bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the prebiotic effect of oligosaccharides on gut microbiome wellness using in vitro fecal fermentation
Authors: Lee Dong Hyeon , Seong Hyunbin , Chang Daniel , Gupta Vinod K. , Kim Jiseung , Cheon Seongwon , Kim Geonhee , Sung Jaeyun , Han Nam Soo 
Published: May 2023

AbstractWe previously proposed the Gut Microbiome Wellness Index (GMWI), a predictor of disease presence based on a gut microbiome taxonomic profile. As an application of this index for food science research, we applied GMWI as a quantitative tool for measuring the prebiotic effect of oligosaccharides. Mainly, in an in vitro anaerobic batch fermentation system, fructooligosaccharides (FOS), galactooligosaccharides (GOS), xylooligosaccharides (XOS), inulin (IN), and 2’-fucosyllactose (2FL), were mixed separately with fecal samples obtained from healthy adult volunteers. To find out how 24 h prebiotic fermentation influenced the GMWI values in their respective microbial communities, changes in species-level relative abundances were analyzed in the five prebiotics groups, as well as in two control groups (no substrate addition at 0 h and for 24 h). The GMWI of fecal microbiomes treated with any of the five prebiotics (IN (0.48 ± 0.06) > FOS (0.47 ± 0.03) > XOS (0.33 ± 0.02) > GOS (0.26 ± 0.02) > 2FL (0.16 ± 0.06)) were positive, which indicates an increase of relative abundances of microbial species previously found to be associated with a healthy, disease-free state. In contrast, the GMWI of samples without substrate addition for 24 h (–0.60 ± 0.05) reflected a non-healthy, disease-harboring microbiome state. Compared to the original prebiotic index (PI) and α-diversity metrics, GMWI provides a more data-driven, evidence-based indexing system for evaluating the prebiotic effect of food components. This study demonstrates how GMWI can be applied as a novel PI in dietary intervention studies, with wider implications for designing personalized diets based on their impact on gut microbiome wellness.
Thermal Bridges on Building Rooftops
Authors: Mayer Zoe , Kahn James , Götz Markus , Hou Yu , Beiersdörfer Tobias , Blumenröhr Nicolas , Volk Rebekka , Streit Achim , Schultmann Frank 
Published: May 2023

AbstractThermal Bridges on Building Rooftops (TBBR) is a multi-channel remote sensing dataset. It was recorded during six separate UAV fly-overs of the city center of Karlsruhe, Germany, and comprises a total of 926 high-resolution images with 6927 manually-provided thermal bridge annotations. Each image provides five channels: three color, one thermographic, and one computationally derived height map channel. The data is pre-split into training and test data subsets suitable for object detection and instance segmentation tasks. All data is organized and structured to comply with FAIR principles, i.e. being findable, accessible, interoperable, and reusable. It is publicly available and can be downloaded from the Zenodo data repository. This work provides a comprehensive data descriptor for the TBBR dataset to facilitate broad community uptake.
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
Authors: Kakuk Balázs , Dörmő Ákos , Csabai Zsolt , Kemenesi Gábor , Holoubek Jiří , Růžek Daniel , Prazsák István , Dani Virág Éva , Dénes Béla , Torma Gábor , Jakab Ferenc , Tóth Gábor E. , Földes Fanni V. , Zana Brigitta , Lanszki Zsófia , Harangozó Ákos , Fülöp Ádám , Gulyás Gábor , Mizik Máté , Kiss András Attila , Tombácz Dóra , Boldogkői Zsolt 
Published: May 2023

AbstractThe recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level.
Quantitative Mass Spectrometry Analysis of Cerebrospinal Fluid Protein Biomarkers in Alzheimer’s Disease
Authors: Watson Caroline M. , Dammer Eric B. , Ping Lingyan , Duong Duc M. , Modeste Erica , Carter E. Kathleen , Johnson Erik C. B. , Levey Allan I. , Lah James J. , Roberts Blaine R. , Seyfried Nicholas T. 
Published: May 2023

AbstractAlzheimer’s disease (AD) is the most common form of dementia, with cerebrospinal fluid (CSF) β-amyloid (Aβ), total Tau, and phosphorylated Tau (pTau) providing the most sensitive and specific biomarkers for diagnosis. However, these diagnostic biomarkers do not reflect the complex changes in AD brain beyond amyloid (A) and Tau (T) pathologies. Here, we report a selected reaction monitoring mass spectrometry (SRM-MS) method with isotopically labeled standards for relative protein quantification in CSF. Biomarker positive (AT+) and negative (AT−) CSF pools were used as quality controls (QCs) to assess assay precision. We detected 62 peptides (51 proteins) with an average coefficient of variation (CV) of ~13% across 30 QCs and 133 controls (cognitively normal, AT−), 127 asymptomatic (cognitively normal, AT+) and 130 symptomatic AD (cognitively impaired, AT+). Proteins that could distinguish AT+ from AT− individuals included SMOC1, GDA, 14-3-3 proteins, and those involved in glycolysis. Proteins that could distinguish cognitive impairment were mainly neuronal proteins (VGF, NPTX2, NPTXR, and SCG2). This demonstrates the utility of SRM-MS to quantify CSF protein biomarkers across stages of AD.
Crowd cluster data in the USA for analysis of human response to COVID-19 events and policies
Authors: Swaminathan B. , Kang J. , Vaidya K. , Srinivasan A. , Kumar P. , Byna S. , Barbarash D. 
Published: May 2023

AbstractWe provide data on daily social contact intensity of clusters of people at different types of Points of Interest (POI) by zip code in Florida and California. This data is obtained by aggregating fine-scaled details of interactions of people at the spatial resolution of 10 m, which is then normalized as a social contact index. We also provide the distribution of cluster sizes and average time spent in a cluster by POI type. This data will help researchers perform fine-scaled, privacy-preserving analysis of human interaction patterns to understand the drivers of the COVID-19 epidemic spread and mitigation. Current mobility datasets either provide coarse-level metrics of social distancing, such as radius of gyration at the county or province level, or traffic at a finer scale, neither of which is a direct measure of contacts between people. We use anonymized, de-identified, and privacy-enhanced location-based services (LBS) data from opted-in cell phone apps, suitably reweighted to correct for geographic heterogeneities, and identify clusters of people at non-sensitive public areas to estimate fine-scaled contacts.
M4Raw: A multi-contrast, multi-repetition, multi-channel MRI k-space dataset for low-field MRI research
Authors: Lyu Mengye , Mei Lifeng , Huang Shoujin , Liu Sixing , Li Yi , Yang Kexin , Liu Yilong , Dong Yu , Dong Linzheng , Wu Ed X. 
Published: May 2023

AbstractRecently, low-field magnetic resonance imaging (MRI) has gained renewed interest to promote MRI accessibility and affordability worldwide. The presented M4Raw dataset aims to facilitate methodology development and reproducible research in this field. The dataset comprises multi-channel brain k-space data collected from 183 healthy volunteers using a 0.3 Tesla whole-body MRI system, and includes T1-weighted, T2-weighted, and fluid attenuated inversion recovery (FLAIR) images with in-plane resolution of ~1.2 mm and through-plane resolution of 5 mm. Importantly, each contrast contains multiple repetitions, which can be used individually or to form multi-repetition averaged images. After excluding motion-corrupted data, the partitioned training and validation subsets contain 1024 and 240 volumes, respectively. To demonstrate the potential utility of this dataset, we trained deep learning models for image denoising and parallel imaging tasks and compared their performance with traditional reconstruction methods. This M4Raw dataset will be valuable for the development of advanced data-driven methods specifically for low-field MRI. It can also serve as a benchmark dataset for general MRI reconstruction algorithms.
Indexing climatic and environmental exposure of refugee camps with a case study in East Africa
Authors: Owen Michael , Kruczkiewicz Andrew , Van Den Hoek Jamon 
Published: May 2023

AbstractThis study presents a novel approach to systematically measure climatic and environmental exposure in refugee camps using remote sensing and geospatial data. Using a case study of seventeen refugee camps across five countries in East Africa, we develop a climatic and environmental exposure index to quantify each camp’s exposure relative to a population of simulated camp locations within the hosting country. Our results show that seven of seventeen refugee camps are within the upper two quartiles of exposure relative to a simulated population, suggesting that more than six-hundred thousand refugees living in these camps face elevated exposure compared to other potential camp locations. This method stands to improve the process of gathering and analyzing climatic and environmental data on geographically remote humanitarian spaces in a reliable, low-cost, and standardized manner. Automation and refinement of this index could enable real-time updates on climatic and environmental exposure to support decision-making related to disaster risk reduction in refugee camp management.
Platelet function suggests cardioembolic aetiology in cryptogenic stroke
Authors: Dev Priya , Ekhlak Mohammad , Dash Debabrata , Pathak Abhishek 
Published: May 2023

AbstractPlatelet-monocyte (PMA) and platelet-neutrophil aggregations (PNA) play critical roles in the evolution of acute ischemic stroke (AIS). The present study investigates the mechanistic basis of platelet responsiveness in cryptogenic stroke compared with cardioembolic stroke. Platelet from 16 subjects, each from cryptogenic and cardioembolic stroke groups and 18 age-matched healthy controls were subjected to different investigations. Compared to healthy controls, platelet-monocyte and platelet-neutrophil interactions were significantly elevated in cryptogenic (2.7 and 2.1 times) and cardioembolic stroke (3.9 and 2.4 times). P-selectin expression on platelet surface was 1.89 and 2.59 times higher in cryptogenic and cardioembolic strokes, respectively, compared to healthy control. Cell population with [Ca2+i] in either stroke group was significantly outnumbered (by 83% and 72%, respectively, in cryptogenic and cardioembolic stroke) in comparison to healthy controls. Noteworthy, TEG experiment revealed that the cryptogenic stroke exhibited significant decline in Reaction Time (R) and amplitude of 20 mm (K) (by 32% and 33%, respectively) while thrombin burst (α-angle) was augmented by 12%, which reflected substantial boost in thrombus formation in cryptogenic stroke. Although TEG analysis reveals a state of hypercoagulability in patients with cryptogenic stroke. However, platelets from both stroke subtypes switch to a ‘hyperactive’ phenotype.
Treatment of hypertension and obstructive sleep apnea counteracts cognitive decline in common neurocognitive disorders in diagnosis-related patterns
Authors: Kujovic Milenko , Lipka Tim , Zalman Mark , Baumann Leonie , Jänner Michaela , Baumann Bruno 
Published: May 2023

AbstractThe aim of this study was to investigate the effect of arterial hypertension (AH) and of obstructive sleep apnea (OSA) on cognitive course in the neurocognitive disorder (NCD) cohort RIFADE which enrolled patients with NCD due to Alzheimer’s disease (AD), vascular NCD (vNCD), and mixed NCD (AD + vNCD = mNCD). Multiple risk factors (RF), including AH and OSA, that contribute to the development of various kinds of dementia have been identified in previous studies. Studies that observed AH lacked investigation of long-term effects and did not isolate it from other RF. Studies involving OSA as a risk factor did not include participants with all stages of NCD. 126 subjects were screened for AH and OSA. Repeated cognitive measurements were performed with the DemTect as primary outcome and the clock drawing test as secondary outcome measure. 90 patients had AH (71.4%) and 40 patients had OSA (31.7%). RF-status had a significant effect on cognitive outcome in models with RF as single factors (AH p = 0.027, OSA p < 0.001), a 2-factor analysis with AH × OSA (AH as main factor p = 0.027) as well as a model including the 3 factors AH × OSA × diagnosis (p = 0.038). Similarly, a 3-factor model was significant for the clock-drawing test, whereas single factor-models remained insignificant. AH and OSA appear to be risk factors in common NCD and cognitive decline can be mitigated by treatment of these RF.
Bio-inspired artificial synapse for neuromorphic computing based on NiO nanoparticle thin film
Authors: Hadiyal Keval , Ganesan Ramakrishnan , Rastogi A. , Thamankar R. 
Published: May 2023

AbstractThe unprecedented need for data processing in the modern technological era has created opportunities in neuromorphic devices and computation. This is primarily due to the extensive parallel processing done in our human brain. Data processing and logical decision-making at the same physical location are an exciting aspect of neuromorphic computation. For this, establishing reliable resistive switching devices working at room temperature with ease of fabrication is important. Here, a reliable analog resistive switching device based on Au/NiO nanoparticles/Au is discussed. The application of positive and negative voltage pulses of constant amplitude results in enhancement and reduction of synaptic current, which is consistent with potentiation and depression, respectively. The change in the conductance resulting in such a process can be fitted well with double exponential growth and decay, respectively. Consistent potentiation and depression characteristics reveal that non-ideal voltage pulses can result in a linear dependence of potentiation and depression. Long-term potentiation (LTP) and Long-term depression (LTD) characteristics have been established, which are essential for mimicking the biological synaptic applications. The NiO nanoparticle-based devices can also be used for controlled synaptic enhancement by optimizing the electric pulses, displaying typical learning-forgetting-relearning characteristics.
Weakly supervised detection and classification of basal cell carcinoma using graph-transformer on whole slide images
Authors: Yacob Filmon , Siarov Jan , Villiamsson Kajsa , Suvilehto Juulia T. , Sjöblom Lisa , Kjellberg Magnus , Neittaanmäki Noora 
Published: May 2023

AbstractThe high incidence rates of basal cell carcinoma (BCC) cause a significant burden at pathology laboratories. The standard diagnostic process is time-consuming and prone to inter-pathologist variability. Despite the application of deep learning approaches in grading of other cancer types, there is limited literature on the application of vision transformers to BCC on whole slide images (WSIs). A total of 1832 WSIs from 479 BCCs, divided into training and validation (1435 WSIs from 369 BCCs) and testing (397 WSIs from 110 BCCs) sets, were weakly annotated into four aggressivity subtypes. We used a combination of a graph neural network and vision transformer to (1) detect the presence of tumor (two classes), (2) classify the tumor into low and high-risk subtypes (three classes), and (3) classify four aggressivity subtypes (five classes). Using an ensemble model comprised of the models from cross-validation, accuracies of 93.5%, 86.4%, and 72% were achieved on two, three, and five class classifications, respectively. These results show high accuracy in both tumor detection and grading of BCCs. The use of automated WSI analysis could increase workflow efficiency.
A system that delivers an antioxidant to mitochondria for the treatment of drug-induced liver injury
Authors: Hibino Mitsue , Maeki Masatoshi , Tokeshi Manabu , Ishitsuka Yoichi , Harashima Hideyoshi , Yamada Yuma 
Published: May 2023

AbstractMitochondria, a major source of reactive oxygen species (ROS), are intimately involved in the response to oxidative stress in the body. The production of excessive ROS affects the balance between oxidative responses and antioxidant defense mechanisms thus perturbing mitochondrial function eventually leading to tissue injury. Therefore, antioxidant therapies that target mitochondria can be used to treat such diseases and improve general health. This study reports on an attempt to establish a system for delivering an antioxidant molecule coenzyme Q10 (CoQ10) to mitochondria and the validation of its therapeutic efficacy in a model of acetaminophen (APAP) liver injury caused by oxidative stress in mitochondria. A CoQ10-MITO-Porter, a mitochondrial targeting lipid nanoparticle (LNP) containing encapsulated CoQ10, was prepared using a microfluidic device. It was essential to include polyethylene glycol (PEG) in the lipid composition of this LNP to ensure stability of the CoQ10, since it is relatively insoluble in water. Based on transmission electron microscope (TEM) observations and small angle X-ray scattering (SAXS) measurements, the CoQ10-MITO-Porter was estimated to be a 50 nm spherical particle without a regular layer structure. The use of the CoQ10-MITO-Porter improved liver function and reduced tissue injury, suggesting that it exerted a therapeutic effect on APAP liver injury.
HCV, HIV AND HBV rapid test diagnosis in non-clinical outreach settings can be as accurate as conventional laboratory tests
Authors: Muñoz-Chimeno Milagros , Valencia Jorge , Rodriguez-Recio Alvaro , Cuevas Guillermo , Garcia-Lugo Alejandra , Manzano Samuel , Rodriguez-Paredes Vanessa , Fernandez Beatriz , Morago Lucía , Casado Concepción , Avellón Ana , Ryan Pablo 
Published: May 2023

AbstractPoint of care rapid diagnostic tests (POC-RDT) for Hepatitis C virus (HCV), Human Immunodeficiency virus (HIV) and Hepatitis B virus (HBV), are ideal for screening in non-clinical outreach settings as they can provide immediate results and facilitate diagnosis, allowing high risk population screening. The aim of this study was to compare POC-RDT with laboratory conventional tests. A total of 301 vulnerable evaluable subjects (drug users, migrants and homeless population) were recruited at a mobile screening unit in outreach settings in Madrid. Fingerprick whole blood capillary samples were tested using the SD BIOLINE HCV POC-RDT, Determine HIV Early Detect and Determine HBsAg 2, and the results were assessed against the LIAISON XL HCV, HIV and Murex-HBsAg-Quant, reference assays, respectively. The feasibility and user satisfaction of the POC-RDT were evaluated through a questionnaire. The resolved sensitivity and resolved specificity and their 95% confidence intervals (95% CI) were as follows, respectively: SD-BIOLINE-HCV: 98.8% (95% CI 93.4, 100.0) and 100.0% (95% CI 98.3, 100.0); Determine HIV Early Detect: 100% (95% CI 85.2, 100.0) and 100% (95% CI 98.7, 100); and Determine HBsAg 2: 66.7% (95% CI 9.4, 99.2) and 100.0% (95% CI 98.7, 100.0). As expected, the number of subjects with a confirmed positive result for HBsAg was very low (n = 4). Therefore, the analytical sensitivity has been evaluated in addition: The Determine HBsAg 2 test demonstrated 100% sensitivity for standard concentrations ≥ 0.125 IU/mL. The subject questionnaire yielded positive feedback for most subjects. The POC-RDT fingerprick blood collection method was well received, and the tests demonstrated a comparable clinical performance with conventional tests in outreach settings and vulnerable high-risk populations.
A mechanical theory of competition between plant root growth and soil pressure reveals a potential mechanism of root penetration
Authors: Tomobe Haruka , Tsugawa Satoru , Yoshida Yuki , Arita Tetsuya , Tsai Allen Yi-Lun , Kubo Minoru , Demura Taku , Sawa Shinichiro 
Published: May 2023

AbstractRoot penetration into the soil is essential for plants to access water and nutrients, as well as to mechanically support aboveground structures. This requires a combination of healthy plant growth, adequate soil mechanical properties, and compatible plant–soil interactions. Despite the current knowledge of the static rheology driving the interactions at the root–soil interface, few theoretical approaches have attempted to describe root penetration with dynamic rheology. In this work, we experimentally showed that radish roots in contact with soil of specific density during a specific growth stage fail to penetrate the soil. To explore the mechanism of root penetration into the soil, we constructed a theoretical model to explore the relevant conditions amenable to root entry into the soil. The theory indicates that dimensionless parameters such as root growth anisotropy, static root–soil competition, and dynamic root–soil competition are important for root penetration. The consequent theoretical expectations were supported by finite element analysis, and a potential mechanism of root penetration into the soil is discussed.
Robust morphogenesis by chaotic dynamics
Authors: Reinitz J. , Vakulenko S. , Sudakow I. , Grigoriev D. 
Published: May 2023

AbstractThis research illustrates that complex dynamics of gene products enable the creation of any prescribed cellular differentiation patterns. These complex dynamics can take the form of chaotic, stochastic, or noisy chaotic dynamics. Based on this outcome and previous research, it is established that a generic open chemical reactor can generate an exceptionally large number of different cellular patterns. The mechanism of pattern generation is robust under perturbations and it is based on a combination of Turing’s machines, Turing instability and L. Wolpert’s gradients. These results can help us to explain the formidable adaptive capacities of biochemical systems.
Damage characteristics of weak rocks with different dip angles during creep
Authors: Miao Haibin , Zhao Na , Meng Lixin , Zhang Yibin , Wang Laigui 
Published: May 2023

AbstractTo investigate the influence of the weak layer dip angle on the creep rupture of the composite rock mass, this paper conducts a graded loading creep experiment on the composite rock mass with different dip angles using the acoustic emission method to examine the fracture evolution process. With increasing load grade, the cumulative total ring count of the rock mass shows a “U”-shaped trend, and the acoustic emission spatial positioning results show that acoustic emission events in the rock mass fracture process are primarily concentrated in the vicinity of the weak layer, while events in other areas are few and dispersed. For rock masses with weak layer dip angles of 0° and 15°, cracks occur in both soft and hard rocks, where shear cracks are dominant in soft rocks, tensile cracks are dominant in hard rocks, and finally, the rock mass mainly exhibits tensile splitting failure. For rock masses with weak layer dip angles of 30° and 45°, most of the cracks exist in the interior of the soft rock, which is dominated by shear cracks. With increasing graded loads, the shear cracks continue to develop along the direction of the weak layer, the upper rock mass keeps slipping and dislocating, and the final failure mode is mainly shear-slip failure. The damage evolution varies with the inclination angle of the weak layer, which can be divided into three stages: initial damage accumulation, damage acceleration, and damage destruction. This demonstrates the ability to predict, prevent, and control the occurrence of creep disasters in rock masses with weak layers.