bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating miRNA profiles in COVID-19 patients and meta-analysis: implications for disease progression and prognosis
Authors: Gao Liangliang , Kyubwa Espoir M. , Starbird Mark A. , Diaz de Leon Jesus , Nguyen Michelle , Rogers Claude J. , Menon Naresh 
Published: December 2023

AbstractWe compared circulating miRNA profiles of hospitalized COVID-positive patients (n = 104), 27 with acute respiratory distress syndrome (ARDS) and age- and sex-matched healthy controls (n = 18) to identify miRNA signatures associated with COVID and COVID-induced ARDS. Meta-analysis incorporating data from published studies and our data was performed to identify a set of differentially expressed miRNAs in (1) COVID-positive patients versus healthy controls as well as (2) severe (ARDS+) COVID vs moderate COVID. Gene ontology enrichment analysis of the genes these miRNAs interact with identified terms associated with immune response, such as interferon and interleukin signaling, as well as viral genome activities associated with COVID disease and severity. Additionally, we observed downregulation of a cluster of miRNAs located on chromosome 14 (14q32) among all COVID patients. To predict COVID disease and severity, we developed machine learning models that achieved AUC scores between 0.81–0.93 for predicting disease, and between 0.71–0.81 for predicting severity, even across diverse studies with different sample types (plasma versus serum), collection methods, and library preparations. Our findings provide network and top miRNA feature insights into COVID disease progression and contribute to the development of tools for disease prognosis and management.
Call combination patterns in Icelandic killer whales (Orcinus orca)
Authors: Selbmann Anna , Miller Patrick J. O. , Wensveen Paul J. , Svavarsson Jörundur , Samarra Filipa I. P. 
Published: December 2023

AbstractAcoustic sequences have been described in a range of species and in varying complexity. Cetaceans are known to produce complex song displays but these are generally limited to mysticetes; little is known about call combinations in odontocetes. Here we investigate call combinations produced by killer whales (Orcinus orca), a highly social and vocal species. Using acoustic recordings from 22 multisensor tags, we use a first order Markov model to show that transitions between call types or subtypes were significantly different from random, with repetitions and specific call combinations occurring more often than expected by chance. The mixed call combinations were composed of two or three calls and were part of three call combination clusters. Call combinations were recorded over several years, from different individuals, and several social clusters. The most common call combination cluster consisted of six call (sub-)types. Although different combinations were generated, there were clear rules regarding which were the first and last call types produced, and combinations were highly stereotyped. Two of the three call combination clusters were produced outside of feeding contexts, but their function remains unclear and further research is required to determine possible functions and whether these combinations could be behaviour- or group-specific.
Model-informed health and socio-economic benefits of enhancing global equity and access to Covid-19 vaccines
Authors: Italia Matteo , Della Rossa Fabio , Dercole Fabio 
Published: December 2023

AbstractWe take a model-informed approach to the view that a global equitable access (GEA) to Covid-19 vaccines is the key to bring this pandemic to an end. We show that the equitable redistribution (proportional to population size) of the currently available vaccines is not sufficient to stop the pandemic, whereas a 60% increase in vaccine access (the global share of vaccinated people) would have allowed the current distribution to stop the pandemic in about a year of vaccination, saving millions of people in poor countries. We then investigate the interplay between access to vaccines and their distribution among rich and poor countries, showing that the access increase to stop the pandemic gets minimized at + 32% by the equitable distribution (− 36% in rich countries and + 60% in poor ones). To estimate the socio-economic benefits of a vaccination campaign with enhanced global equity and access (eGEA), we compare calibrated simulations of the current scenario with a hypothetical, vaccination-intensive scenario that assumes high rollouts (shown however by many rich and poor countries during the 2021–2022 vaccination campaign) and an improved equity from the current 2.5:1 to a 2:1 rich/poor-ratio of the population fractions vaccinated per day. Assuming that the corresponding + 130% of vaccine production is made possible by an Intellectual Property waiver, we show that the money saved on vaccines globally by the selected eGEA scenario overcomes the 5-year profit of the rights holders in the current situation. This justifies compensation mechanisms in exchange for the necessary licensing agreements. The good news is that the benefits of this eGEA scenario are still relevant, were we ready to implement it now.
Physical characterization of late-type contact binary systems observed by LAMOST: a comprehensive statistical analysis
Authors: Abdel Rahman H. I. , Darwish Mohamed 
Published: December 2023

AbstractThis paper presents a catalog of approximately 1800 Eclipsing W UMa systems (EWs) using parameters from LAMOST, VSX, ZTF and Gaia. Our detailed statistical analysis includes frequency distributions of parameters, confidence intervals, and hypothesis testing to provide deeper insights into the physical properties of this important eclipsing binary class. We focus on key parameters, including Period, Effective Temperature, Surface Gravity, metallicity, Radial Velocity, and spectral type of the systems. Our study reveals that the mean values for period, effective temperature, logarithmic surface gravity, metallicity, and radial velocity for EW systems are 0.377 days, 5775 K, 4, -0.185, and -4.085 km/s, respectively. The 95% confidence intervals for these parameters are 0.372 to 0.382 days, 5730 to 5820 K, -0.202 to -0.168, 3.97 to 4.03, and -6.47 to -1.7 km/s, respectively. Hypothesis testing of the estimated intervals results in the acceptance of the null hypothesis, indicating that EW systems are characterized within the specified limits. Our study also confirms that the majority of EW systems are late-type stars, primarily classified as F spectral type, followed by G and K. Interestingly, among the sample, 88 systems are classified as A spectral type, with a mean surface temperature of 7400 K. We examine the correlation between orbital periods and atmospheric parameters in the VSX and ZTF catalogs. While ZTF periods align well with established relations (correlation coefficient: 0.74), a weaker correlation is found in the VSX catalog. This highlights the need for a revision of VSX periods for improved accuracy in the studied sample of EWs.
Fracture-matrix fluid exchange in oil-bearing unconventional mudstones
Authors: Moore Johnathan , Crandall Dustin , Sanguinito Sean , Valenza John J. 
Published: December 2023

AbstractThe poromechanical properties of unconventional reservoir materials are in large part dictated by their mineralogy. Since these properties govern the response to stress experienced during hydraulic fracturing, fluid production, and fluid injection, they play a central role in the formation of microcracks or bedding delaminations which ultimately dominate mass transport. In this work we study access to the porosity of end member unconventional reservoir materials, where the end members are predominantly dictated by carbonate content. Access to the porosity is quantified using state of the art 3D x-ray computed tomography coupled with physics informed data analytics. Xenon gas, which attenuates x-rays, provides a spatiotemporal map of access to the porosity. The accessible porosity is quantified over a range of net confining stress relevant to the manmade disturbances listed above. These experiments demonstrate that heavily carbonated mudstones are nearly impermeable at the core (~ cm) scale, while carbonate free analogues afford better access to the microstructure. Consistent with previous qualitative 2D radiographs, access to the interior of the clastic mudstones is first observed along planar microcracks, followed by slow penetration into the surrounding matrix. Physics informed data analytics of the 3D tomography measurements presented here show that these microcracks do not permit uniform access to the adjacent rock matrix. In addition, variation of the effective pressure elucidates the mechanisms that govern fracture/matrix fluid exchange. Under conditions consistent with hydrocarbon production fluid accumulates in the immediate vicinity of the nearest microcrack. While there is clear evidence that, as intended, part of this accumulation is from the more distant matrix, fluid is also squeezed out of the microcrack. The fluid build-up at the microcrack indicates that migration out of the rock is hindered by the coupled poroelastic response of the microcrack and adjacent rock matrix. We show that these mechanisms ultimately account for the meager oil recovery factors realized in practice. These insights have implications for making reservoir scale predictions based on core scale observations, and provide a basis for devising new asset development techniques to access more porosity, and enhance fluid extraction. Finally, these findings shed light on key features and mechanisms that govern shale storage capacity, with relevance to other important industrial processes, such as geologic CO2 storage.
Reproducible and clinically translatable deep neural networks for cervical screening
Authors: Ahmed Syed Rakin , Befano Brian , Lemay Andreanne , Egemen Didem , Rodriguez Ana Cecilia , Angara Sandeep , Desai Kanan , Jeronimo Jose , Antani Sameer , Campos Nicole , Inturrisi Federica , Perkins Rebecca , Kreimer Aimee , Wentzensen Nicolas , Herrero Rolando , del Pino Marta , Quint Wim , de Sanjose Silvia , Schiffman Mark , Kalpathy-Cramer Jayashree 
Published: December 2023

AbstractCervical cancer is a leading cause of cancer mortality, with approximately 90% of the 250,000 deaths per year occurring in low- and middle-income countries (LMIC). Secondary prevention with cervical screening involves detecting and treating precursor lesions; however, scaling screening efforts in LMIC has been hampered by infrastructure and cost constraints. Recent work has supported the development of an artificial intelligence (AI) pipeline on digital images of the cervix to achieve an accurate and reliable diagnosis of treatable precancerous lesions. In particular, WHO guidelines emphasize visual triage of women testing positive for human papillomavirus (HPV) as the primary screen, and AI could assist in this triage task. In this work, we implemented a comprehensive deep-learning model selection and optimization study on a large, collated, multi-geography, multi-institution, and multi-device dataset of 9462 women (17,013 images). We evaluated relative portability, repeatability, and classification performance. The top performing model, when combined with HPV type, achieved an area under the Receiver Operating Characteristics (ROC) curve (AUC) of 0.89 within our study population of interest, and a limited total extreme misclassification rate of 3.4%, on held-aside test sets. Our model also produced reliable and consistent predictions, achieving a strong quadratic weighted kappa (QWK) of 0.86 and a minimal %2-class disagreement (% 2-Cl. D.) of 0.69%, between image pairs across women. Our work is among the first efforts at designing a robust, repeatable, accurate and clinically translatable deep-learning model for cervical screening.
High resolution simulation of basilar artery infarct and flow within the circle of Willis
Authors: McCullough Jon W. S. , Coveney Peter V. 
Published: December 2023

AbstractOn a global scale, cerebro- and cardiovascular diseases have long been one of the leading causes of death and disability and their prevalence appears to be increasing in recent times. Understanding potential biomarkers and risk factors will help to identify individuals potentially at risk of suffering an ischemic stroke. However, the widely variable construction of the cerebral vasculature makes it difficult to provide a specific assessment without the knowledge of a patient’s physiology. In this paper we use the 3D blood flow simulator HemeLB to study flow within three common structural variations of the circle of Willis during and in the moments after a blockage of the basilar artery. This tool, based on the lattice Boltzmann method, allows the 3D flow entering the basilar artery to be finely controlled to replicate the cessation of blood feeding this particular vessel—we demonstrate this with several examples including a sudden halt to flow and a gradual loss of flow over three heartbeat cycles. In this work we start with an individualised 3D representation of a full circle of Willis and then construct two further domains by removing the left or right posterior communicating arteries from this geometry. Our results indicate how, and how quickly, the circle of Willis is able to redistribute flow following such a stroke. Due to the choice of infarct, the greatest reduction in flow was observed in the posterior cerebral arteries where flow was reduced by up to 70% in some cases. The high resolution domains used in this study permit the velocity magnitude and wall shear stress to be analysed at key points during and following the stroke. The model we present here indicates how personalised vessels are required to provide the best insight into stroke risk for a given individual.
A novel biomarker of MMP-cleaved cartilage intermediate layer protein-1 is elevated in patients with rheumatoid arthritis, ankylosing spondylitis and osteoarthritis
Authors: Port Helena , Hausgaard Cecilie Møller , He Yi , Maksymowych Walter P. , Wichuk Stephanie , Sinkeviciute Dovile , Bay-Jensen Anne-Christine , Holm Nielsen Signe 
Published: December 2023

AbstractRheumatic joints have an altered cartilage turnover. Cartilage intermediate layer protein 1 (CILP-1) is secreted from articular chondrocytes and deposited into the cartilage extracellular matrix. We developed an immunoassay targeting a Matrix Metalloproteinase (MMP)-generated neo-epitope of CILP-1, named CILP-M. Human articular cartilage was cleaved with proteolytic enzymes and CILP-M levels were measured. We also quantified CILP-M in two studies from patients with rheumatoid arthritis (RA), ankylosing spondylitis (AS) and osteoarthritis (OA) and explored the monitoring and prognostic potential of CILP-M in TNF-α inhibitory treatment and modified Stoke AS Spine Score (mSASSS) progression. CILP-M was generated by MMP-1, -8 and -12. In the discovery study, CILP-M was significantly higher in patients with RA, AS and OA than healthy donors (p < 0.01, p < 0.001, p < 0.05) with an area under the curve (AUC) between the diseased groups and healthy donors > 0.95 (p < 0.001). In the validation study, patients with RA and AS had significantly higher CILP-M levels than healthy controls (p < 0.001) and AUC > 0.90 (p < 0.001). Patients with AS treated with TNF- α inhibitory treatment in the validation study had significantly lower CILP-M levels after treatment (p = 0.004). CILP-M may provide useful insights into cartilage degradation processes in rheumatic diseases.
Research on reasonable layout parameters of working faces based on the concept of harmonic extraction to reduce the damage of coal seam waiting for upward mining
Authors: Jing Chai , Zhicheng Han , Weiming Lv , Haitao Zhu , Shuhong Hou 
Published: December 2023

AbstractBased on the idea of harmonic extraction, the problem of reducing the damage of the coal seam waiting for upward mining. Using the theoretical analysis method, a schematic diagram of coordinated mining along the dip direction of coal seam is established, and the calculation method of reasonable layout parameters of coal seam working face early mining is given. Based on the upward mining problem of the No.1 coal seam in the fifth panel of Zaoquan Coal Mine, the influence parameters of the No.2 coal seam, No.6 coal seam and No.7 coal seam mining on the No.1 coal seam were determined by similar simulation test. Then, the layout parameters of working face were determined. The research method of numerical calculation was used to evaluate the degree and uniformity of movement and deformation of the No.1 coal seam, combining five indicators: subsidence, horizontal movement, inclined deformation, curvature deformation, and horizontal deformation. The results indicate that when the working face is arranged using the layout parameters provided in this article, it can promote the further subsidence of the No.1 coal seam at the position of the remaining coal pillar. The movement and deformation indicators of the No.1 coal seam all reach the most uniform degree of the geological mining conditions, which can effectively offset the uneven deformation problem of the No.1 coal seam caused by the influence of the remaining coal pillars, making multiple mining operations a favorable condition for upward mining and achieving the goal of reducing the damage of the No.1 coal seam.
GC-MS profiling of Pistachio vera L., and effect of antioxidant and antimicrobial compounds of it's essential oil compared to chemical counterparts
Authors: Shahdadi Fatemeh , Khorasani Sepideh , Salehi-Sardoei Ali , Fallahnajmabadi Farshad , Fazeli-Nasab Bahman , Sayyed R. Z. 
Published: December 2023

AbstractAll elements of the pistachio tree are considered raw pistachio by-products. The soft hull makes up the majority of these by-products. It contains proteins, fats, minerals, vitamins, phenolics contents (TPC), and antioxidants. Early smiling pistachios are one of the most important sources of pistachio contamination with aflatoxin in the garden and processing stages. The present study aimed to evaluate pistachio hull essential oil (EO) composition, and antioxidant and antimicrobial properties under in vitro conditions. TPC, antioxidant, and antimicrobial activity were measured using the Folin–Ciocalteu reagent, 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging method, and serial dilution titration method, respectively. A gas chromatography system with a mass spectrometer (GC-MS) was utilized to determine the chemical components of the EO. The findings revealed that the quantity of TPC and anti-radical activity in IC50 were 245.43 mg gallic acid/mL and 206.32 µL/L, respectively. The free radical absorption activity of DPPH (%) increased with EO content. The inhibitory activity of EO on Staphylococcus aureus and Bacillus subtilis was much lower than that of streptomycin and penicillin. Aspergillus flavus was effectively inhibited by pistachio hull EO, comparable to fluconazole. The results obtained from GC-MS showed that the major compounds in pistachio hull essential oil include α-pinene (47.36%), terpinolene (10.57%), limonene (9.13%), and L-bornyl acetate (8.57%). The findings indicated that pistachio hull EO has potent antibacterial and antioxidant components and can be employed as a natural antimicrobial and antioxidant in food systems.
Impact of three miRNA signature as potential diagnostic marker for triple negative breast cancer patients
Authors: Kumar Vivek , Gautam Mansi , Chaudhary Amit , Chaurasia Bipin 
Published: December 2023

AbstractBreast cancer is a highly aggressive type of cancer and has several subtypes, including triple-negative breast cancer (TNBC), which accounts for 25% of morbidity related to breast cancer. miRNAs are small non-coding RNA molecules that regulate 60% of human genes. Dysregulated expression of miRNA in liquid biopsy of TNBC patients has the potential as a minimally invasive diagnostic biomarker. The Association of miRNA with TNBC was evaluated using in-silico analysis. Highly enriched miRNAs were selected for functional analysis to evaluate the role of miRNA in the progression of TNBC. The qRT-PCR-based expression analysis of miRNA was performed in 190 serum samples (139 TNBC and 51 healthy). Revealed the elevated expression of miRNA-155 and miRNA-21 in TNBC compared to control samples (P < 0.0001), while miRNA-205 was significantly downregulated in TNBC (P < 0.0001). The combined diagnostic value of the miRNA-205, miRNA-155 and miRNA-21 in cohort-I, cohort-II, and cohort-III was AUC of 96.1% (P < 0.0001), 94.9% (P < 0.0001), and 97.1% (P < 0.0001), respectively. Our study revealed that dysregulated expression of miRNA could be used as an independent indicator for discriminating TNBC from healthy patients. In addition, the combined predictive value of miRNA-205 + miRNA − 155 + miRNA-21 has higher AUC, sensitivity, and specificity in the diagnosis of TNBC in all three cohorts.
Detection of APP gene recombinant in human blood plasma
Authors: Mitsunaga Shigeki , Fujito Naoko , Nakaoka Hirofumi , Imazeki Ryoko , Nagata Eiichiro , Inoue Ituro 
Published: December 2023

AbstractThe pathogenesis of Alzheimer’s disease (AD) is believed to involve the accumulation of amyloid-β in the brain, which is produced by the sequential cleavage of amyloid precursor protein (APP) by β-secretase and γ-secretase. Recently, analysis of genomic DNA and mRNA from postmortem brain neurons has revealed intra-exonic recombinants of APP (gencDNA), which have been implicated in the accumulation of amyloid-β. In this study, we computationally analyzed publicly available sequence data (SRA) using probe sequences we constructed to screen APP gencDNAs. APP gencDNAs were detected in SRAs constructed from both genomic DNA and RNA obtained from the postmortem brain and in the SRA constructed from plasma cell-free mRNA (cf-mRNA). The SRA constructed from plasma cf-mRNA showed a significant difference in the number of APP gencDNA reads between SAD and NCI: the p-value from the Mann–Whitney U test was 5.14 × 10−6. The transcripts were also found in circulating nucleic acids (CNA) from our plasma samples with NGS analysis. These data indicate that transcripts of APP gencDNA can be detected in blood plasma and suggest the possibility of using them as blood biomarkers for Alzheimer's disease.
Implications of seismic and GNSS strain rates in Himachal, Kashmir and Ladakh
Authors: Shrungeshwara T. S. , Narukula Bhavani , Jade Sridevi , Ghavri Sapna , Vivek Chiranjeevi G. , Parvez I. A. 
Published: December 2023

AbstractWe report the present day GNSS velocities (2015–2021) and strain rates in Himachal, Kashmir and Ladakh Himalaya covering the rupture zones of the 2005 Muzaffarabad earthquake and the 1905 Kangra earthquake. Geodetic strain rates estimated from GPS velocities of about 58 sites spanning last two decades of measurements indicate a mean compression rate of − 32.5 ns/year (nanostrain/year) and dilatation of − 37.3 ns/year. Seismic strain rates are estimated using both the instrumental period (1964–2021) and historical earthquakes since 1500 AD in this region. Seismic strain rates during the instrumental period of the past 50 + years indicate a mean compression rate of − 28.1 ns/year and it slightly decreases to − 21.7 ns/year after including the historical earthquakes of the past 520 years. The Azimuth of the seismic strain tensor for the instrumental and historic periods and geodetic strain tensor is broadly consistent with orientation of major faulting in this region suggesting uniform compression over a long-time interval justifying combined analysis of the strain rate field to determine the seismic potential of the region. Composite analysis of geodetic and seismic strain rates and the associated moments estimate the accumulated strain budget of ~ 1E + 21 Nm in the past 520 years which has a potential of generating future earthquake of Mw > 8 in this segment of Northwest Himalaya.