bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequential use of Ad26-based vaccine regimens in NHP to induce immunity against different disease targets
Authors: Khan Selina , Salisch Nadine C. , Gil Ana Izquierdo , Boedhoe Satish , Boer Karin Feddes-de , Serroyen Jan , Schuitemaker Hanneke , Zahn Roland C. 
Published: November 2022

AbstractThe adenovirus (Ad)26 serotype–based vector vaccine Ad26.COV2.S has been used in millions of subjects for the prevention of COVID-19, but potentially elicits persistent anti-vector immunity. We investigated if vaccine-elicited immunity to Ad26 vector–based vaccines significantly influences antigen-specific immune responses induced by a subsequent vaccination with Ad26 vector–based vaccine regimens against different disease targets in non-human primates. A homologous Ad26 vector–based vaccination regimen or heterologous regimens (Ad26/Ad35 or Ad26/Modified Vaccinia Ankara [MVA]) induced target pathogen–specific immunity in animals, but also persistent neutralizing antibodies and T-cell responses against the vectors. However, subsequent vaccination (interval, 26–57 weeks) with homologous and heterologous Ad26 vector–based vaccine regimens encoding different target pathogen immunogens did not reveal consistent differences in humoral or cellular immune responses against the target pathogen, as compared to responses in naïve animals. These results support the sequential use of Ad26 vector–based vaccine regimens targeting different diseases.
Proteomic genotyping of SNP of Complement Factor H (CFH) Y402H and I62V using multiple reaction monitoring (MRM) assays
Authors: Kim Kyoung Lae , Kim Hyerim , Lee Youngju , Lee Cheolju , Joo Kwangsic , Park Sang Jun , Park Kyu Hyung , Park Seong-Jun , Woo Se Joon 
Published: November 2022

AbstractThe single nucleotide polymorphisms (SNPs) of complement factor H (CFH) gene are well-known genetic risk factors for age-related macular degeneration (AMD). To identify whether the measurement of plasma protein concentrations of CFH variants using the multiple reaction monitoring (MRM) assay can determine the genotypes of CFH SNP rs1061170 and rs800292, 120 patients with AMD and 26 controls were included in this study. The number of cases were TT:TC:CC = 121:24:1 in CFH SNP Y402H and GG:AG:AA = 72:57:17 in CFH SNP I62V. Plasma concentrations of tryptic peptides were measured using the MRM assay, and tyrosine/histidine (Y/H) and valine/isoleucine (V/I) CFH variant protein ratios were obtained. To discriminate the genotypes by the plasma protein ratios, cut-off values were set for Y/H ratios (TT: > 4.428; TC: 1.00–4.428; CC: < 1.00) and V/I ratios (GG: > 1.09; AG: 0.0089–1.08; AA: < 0.0089). Correlation analysis revealed that the plasma CFH variant protein ratios and genotypes of CFH were exactly matched (100%) without overlap in the total patients and controls. The measurement of plasma protein CFH variants using the MRM assay can accurately identify the genotypes of CFH SNPs of Y402H and I62V.
Impact of γ-irradiation and SBR content in the compatibility of aminated (PVC/LLDPE)/ZnO for improving their AC conductivity and oil removal
Authors: Sharshir A. I. , Fayek S. A. , El-Gawad Amal F. Abd , Farahat M. A. , Ismail M. I. , Ghobashy Mohamed Mohamady 
Published: November 2022

AbstractIn some cases, blends containing PVC and LLDPE show low compatibility. Adding styrene-butadiene rubber to the PVC/LLDPE mixtures leads to a noticeable increase in tensile strength and compatibility of the blends. Also, an improvement in tensile strength is observed after incorporating SBR compatibilizer resulting in entirely different gamma irradiation doses. Without a compatibilizer, the mixture exhibits a distributed PVC and LLDPE phase with variable sizes and shapes; even a sizable portion of the domains resemble droplets. Styrene butadiene rubber (SBR) and gamma radiation make mixtures of (PVC/LLDPE) more compatible. The SEM study of the blends demonstrated that adding the compatibilizer resulted in finer blend morphologies with less roughness. At the same time, gamma irradiation reduced this droplet and gave a more smooth surface. Poly(vinyl chloride) (PVC) was chemically modified with four different amino compounds, including ethylene diamine (EDA), aniline (An), p-anisidine (pA) and dimethyl aniline (DMA) for improving the electric conductivity and oil removal capability of the blend polymer. All ionomers were prepared by nucleophilic substitution in a solvent/non-solvent system under mild conditions. This work novelty shows a sustainable route for producing oil adsorption materials by recycling plastic waste. After the amination process of poly(vinyl chloride) the oil adsorption was significantly enhanced.
Rapid pathogen identification and phenotypic antimicrobial susceptibility directly from urine specimens
Authors: Burg Larry , Crewe Gretel , DiMeo James , Guo Xin , Li Carmen G. , Mayol Melissa , Tempesta Andrew , Lauzier William , Markham Rachelle , Crissy Katarzyna , Barry Colleen , Walsh Bruce , Kirby James E. , Straus Don 
Published: November 2022

AbstractImplementing effective antimicrobial therapy close to the onset of infection lowers morbidity and mortality and attenuates the spread of antimicrobial resistance. Current antimicrobial susceptibility testing (AST) methods, however, require several days to determine optimal therapies. We present technology and an automated platform that identify (ID) Urinary Tract Infection pathogens in 45 min and provide phenotypic AST results in less than 5 h from urine specimens without colony isolation. The ID and AST tests count cells fluorescently labeled with specific rRNA probes using non-magnified digital imaging. The ID test detected five pathogens at ≤ 7,000 CFU/mL and had a linear range of ~ 4 orders of magnitude. For contrived specimens, AST tests gave 93.1% categorical agreement with 1.3% Very Major Errors (VME), 0.3% Major Errors (ME), and 6.3% minor Errors (mE) compared to the broth microdilution (BMD) reference method. For clinical specimens, the ID test had 98.6% agreement and the AST test had 92.3% categorical agreement with 4.2% mE, 3.4% ME and 4.0% VME compared to BMD. Data presented demonstrates that direct-from-specimen AST tests can accurately determine antimicrobial susceptibility/resistance for each pathogen in a specimen containing two pathogens. The method is robust to urine matrix effects and off-target commensal and contaminating bacteria.
Evaluation of radiomics feature stability in abdominal monoenergetic photon counting CT reconstructions
Authors: Tharmaseelan Hishan , Rotkopf Lukas T. , Ayx Isabelle , Hertel Alexander , Nörenberg Dominik , Schoenberg Stefan O. , Froelich Matthias F. 
Published: November 2022

AbstractFeature stability and standardization remain challenges that impede the clinical implementation of radiomics. This study investigates the potential of spectral reconstructions from photon-counting computed tomography (PCCT) regarding organ-specific radiomics feature stability. Abdominal portal-venous phase PCCT scans of 10 patients in virtual monoenergetic (VM) (keV 40–120 in steps of 10), polyenergetic, virtual non-contrast (VNC), and iodine maps were acquired. Two 2D and 3D segmentations measuring 1 and 2 cm in diameter of the liver, lung, spleen, psoas muscle, subcutaneous fat, and air were obtained for spectral reconstructions. Radiomics features were extracted with pyradiomics. The calculation of feature-specific intraclass correlation coefficients (ICC) was performed by comparing all segmentation approaches and organs. Feature-wise and organ-wise correlations were evaluated. Segmentation-resegmentation stability was evaluated by concordance correlation coefficient (CCC). Compared to non-VM, VM-reconstruction features tended to be more stable. For VM reconstructions, 3D 2 cm segmentation showed the highest average ICC with 0.63. Based on a criterion of ≥ 3 stable organs and an ICC of ≥ 0.75, 12—mainly non-first-order features—are shown to be stable between the VM reconstructions. In a segmentation-resegmentation analysis in 3D 2 cm, three features were identified as stable based on a CCC of > 0.6 in ≥ 3 organs in ≥ 6 VM reconstructions. Certain radiomics features vary between monoenergetic reconstructions and depend on the ROI size. Feature stability was also shown to differ between different organs. Yet, glcm_JointEntropy, gldm_GrayLevelNonUniformity, and firstorder_Entropy could be identified as features that could be interpreted as energy-independent and segmentation-resegmentation stable in this PCCT collective. PCCT may support radiomics feature standardization and comparability between sites.
Manatee calf call contour and acoustic structure varies by species and body size
Authors: Brady Beth , Ramos Eric Angel , May-Collado Laura , Landrau-Giovannetti Nelmarie , Lace Natalija , Arreola Maria Renee , Santos Gabriel Melo , da Silva Vera Maria Ferreira , Sousa-Lima Renata S. 
Published: November 2022

AbstractVocal activity and signal characteristics of mammals are driven by several factors that result in both stability and plasticity over multiple time scales. All three extant species of manatee communicate with several calls that are especially important for maintaining contact between cows and calves. Determining if calf calls differ across manatee species will provide insights into the evolution of species-specific acoustic communication traits. We investigated the interspecific differences in the vocalizations of calves of Amazonian manatees (Trichechus inunguis) and the two subspecies of the West Indian manatee (T. manatus). Vocalizations of individual calves were recorded in rehabilitation centers in Brazil, Puerto Rico, the United States, and Mexico. The acoustic structure of calls produced by manatee calves varied between species and with body size. Amazonian manatee calves produced shorter calls with multiple notes at higher frequency while West Indian calves produced modulated calls that were lower in frequency and longer in duration. Smaller West Indian calves produced frequency modulated, hill-shaped calls that flattened with an increase in body length. Our results provide evidence for divergence in the ontogeny of vocalizations acrossT. manatusandT. inunguisand suggest variation in body size contributed to the evolution of differences in the characteristics of their calls.
Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine
Authors: Hajnic Matea , Alonso-Gil Santiago , Polyansky Anton A. , de Ruiter Anita , Zagrovic Bojan 
Published: November 2022

AbstractCovalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of gene expression by modulating interactions between nucleic acids and protein readers. We derive here the absolute binding free energies and analyze the binding modalities between key modified nucleobases 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (m6A) and all non-prolyl/non-glycyl protein side chains using molecular dynamics simulations and umbrella sampling in both water and methanol, the latter mimicking the low dielectric environment at the dehydrated nucleic-acid/protein interfaces. We verify the derived affinities by comparing against a comprehensive set of high-resolution structures of nucleic-protein complexes involving 5mC. Our analysis identifies protein side chains that are highly tuned for detecting cytosine methylation as a function of the environment and can thus serve as microscopic readers of epigenetic marks. Conversely, we show that the relative ordering of sidechain affinities for 5hmC and m6A does not differ significantly from those for their precursor bases, cytosine and adenine, respectively, especially in the low dielectric environment. For those two modified bases, the effect is more nuanced and manifests itself primarily at the level of absolute changes in the binding free energy. Our results contribute towards establishing a quantitative foundation for understanding, predicting and modulating the interactions between modified nucleic acids and proteins at the atomistic level.
Combining deep learning and crowd-sourcing images to predict housing quality in rural China
Authors: Xu Weipan , Gu Yu , Chen Yifan , Wang Yongtian , Chen Luan , Deng Weihuan , Li Xun 
Published: November 2022

AbstractHousing quality is essential to human well-being, security and health. Monitoring the housing quality is crucial for unveiling the socioeconomic development status and providing political proposals. However, depicting the nationwide housing quality in large-scale and fine detail is exceedingly rare in remote rural areas owing to the high cost of canonical survey methods. Taking rural China as an example, we collect massive rural house images for housing quality assessment by various volunteers and further build up a deep learning model based on the assessed images to realize an automatic prediction for huge raw house images. As a result, the model performance achieves a high R2 of 0.76. Afterward, the housing qualities of 10,000 Chinese villages are estimated based on 50,000 unlabeled geo-images, and an apparent spatial heterogeneity is discovered. Specifically, divided by Qinling Mountains-Huaihe River Line, housing quality in southern China is much better than in northern China. Our method provides high-resolution predictions of housing quality across the extensive rural area, which could be a complementary tool for automatical monitoring of housing change and supporting house-related policymaking.
QTL associated with resistance to Stagonosporopsis citrulli in Citrullus amarus
Authors: Adams Lincoln , McGregor Cecilia 
Published: November 2022

AbstractGummy stem blight (GSB) is a fungal disease affecting cucurbit crops, including watermelon (Citrullus lanatus), leading to significant yield losses. The disease is caused by three Stagonosporopsis species, of which Stagonosporopsis citrulli is the most common in the southeastern United States. Currently no gummy stem blight-resistant watermelon cultivars are available to growers. In this study, QTL-seq in an interspecific population developed from Sugar Baby × PI 189225 (Citrullus amarus) identified QTL on chromosomes 2, 5, 9 and 11. A novel QTL on chromosome 5 (Qgsb5.2) associated with resistance to S. citrulli (PVE = 13.3%) was confirmed by genetic mapping. KASP marker assays were developed for selection of Qgsb5.2 to allow breeders to track the allele contributing resistance to GSB, reducing the need for laborious phenotyping. Pyramiding different GSB resistance QTL could be a useful strategy to develop GSB resistant watermelon cultivars.
Impacts of breast cancer and chemotherapy on gut microbiome, cognitive functioning, and mood relative to healthy controls
Authors: Bilenduke Emily , Sterrett John D. , Ranby Krista W. , Borges Virginia F. , Grigsby Jim , Carr Alaina L. , Kilbourn Kristin , Lowry Christopher A. 
Published: November 2022

AbstractWomen diagnosed with breast cancer undergoing chemotherapy experience cognitive impairment, symptoms of anxiety and depression, and physical side effects including disruption in the diversity and community composition of the gut microbiome. To date, there is limited research exploring the associations among these specific challenges. The present cross-sectional study explored the associations of self-reported cognitive functioning, depression, and anxiety symptoms, and gut microbiome diversity and community composition in women who were diagnosed with and undergoing chemotherapy treatment for breast cancer (BC) compared to cancer-free healthy controls (HC). The BC group displayed higher rates of cognitive dysfunction (p < 0.001) and depressive symptoms (p < 0.05) relative to HC. There was a significant difference in microbiome community composition between BC and HC, particularly characterized by a decreased relative abundance of the mucin-degrading genus Akkermansia in BC compared to HC (p < 0.05). Association models identified significant associations among group, cognitive, depression, and microbiome variables (p < 0.001). Overall, the study identified that BC participants experienced significant differences in self-reported cognitive functioning, self-reported depression symptoms, microbiome community composition, and mucin-degrading bacteria of the gut-mucosal barrier, relative to HC. The present study is consistent with the hypothesis that gut microbiome community composition impacts a woman’s experience with breast cancer and treatment suggesting that microbiome-based interventions have potential for improving quality of life outcomes in individuals with breast cancer.
Cardiac function in relation to functional status and fatigue in patients with post-COVID syndrome
Authors: Baum Paul , Do Lisa , Deterding Lea , Lier Julia , Kunis Ines , Saur Dorothee , Classen Joseph , Wirtz Hubert , Laufs Ulrich 
Published: November 2022

AbstractPatients with Post-COVID syndrome (PCS) are frequently referred for cardiologic evaluation. We assessed cardiac function and biomarkers in relation to functional status and fatigue in patients with PCS. This prospective single-center cohort study included 227 patients with persisting symptoms after COVID-19 infection. Most frequent complaints were fatigue (70%), dyspnea (56%), neurocognitive symptoms (34%) and chest pain (28%). Standardized questionnaires were used to assess Post-COVID-Functional-Scale (PCFS) and fatigue (MFI-20). The fatigue severity was inversely related to age and did not correlate with cardiovascular diseases, echocardiographic findings, or biomarkers. Similarly, mild to moderate functional impairment (PCFS 1–3) did not correlate with cardiovascular alterations. However, the subgroup of patients with significant functional impairment (PCFS = 4) had more frequent cardiovascular comorbidities, biomarkers and impaired global longitudinal strain (GLS). Patients with elevated troponin T showed abnormal GLS, reduced left ventricular ejection fraction and impaired tricuspid annular plane systolic excursion. The majority of patients with PCS shows a normal cardiac function. Only the small subgroup of patients with severe functional impairment and patients with elevated troponin T is at risk for impaired cardiac function and likely to benefit from specialized care by a cardiologist.
Prognostic model for survival of patients with abdominal aortic aneurysms treated with endovascular aneurysm repair
Authors: Meuli Lorenz , Zimmermann Alexander , Menges Anna-Leonie , Stefanikova Sandra , Reutersberg Benedikt , Makaloski Vladimir 
Published: November 2022

AbstractThe role of endovascular aneurysm repair (EVAR) in patients with asymptomatic abdominal aortic aneurysm (AAA) who are unfit for open surgical repair has been questioned. The impending risk of aneurysm rupture, the risk of elective repair, and the life expectancy must be balanced when considering elective AAA repair. This retrospective observational cohort study included all consecutive patients treated with standard EVAR for AAA at a referral centre between 2001 and 2020. A previously published predictive model for survival after EVAR in patients treated between 2001 and 2012 was temporally validated using patients treated at the same institution between 2013 and 2020 and updated using the overall cohort. 558 patients (91.2% males, mean age 74.9 years) were included. Older age, lower eGFR, and COPD were independent predictors for impaired survival. A risk score showed good discrimination between four risk groups (Harrel’s C = 0.70). The 5-years survival probabilities were only 40% in “high-risk” patients, 68% in “moderate-to-high-risk” patients, 83% in “low-to-moderate-risk”, and 89% in “low-risk” patients. Low-risk patients with a favourable life expectancy are likely to benefit from EVAR, while high-risk patients with a short life expectancy may not benefit from EVAR at the current diameter threshold.
Microfluidic dose–response platform to track the dynamics of drug response in single mycobacterial cells
Authors: Mistretta Maxime , Gangneux Nicolas , Manina Giulia 
Published: November 2022

AbstractPreclinical analysis of drug efficacy is critical for drug development. However, conventional bulk-cell assays statically assess the mean population behavior, lacking resolution on drug-escaping cells. Inaccurate estimation of efficacy can lead to overestimation of compounds, whose efficacy will not be confirmed in the clinic, or lead to rejection of valuable candidates. Time-lapse microfluidic microscopy is a powerful approach to characterize drugs at high spatiotemporal resolution, but hard to apply on a large scale. Here we report the development of a microfluidic platform based on a pneumatic operating principle, which is scalable and compatible with long-term live-cell imaging and with simultaneous analysis of different drug concentrations. We tested the platform with mycobacterial cells, including the tubercular pathogen, providing the first proof of concept of a single-cell dose–response assay. This dynamic in-vitro model will prove useful to probe the fate of drug-stressed cells, providing improved predictions of drug efficacy in the clinic.
Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion
Authors: Claudel Iris , Brouazin Ronan , Lancelot Renaud , Gouagna Louis-Clément , Dupraz Marlène , Baldet Thierry , Bouyer Jérémy 
Published: November 2022

AbstractCompetent arbovirus vectors are found in the culicid mosquito fauna of south-west Indian Ocean (SWIO) islands. In La Reunion, Aedes albopictus and Aedes aegypti mosquitoes are known vectors of dengue and chikungunya viruses. Culex quinquefasciatus is a potential vector of Rift Valley fever and West Nile viruses. To prepare a vector-control field trial against Ae. aegypti, this study aimed at identifying the best trapping strategy to catch adult Ae. aegypti, using BG-Sentinel traps (Biogents, Germany). It was implemented in two sites in southern La Reunion. Catches of Ae. albopictus and Cx. quinquefasciatus mosquitoes were also recorded. A Latin square design was used to estimate the detection probability and the apparent daily density—according to the BG-Sentinel trapping strategy: none, carbon dioxide (CO2), a commercial attractant—BG-Lure (Biogents, Germany), or both. The use of CO2 alone was associated with a higher detection probability for Ae. aegypti and Cx. quinquefasciatus mosquitoes, as well as a large increase in their apparent density. Traps with BG-Lure—alone or in combination with CO2, did not improve the detection probability of Ae. aegypti and Cx. quinquefasciatus mosquitoes. The same result was found for male Ae. albopictus. For females, baiting BG-Sentinel traps with CO2 or BG-Lure had no significant effect. The same apparent densities were found for Ae. aegypti and Ae. albopictus mosquitoes in both study sites—where Ae. aegypti mosquitoes were found at very low densities during previous surveys.