bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing
Authors: Ali Jawad , Johansen Wenche , Ahmad Rafi 
Published: March 2024

AbstractBloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2–4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102–104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103–107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.
Uncovering the molecular mechanisms of russet skin formation in Niagara grapevine (Vitis vinifera × Vitis labrusca)
Authors: Niederauer Guilherme Francio , de Oliveira Geovani Luciano , Aono Alexandre Hild , da Silva Graciano Diego , Carmello-Guerreiro Sandra Maria , Moura Mara Fernandes , de Souza Anete Pereira 
Published: March 2024

AbstractGrape breeding programs are mostly focused on developing new varieties with high production volume, sugar contents, and phenolic compound diversity combined with resistance and tolerance to the main pathogens under culture and adverse environmental conditions. The ‘Niagara’ variety (Vitis labrusca$$\times$$
×
Vitis vinifera) is one of the most widely produced and commercialized table grapes in Brazil. In this work, we selected three Niagara somatic variants with contrasting berry phenotypes and performed morphological and transcriptomic analyses of their berries. Histological sections of the berries were also performed to understand anatomical and chemical composition differences of the berry skin between the genotypes. An RNA-Seq pipeline was implemented, followed by global coexpression network modeling. ‘Niagara Steck’, an intensified russet mutant with the most extreme phenotype, showed the largest difference in expression and showed selection of coexpressed network modules involved in the development of its russet-like characteristics. Enrichment analysis of differently expressed genes and hub network modules revealed differences in transcription regulation, auxin signaling and cell wall and plasmatic membrane biogenesis. Cutin- and suberin-related genes were also differently expressed, supporting the anatomical differences observed with microscopy.
Close negative correlation of local and circulating Dickkopf-1 and Sclerostin levels during human fracture healing
Authors: Starlinger Julia , Santol Jonas , Kaiser Georg , Sarahrudi Kambiz 
Published: March 2024

AbstractWnt signaling is critically involved in fracture healing. Existing data predominantly relies on rodent models. Here, we explored local and circulating Dickkopf-1 (DKK1) levels in patients with respect to fracture healing and explore its association to sclerostin (SOST). 69 patients after surgical stabilization of long bone fractures of which six patients had impaired fracture healing were included in this study. Life-style and patient related factors with a known effect on DKK1 and SOST were recorded. DKK1 and SOST concentrations were measured using enzyme-linked immunosorbent assay (ELISA) at the fracture site and in circulation. DKK1 and SOST showed a close inverse correlation. In fracture hematoma and immediately after trauma DKK1 levels were significantly reduced while SOST levels were significantly increased, compared to healthy control. Postoperatively, DKK1 peaked at week 2 and SOST at week 8, again demonstrating a close negative correlation. Age and smoking status affected the balance of DKK1 and SOST, while type 2 diabetes and sex did not demonstrate a significant influence. Early postoperative elevation of SOST without compensatory DKK1 decrease was associated with fracture non-union in younger patients (< 50a). The close inverse correlation and very rapid dynamics of DKK1 and SOST locally as well as systemically suggest their critical involvement during human fracture healing. Importantly, as immediate compensatory feedback mechanism are apparent, we provide evidence that dual-blockade of DKK1 and SOST could be critical to allow for therapeutic efficiency of Wnt targeted therapies for fracture healing.
Lightweight federated learning for STIs/HIV prediction
Authors: Nguyen Thi Phuoc Van , Yang Wencheng , Tang Zhaohui , Xia Xiaoyu , Mullens Amy B. , Dean Judith A. , Li Yan 
Published: March 2024

AbstractThis paper presents a solution that prioritises high privacy protection and improves communication throughput for predicting the risk of sexually transmissible infections/human immunodeficiency virus (STIs/HIV). The approach utilised Federated Learning (FL) to construct a model from multiple clinics and key stakeholders. FL ensured that only models were shared between clinics, minimising the risk of personal information leakage. Additionally, an algorithm was explored on the FL manager side to construct a global model that aligns with the communication status of the system. Our proposed method introduced Random Forest Federated Learning for assessing the risk of STIs/HIV, incorporating a flexible aggregation process that can be adjusted to accommodate the capacious communication system. Experimental results demonstrated the significant potential of a solution for estimating STIs/HIV risk. In comparison with recent studies, our approach yielded superior results in terms of AUC (0.97) and accuracy ($$93\%$$93%). Despite these promising findings, a limitation of the study lies in the experiment for man’s data, due to the self-reported nature of the data and sensitive content. which may be subject to participant bias. Future research could check the performance of the proposed framework in partnership with high-risk populations (e.g., men who have sex with men) to provide a more comprehensive understanding of the proposed framework’s impact and ultimately aim to improve health outcomes/health service optimisation.
Data-driven simulations for training AI-based segmentation of neutron images
Authors: Sathe Pushkar S. , Wolf Caitlyn M. , Kim Youngju , Robinson Sarah M. , Daugherty M. Cyrus , Murphy Ryan P. , LaManna Jacob M. , Huber Michael G. , Jacobson David L. , Kienzle Paul A. , Weigandt Katie M. , Klimov Nikolai N. , Hussey Daniel S. , Bajcsy Peter 
Published: March 2024

AbstractNeutron interferometry uniquely combines neutron imaging and scattering methods to enable characterization of multiple length scales from 1 nm to 10 µm. However, building, operating, and using such neutron imaging instruments poses constraints on the acquisition time and on the number of measured images per sample. Experiment time-constraints yield small quantities of measured images that are insufficient for automating image analyses using supervised artificial intelligence (AI) models. One approach alleviates this problem by supplementing annotated measured images with synthetic images. To this end, we create a data-driven simulation framework that supplements training data beyond typical data-driven augmentations by leveraging statistical intensity models, such as the Johnson family of probability density functions (PDFs). We follow the simulation framework steps for an image segmentation task including Estimate PDFs $$\,\rightarrow \,$$

→

Validate PDFs $$\,\rightarrow \,$$

→

Design Image Masks $$\,\rightarrow \,$$

→

Generate Intensities $$\,\rightarrow \,$$

→

Train AI Model for Segmentation. Our goal is to minimize the manual labor needed to execute the steps and maximize our confidence in simulations and segmentation accuracy. We report results for a set of nine known materials (calibration phantoms) that were imaged using a neutron interferometer acquiring four-dimensional images and segmented by AI models trained with synthetic and measured images and their masks.
Taiwan ended third COVID-19 community outbreak as forecasted
Authors: Wu Yu-Heng , Nordling Torbjörn E. M. 
Published: March 2024

AbstractAccurate forecasting of community outbreaks is crucial for governments to allocate healthcare resources correctly and implement suitable non-pharmaceutical interventions. Additionally, companies must address critical questions about stock and staff management. Society’s key concern is when businesses and organizations can resume normal operations. Between December 31st 2019 and 2021, Taiwan experienced three separate COVID-19 community outbreaks with significant time intervals in between, suggesting that each outbreak eventually came to an end. We identified the ratio of the 7-day average of local & unknown confirmed to suspected cases as the key control variable and forecasted the end of the third outbreak by the exponential model. We forecasted the end of the third outbreak on Aug. 16th with threshold ratios of $$1.2\cdot 10^{-4}$$

1.2
·

10

-
4

. The real observations crossed the threshold on Aug. 27th, eleven days later than forecasted, with the last case of the third outbreak confirmed and quarantined on Sept. 20th. This demonstrated the accuracy of the proposed forecasting method in predicting the end of a local outbreak. Furthermore, we highlight that the ratio reflects the effectiveness of contact tracing. Effective contact tracing together with testing and isolation of infected individuals is crucial for ending community outbreaks.
5-HT_FAsTR: a versatile, label-free, high-throughput, fluorescence-based microplate assay to quantify serotonin transport and release
Authors: Bukowski Lina , Strøm Markus Emanuel , Andersen Jens Lindengren , Maesen Jannick Bang , Tian Lin , Sinning Steffen 
Published: March 2024

AbstractThe neurotransmitter serotonin plays a pivotal role in mood and depression. It also acts as a vasoconstrictor within blood vessels and is the main neurotransmitter in the gastrointestinal system. In neurotransmission, released serotonin is taken up by serotonin transporters, which are principal targets of antidepressants and the psychostimulant, ecstasy. The investigation of serotonin transporters have relied almost exclusively on the use of radiolabeled serotonin in heterogenous end-point assays. Here we adapt the genetically encoded fluorescent biosensor, iSeroSnFR, to establish and validate the Serotonin (5-HT) Fluorescence Assay for Transport and Release (5-HT_FAsTR) for functional and pharmacological studies of serotonin transport and release. We demonstrate the applicability of the method for the study of a neuronal, high-affinity, low-capacity serotonin transporter (SERT) as well as an extraneuronal low-affinity, high-capacity organic cation transporter and mutants thereof. 5HT_FAsTR offers an accessible, versatile and reliable semi-homogenous assay format that only relies on a fluorescence plate reader for repeated, real-time measurements of serotonin influx and efflux. 5HT_FAsTR accelerates and democratizes functional characterization and pharmacological studies of serotonin transporters and genetic variants thereof in disease states such as depression, anxiety and ADHD.
The Pleistocene high-elevation environments between 2.02 and 0.6 Ma at Melka Kunture (Upper Awash Valley, Ethiopia) based upon stable isotope analysis
Authors: Briatico Giuseppe , Bocherens Hervé , Geraads Denis , Melis Rita T. , Mussi Margherita 
Published: March 2024

AbstractPleistocene environments are among the most studied issues in paleoecology and human evolution research in eastern Africa. Many data have been recorded from archaeological sites located at low and medium elevations (≤ 1500 m), whereas few contexts are known at 2000 m and above. Here, we present a substantial isotopic study from Melka Kunture, a complex of prehistoric sites located at 2000—2200 m above sea level in the central Ethiopian highlands. We analyzed the stable carbon and oxygen isotopic composition of 308 faunal tooth enamel samples from sites dated between 2.02 and 0.6 Ma to investigate the animal diets and habitats. The carbon isotopic results indicate that the analyzed taxa had C4-dominated and mixed C3-C4 diets with no significant diachronic changes in feeding behavior with time. This is consistent with faunal and phytolith analyses, which suggested environments characterized by open grasslands (with both C3 and C4 grasses), patches of bushes and thickets, and aquatic vegetation. However, palynological data previously documented mountain forests, woodlands, and high-elevation grasslands. Additionally, the carbon isotopic comparison with other eastern African localities shows that differences in elevation did not influence animal feeding strategies and habitat partitioning, even though plant species vary according to altitudinal gradients. In contrast, the oxygen isotopic comparison suggests significant differences consistent with the altitude effect. Our approach allows us to detect diverse aspects of animal behavior, habitat, and vegetation that should be considered when reconstructing past environments.
CDK12 is a potential biomarker for diagnosis, prognosis and immunomodulation in pan-cancer
Authors: Lu Ke-Qi , Li Zuo-Lin , Zhang Qian , Yin Qing , Zhang Yi-Lin , Ni Wei-Jie , Jiang LiangYun-Zi , He Wei , Wang Bin 
Published: March 2024

AbstractCell cycle-dependent protein kinase 12 (CDK12) plays a key role in a variety of carcinogenesis processes and represents a promising therapeutic target for cancer treatment. However, to date, there have been no systematic studies addressing its diagnostic, prognostic and immunological value across cancers. Here, we found that CDK12 was significantly upregulated in various types of cancers, and it expression increased with progression in ten cancer types, including breast cancer, cholangiocarcinoma and colon adenocarcinoma. Moreover, the ROC curves indicated that CDK12 showed diagnostic value in eight cancer types. High CDK12 expression was associated with poor prognosis in eight types of cancer, including low-grade glioma, mesothelioma, melanoma and pancreatic cancer. Furthermore, we conducted immunoassays to explore the exact mechanisms underlying CDK12-induced carcinogenesis, which revealed that increased expression of CDK12 allowed tumours to evade immune surveillance and upregulate immune checkpoint genes. Additionally, mutational studies have shown that amplification and missense mutations are the predominant mutational events affecting CDK12 across cancers. These findings establish CDK12 as a significant biological indicator of cancer diagnosis, prognosis, and immunotherapeutic targeting. Early surveillance and employment of CDK12 inhibitors, along with concomitant immunotherapy interventions, may enhance the clinical outcomes of cancer patients.
Subsurface temperature estimates from a Regional Ocean Modelling System (ROMS) reanalysis provide accurate coral heat stress indices across the Main Hawaiian Islands
Authors: Perelman Jessica N. , Tanaka Kisei R. , Smith Joy N. , Barkley Hannah C. , Powell Brian S. 
Published: March 2024

AbstractAs ocean temperatures continue to rise, coral bleaching events around the globe are becoming stronger and more frequent. High-resolution temperature data is therefore critical for monitoring reef conditions to identify indicators of heat stress. Satellite and in situ measurements have historically been relied upon to study the thermal tolerances of coral reefs, but these data are quite limited in their spatial and temporal coverage. Ocean circulation models could provide an alternative or complement to these limited data, but a thorough evaluation against in situ measurements has yet to be conducted in any Pacific Islands region. Here we compared subsurface temperature measurements around the nearshore Main Hawaiian Islands (MHI) from 2010 to 2017 with temperature predictions from an operational Regional Ocean Modeling System (ROMS) to evaluate the potential utility of this model as a tool for coral reef management. We found that overall, the ROMS reanalysis presents accurate subsurface temperature predictions across the nearshore MHI region and captures a significant amount of observed temperature variability. The model recreates several temperature metrics used to identify coral heat stress, including predicting the 2014 and 2015 bleaching events around Hawaiʻi during the summer and fall months of those years. The MHI ROMS simulation proves to be a useful tool for coral reef management in the absence of, or to supplement, subsurface and satellite measurements across Hawaiʻi and likely for other Pacific Island regions.
Denoising OCT videos based on temporal redundancy
Authors: Richer Emmanuelle , Solano Marissé Masís , Cheriet Farida , Lesk Mark R. , Costantino Santiago 
Published: March 2024

AbstractThe identification of eye diseases and their progression often relies on a clear visualization of the anatomy and on different metrics extracted from Optical Coherence Tomography (OCT) B-scans. However, speckle noise hinders the quality of rapid OCT imaging, hampering the extraction and reliability of biomarkers that require time series. By synchronizing the acquisition of OCT images with the timing of the cardiac pulse, we transform a low-quality OCT video into a clear version by phase-wrapping each frame to the heart pulsation and averaging frames that correspond to the same instant in the cardiac cycle. Here, we compare the performance of our one-cycle denoising strategy with a deep-learning architecture, Noise2Noise, as well as classical denoising methods such as BM3D and Non-Local Means (NLM). We systematically analyze different image quality descriptors as well as region-specific metrics to assess the denoising performance based on the anatomy of the eye. The one-cycle method achieves the highest denoising performance, increases image quality and preserves the high-resolution structures within the eye tissues. The proposed workflow can be readily implemented in a clinical setting.
Quantifying forest disturbance regimes within caribou (Rangifer tarandus) range in British Columbia
Authors: Maltman James C. , Coops Nicholas C. , Rickbeil Gregory J. M. , Hermosilla Txomin , Burton A. Cole 
Published: March 2024

Abstract
Habitat disturbance is a major driver of the decline of woodland caribou (Rangifer tarandus caribou) in Canada. Different disturbance agents and regimes negatively impact caribou populations to different degrees. It is therefore critical that land managers and scientists studying caribou have a detailed understanding of the disturbance regimes affecting caribou habitat. In this work we use recent advances in satellite-based disturbance detection to quantify polygonal forest disturbance regimes affecting caribou ecotypes and herds in British Columbia (BC) from 1985 to 2019. Additionally, we utilize this data to investigate harvesting rates since the implementation of the Species at Risk Act (SARA) and publication of recovery strategies for caribou in BC. Southern Mountain caribou herds are the most threatened yet experienced the highest rates of disturbance, with 22.75% of forested habitat within their ranges disturbed during the study period. Over the study period, we found that in total, 16.4% of forested area was disturbed across all caribou herd ranges. Our findings indicate that caribou in BC face high, and in many cases increasing, levels of habitat disturbance. Our results provide a detailed understanding of the polygonal disturbance regimes affecting caribou in BC at the herd scale, and highlight the need for effective implementation of policies aimed at preserving caribou habitat.
Multi-objective and multi constrained task scheduling framework for computational grids
Authors: Hegde Sujay N. , Srinivas D. B. , Rajan M. A. , Rani Sita , Kataria Aman , Min Hong 
Published: March 2024

AbstractGrid computing emerged as a powerful computing domain for running large-scale parallel applications. Scheduling computationally intensive parallel applications such as scientific, commercial etc., computational grids is a NP-complete problem. Many researchers have proposed several task scheduling algorithms on grids based on formulating and solving it as an optimization problem with different objective functions such as makespan, cost, energy etc. Further to address the requirements/demands/needs of the users (lesser cost, lower latency etc.) and grid service providers (high utilization and high profitability), a task scheduler needs to be designed based on solving a multi-objective optimization problem due to several trade-offs among the objective functions. In this direction, we propose an efficient multi-objective task scheduling framework to schedule computationally intensive tasks on heterogeneous grid networks. This framework minimizes turnaround time, communication, and execution costs while maximizing grid utilization. We evaluated the performance of our proposed algorithm through experiments conducted on standard, random, and scientific task graphs using the GridSim simulator.
Absorption peak decomposition of an inhomogeneous nanoparticle ensemble of hexagonal tungsten bronzes using the reduced Mie scattering integration method
Authors: Machida Keisuke , Adachi Kenji 
Published: March 2024

AbstractRecent optical analyses of cesium-doped hexagonal tungsten bronze have accurately replicated the absorption peak and identified both plasmonic and polaronic absorptions in the near-infrared region, which have been exploited in various technological applications. However, the absorption peaks of tungsten oxides and bronzes have not generally been reproduced well, including those of the homologous potassium- and rubidium-doped hexagonal tungsten bronzes that lacked evidence of polaronic subpeaks. The present study reports a modified and simplified Mie scattering integration method which incorporates the ensemble inhomogeneity effect and allows precise peak decomposition and determination of the physical parameters of nanoparticles. The decomposed peaks were interpreted in terms of electronic structures, screening effect, and modified dielectric functions. The analysis revealed that the plasma frequencies, polaron energies, and the number of oxygen vacancies decrease in the dopant order Cs → Rb → K. The coexistence of plasmonic and polaronic excitations was confirmed for all the alkali-doped hexagonal tungsten bronzes.