergo positive selection for various types of genetic alterations, including gain-of-function or loss-of-function mutations and copy number alterations (CNA). We investigated the landscape of different types of alterations affecting driver genes in 17,644 cancer exomes and genomes. We find that oncogenes may simultaneously exhibit signatures of positive selection and also negative selection in different gene segments, suggesting a method to identify additional tumor types where an oncogene is a driver or a vulnerability. Next, we characterize the landscape of CNA-dependent selection effects, revealing a general trend of increased positive selection on oncogene mutations not only upon CNA gains but also upon CNA deletions. Similarly, we observe a positive interaction between mutations and CNA gains in tumor suppressor genes. Thus, two-hit events involving point mutations and CNA are universally observed regardless of the type of CNA and may signal new therapeutic opportunities. An analysis with focus on the somatic CNA two-hit events can help identify additional driver genes relevant to a tumor type. By a global inference of point mutation and CNA selection signatures and interactions thereof across genes and tissues, we identify 9 evolutionary archetypes of driver genes, representing different mechanisms of (in)activation by genetic alterations.
Self-powered and speed-adjustable sensor for abyssal ocean current measurements based on triboelectric nanogenerators
Authors: Pan Yuan Chao , Dai Zhuhang , Ma Haoxiang , Zheng Jinrong , Leng Jing , Xie Chao , Yuan Yapeng , Yang Wencai , Yalikun Yaxiaer , Song Xuemei , Han Chang Bao , Shang Chenjing , Yang Yang 
Published: July 2024

AbstractThe monitoring of currents in the abyssal ocean is an essential foundation of deep-sea research. The state-of-the-art current meter has limitations such as the requirement of a power supply for signal transduction, low pressure resistance, and a narrow measurement range. Here, we report a fully integrated, self-powered, highly sensitive deep-sea current measurement system in which the ultra-sensitive triboelectric nanogenerator harvests ocean current energy for the self-powered sensing of tiny current motions down to 0.02 m/s. Through an unconventional magnetic coupling structure, the system withstands immense hydrostatic pressure exceeding 45 MPa. A variable-spacing structure broadens the measuring range to 0.02–6.69 m/s, which is 67% wider than that of commercial alternatives. The system successfully operates at a depth of 4531 m in the South China Sea, demonstrating the record-deep operations of triboelectric nanogenerator-based sensors in deep-sea environments. Our results show promise for sustainable ocean current monitoring with higher spatiotemporal resolution.
International survey on invasive lobular breast cancer identifies priority research questions
Authors: Oesterreich Steffi , Pate Leigh , Lee Adrian V. , Chen Fangyuan , Jankowitz Rachel C. , Mukhtar Rita , Metzger Otto , Sikora Matthew J. , Li Christopher I. , Sotiriou Christos , Shah Osama S. , Koorman Thijs , Ulaner Gary , Reis-Filho Jorge S. , Davidson Nancy M. , Van Baelen Karen , Hutcheson Laurie , Freeney Siobhan , Migyanka Flora , Turner Claire , Derksen Patrick , Bear Todd , Desmedt Christine 
Published: July 2024

AbstractThere is growing awareness of the unique etiology, biology, and clinical presentation of invasive lobular breast cancer (ILC), but additional research is needed to ensure translation of findings into management and treatment guidelines. We conducted a survey with input from breast cancer physicians, laboratory-based researchers, and patients to analyze the current understanding of ILC, and identify consensus research questions. 1774 participants from 66 countries respondents self-identified as clinicians (N = 413), researchers (N = 376), and breast cancer patients and advocates (N = 1120), with some belonging to more than one category. The majority of physicians reported being very/extremely (41%) to moderately (42%) confident in describing the differences between ILC and invasive breast cancer of no special type (NST). Knowledge of histology was seen as important (73%) and as affecting treatment decisions (51%), and most agreed that refining treatment guidelines would be valuable (76%). 85% of clinicians have never powered a clinical trial to allow subset analysis for histological subtypes, but the majority would consider it, and would participate in an ILC clinical trials consortium. The majority of laboratory researchers, reported being and very/extremely (48%) to moderately (29%) confident in describing differences between ILC and NST. They reported that ILCs are inadequately presented in large genomic data sets, and that ILC models are insufficient. The majority have adequate access to tissue or blood from patients with ILC. The majority of patients and advocates (52%) thought that their health care providers did not sufficiently explain the unique features of ILC. They identified improvement of ILC screening/early detection, and identification of better imaging tools as top research priorities. In contrast, both researchers and clinicians identified understanding of endocrine resistance and identifying novel drugs that can be tested in clinical trials as top research priority. In summary, we have gathered information from an international community of physicians, researchers, and patients/advocates that we expect will lay the foundation for a community-informed collaborative research agenda, with the goal of improving management and personalizing treatment for patients with ILC.
Nasal microbiome and the effect of nasal decolonization with a novel povidone-iodine antiseptic solution: a prospective and randomized clinical trial
Authors: Fernández-Rodríguez Diana , Cho Jeongeun , Chisari Emanuele , Citardi Martin J. , Parvizi Javad 
Published: July 2024

AbstractThe aim of this study was to assess the profile of nasal microbiome and evaluate the effect of a specific nasal decolonization solution on the microbiome. We conducted a randomized, placebo-controlled, and parallel-group clinical study of 50 volunteers aged 18 years and older. The subjects were randomly assigned to receive a nasal antiseptic solution, containing povidone-iodine as the main ingredient, (n = 25) or a control solution (n = 25). Nasal swabs were obtained before application (baseline) and at 3 timepoints after application (5 min, 2 h, 24 h). Nasal swabs were subjected to next generation sequencing analysis and cultured in agar plates. At baseline, there were substantial associations between anaerobic species, Corynebacterium spp., Staphylococcus spp., and Dolosigranulum spp. Then, a high bioburden reduction was observed after the application of povidone-iodine (log10 3.68 ± 0.69 at 5 min; log10 3.57 ± 0.94 at 2 h; log10 1.17 ± 1.40 at 24 h), compared to the control. The top species affected by the treatment were Cutibacterium acnes, Staphylococcus, and Corynebacterium species. None of the subjects experienced any adverse effects, nor increases in mucociliary clearance time. Antiseptic solutions applied to the anterior nares can transiently and markedly reduce the bioburden of the nose. The registration number for this clinical trial is NCT05617729.
Automated segmentation of the median nerve in patients with carpal tunnel syndrome
Authors: Moser Florentin , Muller Sébastien , Lie Torgrim , Langø Thomas , Hoff Mari 
Published: July 2024

AbstractMachine learning and deep learning are novel methods which are revolutionizing medical imaging. In our study we trained an algorithm with a U-Net shaped network to recognize ultrasound images of the median nerve in the complete distal half of the forearm and to measure the cross-sectional area at the inlet of the carpal tunnel. Images of 25 patient hands with carpal tunnel syndrome (CTS) and 26 healthy controls were recorded on a video loop covering 15 cm of the distal forearm and 2355 images were manually segmented. We found an average Dice score of 0.76 between manual and automated segmentation of the median nerve in its complete course, while the measurement of the cross-sectional area at the carpal tunnel inlet resulted in a 10.9% difference between manually and automated measurements. We regard this technology as a suitable device for verifying the diagnosis of CTS.
A study of the effects of early diagenesis on the geotechnical properties of carbonate sediments (North West Shelf, Australia)
Authors: Lebrec Ulysse , Sharma Shambhu , Watson Phil , Riera Rosine , Joer Hackmet , Beemer Ryan , Gaudin Christophe 
Published: July 2024

AbstractCarbonate sediments are often regarded as problematic in geotechnical engineering due to the high variability of their properties. Understanding and quantifying this variability will become increasingly critical in the years ahead, notably with respect to upcoming developments in offshore renewable energy, for which limited in-situ data are typically available to characterise large areas. Here, six intervals from the North West Shelf of Australia, each composed of similar carbonate grains but accumulated in different environments, are investigated to better understand how the post-depositional cementation, alteration and dissolution of sediments, known as diagenesis, impact their geotechnical properties. Intervals are primarily affected by mineralogy-driven meteoric diagenesis, comprising in-situ dissolution of metastable grains and subsequent precipitation of cement that occurred when the shelf was exposed during lower sea-levels, and by marine diagenesis. In both cases, increased diagenesis results in a higher cement-to-solid ratio and compressive strength. However, while marine diagenesis is associated with a reduction in void ratio, this is not initially observed with mineralogy-driven meteoric diagenesis. Additionally, for a similar cement-to-solid ratio, microcrystalline cement results in higher compressive strength than sparite cement. The data further reveal that the level of meteoric cementation and the compressive strength increase as a function of the duration of exposure and of the regional climate, along with a reduction of the specific gravity related to the replacement of aragonite by calcite. However, increased meteoric diagenesis also leads to the formation of macro-scale heterogeneities such as calcrete layers and karsts that can affect the holistic geotechnical behaviour of such deposits.