bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution
Authors: Eastburn Dennis J. , White Kevin S. , Jayne Nathan D. , Camiolo Salvatore , Montis Gioele , Ha Seungeun , Watson Kendall G. , Yeakley Joanne M. , McComb Joel , Seligmann Bruce 
Published: December 2024

AbstractWe report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000 + cells per sample. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC offers a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has a multiplet rate of less than 1.1% and a cell capture rate of ~ 50%. Although the assay can accurately profile the whole transcriptome (19,683 human, 21,400 mouse and 21,119 rat genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest – thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of more than 90,000 cells across multiple species and sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate more than 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies with high data quality.
A ridge-loaded staggered double-vane slow wave structure for terahertz radiation sources
Authors: Latif Jibran , Wang Zhanliang , Jameel Atif , Ali Bilawal , Nadeem Muhammad Khawar , Gong Yubin 
Published: December 2024

AbstractA ridge-loaded staggered double-vane slow-wave structure is proposed for terahertz radiation sources employing a sheet electron beam. This slow-wave structure has the advantages of enhanced electric field and energy density distribution and improved interaction impedance in the beam-wave interaction region. High-frequency characteristics are investigated for the proposed slow wave structure and compared with those of the staggered double-vane slow wave structure. The slow wave structure is fabricated and experimentally tested for transmission and reflection properties, revealing $$S_{21}$$ above -2 dB and $$S_{11}$$ below -17 dB at 0.34 THz for a backward wave oscillator. Steady transmission of the 21.7 kV sheet electron beam is achieved by designing a periodic cusped magnetic system (0.2 T) along with a sheet electron beam gun (50 mA). Beam-wave interaction simulations utilizing 100 periods demonstrate a peak power of 14 W and continuous frequency tuning from 0.295-0.375 THz for the proposed slow wave structure, whereas the staggered double-vane slow wave structure achieves 8.5 W peak power and frequency tuning from 0.308-0.366 THz. The sensitivity of the output power to the added ridge geometry is also analyzed. These findings indicate that the novel ridge-loaded staggered double vane slow-wave structure is promising for developing high-power broad frequency tunable terahertz radiation sources.
Effect of exogenous treatment with zaxinone and its mimics on rice root microbiota across different growth stages
Authors: Mazzarella Teresa , Chialva Matteo , de Souza Leonardo Perez , Wang Jian You , Votta Cristina , Tiozon Rhowell , Vaccino Patrizia , Salvioli di Fossalunga Alessandra , Sreenivasulu Nese , Asami Tadao , Fernie Alisdair R. , Al-Babili Salim , Lanfranco Luisa , Fiorilli Valentina 
Published: December 2024

AbstractEnhancing crops productivity to ensure food security is one of the major challenges encountering agriculture today. A promising solution is the use of biostimulants, which encompass molecules that enhance plant fitness, growth, and productivity. The regulatory metabolite zaxinone and its mimics (MiZax3 and MiZax5) showed promising results in improving the growth and yield of several crops. Here, the impact of their exogenous application on soil and rice root microbiota was investigated. Plants grown in native paddy soil were treated with zaxinone, MiZax3, and MiZax5 and the composition of bacterial and fungal communities in soil, rhizosphere, and endosphere at the tillering and the milky stage was assessed. Furthermore, shoot metabolome profile and nutrient content of the seeds were evaluated. Results show that treatment with zaxinone and its mimics predominantly influenced the root endosphere prokaryotic community, causing a partial depletion of plant-beneficial microbes at the tillering stage, followed by a recovery of the prokaryotic community structure during the milky stage. Our study provides new insights into the role of zaxinone and MiZax in the interplay between rice and its root-associated microbiota and paves the way for their practical application in the field as ecologically friendly biostimulants to enhance crop productivity.
A new diminutive species of bohaiornithid enantiornithine (Aves: Ornithothoraces) from the Lower Cretaceous Jehol Group, northern China
Authors: Shen Caizhi , Clark Alexander D. , Fang Hui , Chen Shaokun , Jiang Hongxia , Ji Qiang , O’Connor Jingmai K. 
Published: December 2024

AbstractEnantiornithes are the most successful early-diverging avian clade, their fossils revealing important information regarding the structure of Cretaceous avifaunas and the parallel refinement of flight alongside the ornithuromorph lineage that includes modern birds. The most diverse recognized family of Early Cretaceous enantiornithines is the Bohaiornithidae, known from the Jehol Biota in northeastern China. Members of this clade enhance our understanding of intraclade morphological diversity and elucidate the independent evolution of this unique lineage. Here, we report on a new specimen of bohaiornithid, Neobohaiornis lamadongensis gen. et sp. nov., from the Lower Cretaceous Jiufotang Formation in western Liaoning, China. The holotype specimen is considerably smaller than all other known bohaiornithids (roughly half the size of Bohaiornis). The presence of complete fusion in compound elements strongly suggests it represents a mature or nearly mature individual, and therefore substantially increases the known size range of this clade. This specimen further differs from known bohaiornithids in that it exhibits reduced manual unguals and an increased number of sacral vertebrae, which indicates bohaiornithids evolved increased flight capabilities in parallel to other enantiornithine lineages, such as the Longipterygidae. Traces of the plumage, which are rarely preserved in bohaiornithids, reveal the presence of remiges with rounded distal margins and short crural feathers.
Predictive nomogram of ultrasound indicators for the termination outcome of caesarean scar pregnancy
Authors: Xiao Xiaoyi , Feng Zhichao , Li Ting , Qiao Hong , Zhu Yun 
Published: December 2024

AbstractTo develop and validate a nomogram for predicting the risk of adverse events (intraoperative massive haemorrhage or retained products of conception) associated with the termination of Caesarean scar pregnancy (CSP). Data were retrospectively collected from patients diagnosed with CSP who underwent Dilation and Curettage (D&C) at two hospitals. This data was divided into internal and external cohorts for analysis. The internal cohort was randomly split, with 70% of the data designated for a training set and 30% for an internal validation set. The external cohort served exclusively as the external validation set. LASSO and logistic regression techniques were employed to select variables and construct the nomogram. The performance of the nomogram was evaluated using various methods, including C-index, calibration curve, decision curve analysis (DCA), and clinical impact curve analysis (CICA), to assess its identification, calibration, and clinical effectiveness. The prediction nomogram included several predictors, such as scar thickness, type of CSP, gestational sac diameter, and blood flow. It demonstrated strong discrimination, with a C-index of 0.83 (95% confidence interval: 0.77–0.89). Furthermore, in the internal validation set, a high C-index of 0.78 was achieved, while in the external validation set, it reached 0.83. Additional assessments using calibration curve analysis, DCA, and CICA indicated robust agreement between the nomogram’s predictions and actual observations, highlighting its utility and reliability. The developed nomogram shows excellent discriminative ability and calibration, with the potential for effective local prediction of adverse events in CSP.
Biopreservation and reversal of oxidative injury during blood storage by a novel curcumin-based gel formulation
Authors: Hicks Wayne , Jana Sirsendu , Kassa Tigist , Prince Richard , Cabrales Pedro , Friedman Joel , Alayash Abdu I. 
Published: December 2024

AbstractBlood storage lesion induces cytosolic and membrane changes driven in part by hemoglobin (Hb) oxidation reactions within red blood cells (RBCs). A novel gel formulation containing the antioxidant curcuminoids in a biocompatible solvent system was used to deliver curcumin into RBCs. Incubation of peroxide treated RBCs stored in PBS with curcumin gel led to a reduction in prooxidant ferrylHb and recovery in ATP. Curcumin treatment prevented band 3 tyrosine (Y359 and Y21) phosphorylation. RBCs stored in AS-3 solutions for 28, 35, 42 and 49 days, following a single-dose of 100µM curcuminoids at each time points, caused reduction in protein carbonylation and considerable recovery in ATP levels. Proteomic analysis revealed minimal changes in the proteomic landscape in 35 days. However, a downregulation in fibrinogen was observed in the treated samples which may reduce RBC aggregation. Additionally, we used a guinea pig model where the circulation of infused aged RBCs can be extended (approximately 10%) when treated with curcumin gel at the start of storage. Our data therefore provide mechanistic insights and supportive animal data into benefits of treating stored RBCs with a novel curcuminoid formulation based on the biopreservation of RBC membrane integrity, redox balance, and increased longevity in circulation.
New-onset cardiovascular diseases post SARS-CoV-2 infection in an urban population in the Bronx
Authors: Lu Jason Y. , Lu Justin Y. , Wang Stephen H. , Duong Katie S. , Hou Wei , Duong Tim Q. 
Published: December 2024

AbstractThis study investigated the incidence of new-onset cardiovascular disorders up to 3.5 years post SARS-CoV-2 infection for 56,400 individuals with COVID-19 and 1,093,904 contemporary controls without COVID-19 in the Montefiore Health System (03/11/2020 to 07/01/2023). Outcomes were new incidence of major adverse cardiovascular event (MACE), arrhythmias, inflammatory heart disease, thrombosis, cerebrovascular disorders, ischemic heart disease and other cardiac disorders between 30 days and (up to) 3.5 years post index date. Results were also compared with a pre-pandemic cohort over similar observation duration (N = 64,541). Cumulative incidence and hazard ratios adjusted for competitive risks were analyzed. Compared to contemporary controls, hospitalized COVID-19 patients had significantly higher risk of developing MACE (aHR = 2.29, 95% confidence interval [2.27, 2.31], p < 0.001), arrhythmias (aHR = 2.54[2.50, 2.58], p < 0.001), inflammatory heart disease (aHR = 5.34[4.79, 5.96], p < 0.001), cerebrovascular (aHR = 2.05[2.00, 2.11], p < 0.001), other cardiac disorders (aHR = 2.31[2.26, 2.35], p < 0.001), thrombosis (aHR = 4.25[4.15, 4.36], p < 0.001), and ischemic heart disease (aHR = 1.89[1.86, 1.92], p < 0.001). Non-hospitalized COVID-19 patients had slightly higher risk of developing MACE (aHR = 1.04[1.03, 1.06], p < 0.001), arrhythmias (aHR = 1.10[1.08, 1.12], p < 0.001), inflammatory heart disease (aHR = 2.29 [2.03, 2.59], p < 0.001), cerebrovascular (aHR = 1.11[1.07, 1.15], p < 0.001), and ischemic heart disease (aHR = 1.10[1.08, 1.13], p < 0.001). Race and ethnicity were mostly not associated with increased risks (p > 0.05). aHRs with contemporary controls as a reference were similar to those with pre-pandemic cohort as a reference. We concluded that new incident cardiovascular disorders in COVID-19 patients, especially those hospitalized for COVID-19, were higher than those in controls. Identifying risk factors for developing new-onset cardiovascular disorders may draw clinical attention for the need for careful follow-up in at-risk individuals.
Exploiting full-duplex opportunities in WLANs via a reinforcement learning-based medium access control protocol
Authors: Liu Song , Wei Peng 
Published: December 2024

AbstractIn-band full-duplex communication has the potential to double the wireless channel capacity. However, how to efficiently transform the full-duplex gain at the physical layer into network throughput improvement is still a challenge, especially in dynamic communication environments. This paper presents a reinforcement learning-based full-duplex (RLFD) medium access control (MAC) protocol for wireless local-area networks (WLANs) with full-duplex access points. To solve the channel contention problem and fully utilize the full-duplex transmission opportunities, we first design a two-way handshake transmission mechanism and make an investigation on the effects of transmission scheduling in full-duplex transmission. Then the transmission scheduling problem is theoretically formulated as a non-stationary multi-armed bandit problem in which our objective is to maximize the network throughput. Thus, we develop a Window-Constraint Bayesian (WCB) algorithm to generate optimized scheduling policies online. And full-duplex opportunities are fully utilized by transmitting packets according to the optimized scheduling policies. Besides, an analytical model is developed to characterize the performance of RLFD. The performance of RLFD is evaluated by simulation. And the results show that RLFD can improve the network throughput by 80% compared with the IEEE 802.11 distributed coordination function with Request-To-Send/Clear-To-Send. Moreover, with the proposed WCB algorithm, the network throughput can remain steady as the communication environment dynamically changes.
Metabolic profiling reveals altered amino acid and fatty acid metabolism in children with Williams Syndrome
Authors: Chen Weijun , Yang Yang , Zhang Yu , Sun Changxuan , Ji Chai , Shen Jiyang , Li Fangfang , Xiao Yingping , Wen Yang , Liu Qian , Zou Chaochun 
Published: December 2024

AbstractWilliams Syndrome (WS) is a rare neurodevelopmental disorder with a prevalence of 1 in 7500 to 1 in 20,000 individuals, caused by a microdeletion in chromosome 7q11.23. Despite its distinctive clinical features, the underlying metabolic alterations remain largely unexplored. This study employs targeted metabolomics to investigate the metabolic characteristics of children with WS. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified significant dysregulation of 15 metabolites, with 11 upregulated and 4 downregulated. Notably, amino acids such as alanine, proline, and arginine were significantly elevated. Fatty acid metabolism showed pronounced upregulation of long-chain saturated fatty acids (C18:0, C20:0, C22:0, C24:0, C26:0, and C28:0) and downregulation of long-chain unsaturated fatty acids (C18:2 LA, C22:6 DHA, C16:1 PLA, and t-C18:1 EA), except for upregulated nervonic acid (C24:1) and arachidonic acid (C20:4). Metabolic pathway analysis highlighted disruptions in arginine synthesis, arginine/proline metabolism, alanine, aspartate and glutamate metabolism, biosynthesis of unsaturated fatty acids, linoleic acid metabolism, and arachidonic acid metabolism. This study provides the first comprehensive analysis of amino acid and fatty acid metabolism in children with WS, offering insights into the disorder’s complex metabolic landscape. Further validation in larger cohorts is essential to confirm these findings and their potential as biomarkers and therapeutic targets.
405 nm violet-blue light inactivates hepatitis C cell culture virus (HCVcc) in ex vivo human platelet concentrates and plasma
Authors: Jackson Joseph W. , Kaldhone Pravin R. , Stewart Caitlin , Anderson John , MacGregor Scott , Maclean Michelle , Major Marian , Atreya Chintamani D. 
Published: December 2024

AbstractAdded safety measures coupled with the development and use of pathogen reduction technologies (PRT) significantly reduces the risk of transfusion-transmitted infections (TTIs) from blood products. Current approved PRTs utilize chemical and/or UV-light based inactivation methods. While the effectiveness of these PRTs in reducing pathogens are well documented, these can cause tolerable yet unintended consequences on the quality and efficacy of the transfusion products. As an alternative to UV-based approaches, we have previously demonstrated that 405 nm violet-blue light exposure successfully inactivates a variety of pathogens, including bacteria, parasites, and viruses, in both platelet concentrates (PCs) and plasma. Herein, we show that 405 nm light treatment effectively inactivates hepatitis C cell culture virus (HCVcc) by up to ~ 3.8 log10 in small volumes of a variety of matrices, such as cell culture media, PBS, plasma, and PCs with 27 J/cm2 of light exposure, and total inactivation of HCVcc after 162 J/cm2 light exposure. Furthermore, we demonstrate that carry-over of media supplemented with fetal bovine serum enhances the production of reactive oxygen species (ROS), providing mechanistic insights to 405 nm light-mediated viral inactivation. Overall, 405 nm light successfully inactivates HCVcc, further strengthening this method as a novel PRT for platelets and plasma.
A novel sweat sensor detects inflammatory differential rhythmicity patterns in inpatients and outpatients with cirrhosis
Authors: Davis Brian C. , Lin Kai-Chun , Shahub Sarah , Ramasubramanya Annapoorna , Fagan Andrew , Muthukumar Sriram , Prasad Shalini , Bajaj Jasmohan S. 
Published: December 2024

AbstractPatients with cirrhosis have high systemic inflammation (TNFα, CRP, and IL-6) that is associated with poor outcomes. These biomarkers need continuous non-invasive monitoring, which is difficult with blood. We studied the AWARE sweat-sensor to measure these in passively expressed sweat in healthy people (N = 12) and cirrhosis (N = 32, 10 outpatients/22 inpatients) for 3 days. Blood CRP, TNFα, IL6, levels, and liver function and quality of life were measured. We found that CRP, TNFα, and IL6 were correlated in sweat and serum among both groups and were evaluated in inpatients versus outpatients/controls. IL6 is associated with lower transplant-free survival. Sweat monitoring nocturnal CRP/IL6 elevations in cirrhosis versus controls. Outpatients with cirrhosis had inflammation levels that elevated during the evening and peaked towards the early night periods. The levels start to fall much later at night and early morning. These data suggest that further investigation of continuous measurement of sweat biomarkers in cirrhosis is warranted.
An Online Tool for Correcting Performance Measures of Electronic Phenotyping Algorithms for Verification Bias
Authors: Bhasin Ajay , Bielinski Sue , Kho Abel N. , Larson Nicholas , Rasmussen-Torvik Laura J. 
Published: December 2024

Abstract
Objectives Computable or electronic phenotypes of patient conditions are becoming more commonplace in quality improvement and clinical research. During phenotyping algorithm validation, standard classification performance measures (i.e., sensitivity, specificity, positive predictive value, negative predictive value, and accuracy) are often employed. When validation is performed on a randomly sampled patient population, direct estimates of these measures are valid. However, studies will commonly sample patients conditional on the algorithm result prior to validation, leading to a form of bias known as verification bias.
Methods We illustrate validation study sampling design and naïve and bias-corrected validation performance through both a concrete example (1,000 cases, 100 noncases, 1:1 sampling on predicted status) and a more thorough simulation study under varied realistic scenarios. We additionally describe the development of a free web calculator to adjust estimates for people validating phenotyping algorithms.
Results In our illustrative example, naïve performance estimates corresponded to 0.942 sensitivity, 0.979 specificity, and 0.960 accuracy; these contrast proper estimates of 0.620 sensitivity, 0.999 specificity, and 0.944 accuracy after adjusting for verification bias using our free calculator. Our simulation results demonstrate increasing positive bias for sensitivity and negative bias for specificity as the disease prevalence approaches zero, with decreasing positive predictive value moderately exacerbating these biases.
Conclusion Novel computable phenotypes of patient conditions must account for verification bias when calculating performance measures of the algorithm. The performance measures may vary significantly based on disease prevalence in the source population so use of a free web calculator to adjust these measures is desirable.
Vascular Air Embolism in Neonates: A Literature Review
Authors: Zhou Qi , Lee Shoo K. 
Published: December 2024

Neonatal vascular air embolism is a rare but often fatal condition. The literature comprises mostly case reports and a few dated systematic reviews. Our objective was to review all case reports of neonatal vascular air embolism to date and provide up-to-date information about patient characteristics, clinical presentations, outcomes, pathogenesis, diagnosis, prevention, treatment, and prognosis. We searched the literature for case reports of neonatal vascular air embolism, using MEDLINE, CINAHL, and EMBASE, and the keywords “neonates” and “vascular air embolism.” Results were summarized. There were 117 cases of neonatal vascular air embolism, with a mean gestational age of 30.4 weeks (range: 23–40), mean birth weight of 1,422 g (range 830–3,844), and median age of occurrence of 2 days (range: 1–540) after birth. The majority were preterm (75.2%), male (62.7%), on assisted respiratory support (90.5%), and had air leak syndrome (52.9%). The most common clinical presentation was sudden acute clinical deterioration, sometimes accompanied by crying, cardiac rhythm abnormalities, skin discoloration, and a decrease in end-tidal carbon dioxide concentration. Incidence of mortality and adverse neurological sequelae among survivors was 73.9 and 16.6%, respectively, overall, but significantly (p < 0.05) higher among preterm infants (81.8 and 31.2%, respectively) and lower among surgical infants (23.8 and 0%, respectively). Diagnosis included visualizing air in infusion lines or retinal vessels, a decrease in the end-tidal carbon dioxide levels, and radiographic, doppler ultrasound, transesophageal echocardiography, or computed tomography (CT) imaging. The prognosis for neonatal air embolism is poor, especially for preterm infants requiring mechanical ventilation. Prevention is key and treatment is supportive.
Key Points