bluuebunny/crossref_metadata_2025_split huggingface dataset:
A third vaccination with a single T cell epitope confers protection in a murine model of SARS-CoV-2 infection
Authors: Pardieck Iris N. , van der Sluis Tetje C. , van der Gracht Esmé T. I. , Veerkamp Dominique M. B. , Behr Felix M. , van Duikeren Suzanne , Beyrend Guillaume , Rip Jasper , Nadafi Reza , Beyranvand Nejad Elham , Mülling Nils , Brasem Dena J. , Camps Marcel G. M. , Myeni Sebenzile K. , Bredenbeek Peter J. , Kikkert Marjolein , Kim Yeonsu , Cicin-Sain Luka , Abdelaal Tamim , van Gisbergen Klaas P. J. M. , Franken Kees L. M. C. , Drijfhout Jan Wouter , Melief Cornelis J. M. , Zondag Gerben C. M. , Ossendorp Ferry , Arens Ramon 
Published: July 2022

AbstractUnderstanding the mechanisms and impact of booster vaccinations are essential in the design and delivery of vaccination programs. Here we show that a three dose regimen of a synthetic peptide vaccine elicits an accruing CD8+ T cell response against one SARS-CoV-2 Spike epitope. We see protection against lethal SARS-CoV-2 infection in the K18-hACE2 transgenic mouse model in the absence of neutralizing antibodies, but two dose approaches are insufficient to confer protection. The third vaccine dose of the single T cell epitope peptide results in superior generation of effector-memory T cells and tissue-resident memory T cells, and these tertiary vaccine-specific CD8+ T cells are characterized by enhanced polyfunctional cytokine production. Moreover, fate mapping shows that a substantial fraction of the tertiary CD8+ effector-memory T cells develop from re-migrated tissue-resident memory T cells. Thus, repeated booster vaccinations quantitatively and qualitatively improve the CD8+ T cell response leading to protection against otherwise lethal SARS-CoV-2 infection.
Diurnal modulation of subthalamic beta oscillatory power in Parkinson’s disease patients during deep brain stimulation
Authors: van Rheede Joram J. , Feldmann Lucia K. , Busch Johannes L. , Fleming John E. , Mathiopoulou Varvara , Denison Timothy , Sharott Andrew , Kühn Andrea A. 
Published: July 2022

AbstractBeta-band activity in the subthalamic local field potential (LFP) is correlated with Parkinson’s disease (PD) symptom severity and is the therapeutic target of deep brain stimulation (DBS). While beta fluctuations in PD patients are well characterized on shorter timescales, it is not known how beta activity evolves around the diurnal cycle, outside a clinical setting. Here, we obtained chronic recordings (34 ± 13 days) of subthalamic beta power in PD patients implanted with the Percept DBS device during high-frequency DBS and analysed their diurnal properties as well as sensitivity to artifacts. Time of day explained 41 ± 9% of the variance in beta power (p < 0.001 in all patients), with increased beta during the day and reduced beta at night. Certain movements affected LFP quality, which may have contributed to diurnal patterns in some patients. Future DBS algorithms may benefit from taking such diurnal and artifactual fluctuations in beta power into account.
CovidPubGraph: A FAIR Knowledge Graph of COVID-19 Publications
Authors: Pestryakova Svetlana , Vollmers Daniel , Sherif Mohamed Ahmed , Heindorf Stefan , Saleem Muhammad , Moussallem Diego , Ngomo Axel-Cyrille Ngonga 
Published: July 2022

AbstractThe rapid generation of large amounts of information about the coronavirus SARS-CoV-2 and the disease COVID-19 makes it increasingly difficult to gain a comprehensive overview of current insights related to the disease. With this work, we aim to support the rapid access to a comprehensive data source on COVID-19 targeted especially at researchers. Our knowledge graph, CovidPubGraph, an RDF knowledge graph of scientific publications, abides by the Linked Data and FAIR principles. The base dataset for the extraction is CORD-19, a dataset of COVID-19-related publications, which is updated regularly. Consequently, CovidPubGraph is updated biweekly. Our generation pipeline applies named entity recognition, entity linking and link discovery approaches to the original data. The current version of CovidPubGraph contains 268,108,670 triples and is linked to 9 other datasets by over 1 million links. In our use case studies, we demonstrate the usefulness of our knowledge graph for different applications. CovidPubGraph is publicly available under the Creative Commons Attribution 4.0 International license.
Predicting the impacts of land management for sustainable development on depression risk in a Ugandan case study
Authors: Pienkowski Thomas , Keane Aidan , Kinyanda Eugene , Asiimwe Caroline , Milner-Gulland E. J. 
Published: July 2022

AbstractAgricultural intensification and expanding protected areas are proposed sustainable development approaches. But, their consequences for mental health are poorly understood. This study aims to predict how forest conservation and contract farming may alter resource access and depression risk in rural Uganda. Residents (N = 695) in 11 communities in Masindi District were asked about their expectations under land management scenarios using scenario-based interviews, household characteristics and depression symptoms. Over 80% of respondents presented with a ‘business-as-usual forest access’ scenario expected reduced access to forest income and food over the next decade; this number climbed above 90% among ‘restricted forest access’ scenario respondents. Over 99% of those presented with two land access scenarios (‘business-as-usual land access’ and ‘sugarcane expansion land access’) expected wealthy households to gain land but poorer families to lose it, threatening to increase poverty and food insecurity among small-scale farmers. Bayesian structural equation modelling suggested that depression severity was positively associated with food insecurity (0.20, 95% CI = 0.12–0.28) and economic poverty (0.11, 95% CI 0.02–0.19). Decision-makers should evaluate the mental health impacts of conservation and agricultural approaches that restrict access to livelihood resources. Future research could explore opportunities to support mental health through sustainable use of nature.
A novel prognostic model for malignant patients with Gram-negative bacteremia based on real-world research
Authors: Ni Sujiao , Xu Pingyao , Zhang Kaijiong , Zou Haiming , Luo Huaichao , Liu Chang , Li Yuping , Li Yan , Wang Dongsheng , Zhang Renfei , Zu Ruiling 
Published: July 2022

AbstractGram-negative bacteremia (GNB) is a common complication in malignant patients. Identifying risk factors and developing a prognostic model for GNB might improve the survival rate. In this observational and real-world study, we retrospectively analyzed the risk factors and outcomes of GNB in malignant patients. Multivariable regression was used to identify risk factors for the incidence of GNB, while Cox regression analysis was performed to identify significant prognostic factors. A prognostic model was constructed based on Cox regression analysis and presented on a nomogram. ROC curves, calibration plots, and Kaplan–Meier analysis were used to estimate the model. It comprised 1004 malignant patients with Bloodstream infection (BSI) in the study cohort, 65.7% (N = 660) acquired GNB. Multivariate analysis showed gynecologic cancer, hepatobiliary cancer, and genitourinary cancer were independent risk factors related to the incidence of GNB. Cox regression analysis raised that shock, admission to ICU before infection, pulmonary infection, higher lymphocyte counts, and lower platelet counts were independent risk factors for overall survival (OS). The OS was significantly different between the two groups classified by optimal cut-off value (log-rank, p < 0.001). Above all, a nomogram was created based on the prognostic model, which was presented on a website freely. This real-world study was concentrated on the malignant patients with GNB and proved that shock, admission to ICU before infection, pulmonary infection, higher lymphocyte counts, and lower platelet counts were related to the death of these patients. And a prognostic model was constructed to estimate the risk score of mortality, further to reduce the risk of death.
CyberSco.Py an open-source software for event-based, conditional microscopy
Authors: Chiron Lionel , Le Bec Matthias , Cordier Céline , Pouzet Sylvain , Milunov Dimitrije , Banderas Alvaro , Di Meglio Jean-Marc , Sorre Benoit , Hersen Pascal 
Published: July 2022

AbstractTimelapse fluorescence microscopy imaging is routinely used in quantitative cell biology. However, microscopes could become much more powerful investigation systems if they were endowed with simple unsupervised decision-making algorithms to transform them into fully responsive and automated measurement devices. Here, we report CyberSco.Py, Python software for advanced automated timelapse experiments. We provide proof-of-principle of a user-friendly framework that increases the tunability and flexibility when setting up and running fluorescence timelapse microscopy experiments. Importantly, CyberSco.Py combines real-time image analysis with automation capability, which allows users to create conditional, event-based experiments in which the imaging acquisition parameters and the status of various devices can be changed automatically based on the image analysis. We exemplify the relevance of CyberSco.Py to cell biology using several use case experiments with budding yeast. We anticipate that CyberSco.Py could be used to address the growing need for smart microscopy systems to implement more informative quantitative cell biology experiments.
Temporal quality degradation in AI models
Authors: Vela Daniel , Sharp Andrew , Zhang Richard , Nguyen Trang , Hoang An , Pianykh Oleg S. 
Published: July 2022

AbstractAs AI models continue to advance into many real-life applications, their ability to maintain reliable quality over time becomes increasingly important. The principal challenge in this task stems from the very nature of current machine learning models, dependent on the data as it was at the time of training. In this study, we present the first analysis of AI “aging”: the complex, multifaceted phenomenon of AI model quality degradation as more time passes since the last model training cycle. Using datasets from four different industries (healthcare operations, transportation, finance, and weather) and four standard machine learning models, we identify and describe the main temporal degradation patterns. We also demonstrate the principal differences between temporal model degradation and related concepts that have been explored previously, such as data concept drift and continuous learning. Finally, we indicate potential causes of temporal degradation, and suggest approaches to detecting aging and reducing its impact.
Inactivity and Ca2+ signaling regulate synaptic compensation in motoneurons following hibernation in American bullfrogs
Authors: Zubov Tanya , do Amaral-Silva Lara , Santin Joseph M. 
Published: July 2022

AbstractNeural networks tune synaptic and cellular properties to produce stable activity. One form of homeostatic regulation involves scaling the strength of synapses up or down in a global and multiplicative manner to oppose activity disturbances. In American bullfrogs, excitatory synapses scale up to regulate breathing motor function after inactivity in hibernation, connecting homeostatic compensation to motor behavior. In traditional models of homeostatic synaptic plasticity, inactivity is thought to increase synaptic strength via mechanisms that involve reduced Ca2+ influx through voltage-gated channels. Therefore, we tested whether pharmacological inactivity and inhibition of voltage-gated Ca2+ channels are sufficient to drive synaptic compensation in this system. For this, we chronically exposed ex vivo brainstem preparations containing the intact respiratory network to tetrodotoxin (TTX) to stop activity and nimodipine to block L-type Ca2+ channels. We show that hibernation and TTX similarly increased motoneuron synaptic strength and that hibernation occluded the response to TTX. In contrast, inhibiting L-type Ca2+ channels did not upregulate synaptic strength but disrupted the apparent multiplicative scaling of synaptic compensation typically observed in response to hibernation. Thus, inactivity drives up synaptic strength through mechanisms that do not rely on reduced L-type channel function, while Ca2+ signaling associated with the hibernation environment independently regulates the balance of synaptic weights. Altogether, these results point to multiple feedback signals for shaping synaptic compensation that gives rise to proper network function during environmental challenges in vivo.
Monolithic integration of a 10 μm cut-off wavelength InAs/GaSb type-II superlattice diode on GaAs platform
Authors: Kwan D. C. M. , Kesaria M. , Jiménez J. J. , Srivastava V. , Delmas M. , Liang B. L. , Morales F. M. , Huffaker D. L. 
Published: July 2022

AbstractAt room temperature, a 10 µm cut-off wavelength coincides with an infrared spectral window and the peak emission of blackbody objects. We report a 10 µm cut-off wavelength InAs/GaSb T2SL p-i-n diode on a GaAs substrate with an intentional interfacial misfit (IMF) array between the GaSb buffer layer and GaAs substrate. Transmission electron microscopy and energy-dispersive X-ray spectroscopy revealed that the heterostructure on GaSb-on-GaAs is epitaxial, single-crystalline but with a reduced material homogeneity, extended lattice defects and atomic segregation/intermixing in comparison to that on the GaSb substrate. Strain-induced degradation of the material quality is observed by temperature-dependent current–voltage measurements. The T2SL with the IMF array appears as a potentially effective route to mitigate the impact of the lattice mismatch once its fabrication is fully optimized for these systems, but additional strain compensating measures can enable a low cost, scalable manufacturing of focal plane arrays (FPA) for thermal imaging cameras for spectroscopy, dynamic scene projection, thermometry, and remote gas sensing.
A novel and non-invasive method for DNA extraction from dry bee specimens
Authors: Cilia Giovanni , Flaminio Simone , Quaranta Marino 
Published: July 2022

AbstractIn recent years molecular techniques have been used on museum material as integrative support for classic taxonomy. This cumulative systematics approach is especially for rare or extinct specimens, and genetic analysis may be useful to discern information that is not possible to glean from live materials or morphology. To date, the extraction of DNA required at least a partial destruction of the specimens, which is not possible for all individuals, especially the types. In this study, we described a novel method to extract mitochondrial DNA (mtDNA) from pinned museum bee individuals to avoid any external morphological damage. This method was able to amplify the mtDNA Cytochrome C oxidase subunit I (COI) gene in bee samples collected up to 27 years ago. We tested the efficacy of this method on 72 preserved be specimens belonging to nine species among four families, it could be used on many museums’ rare and/or extinct bee species because it does not provide external morphological damages. The method could be helpful for providing ecological, taxonomic, and phylogenetic information about specimens preserved in museum collections.
Presence of periodontitis may synergistically contribute to cancer progression via Treg and IL-6
Authors: Kajihara Ryo , Sakai Hironori , Han Yibing , Amari Kei , Kawamoto Makiko , Hakoyama Yusuke , Nagashio Sachiho , Yamada Shin-ichi , Sanjo Hideki , Kurita Hiroshi 
Published: July 2022

AbstractA close causal relationship has been suggested to exist between cancer and periodontitis. We hypothesized that the immune surveillance system is impaired in patients with periodontitis, which contributes to cancer development and growth. Therefore, the present study investigated the relationship between immune surveillance mechanisms and periodontitis in cancer patients. The presence or absence of periodontitis was assessed and the peripheral blood (PB) concentrations of IL-6, immunosuppressive cytokines (VEGF, TGF-β1, and CCL22) and proportion of T regulatory cells (Treg, CD3 + CD4 + CD25 + Foxp3 +) were measured. Subjects were classified into the following four groups: non-cancer patients without periodontitis (C − P −), non-cancer patients with periodontitis (C − P +), cancer patients without periodontitis (C + P −), and cancer patients with periodontitis (C + P +). The results of a multivariate analysis showed that the PB concentration of IL-6 was significantly higher in C + than in C- and higher in C + P + than in C + P −. The PB proportion of Treg was significantly higher in C + P + than in C + P −, C − P + , and C − P −. The results of this study suggested that the presence of periodontitis and cancer synergistically increased Treg in PB, which may be one of the underlying causes of immunosuppression and immune evasion in cancer. It was also suggested that the presence of periodontal disease and/or cancer also increases IL-6 in PB, which would be associated with cancer progression. These results suggest the possibility that the presence of periodontitis might synergistically contribute to cancer progression.
Mosses in the Kopački Rit Nature Park, Croatia, as bioindicators of a potential radioactive contamination of the middle Danube River basin
Authors: Petrinec Branko , Babić Dinko , Meštrović Tomislav , Bogdanović Tomislav , Popijač Marina , Rašeta Davor 
Published: July 2022

AbstractWe studied activity concentrations of radionuclides in the Kopački Rit Nature Park using mosses as bioindicators. This area of intact nature is at the tripoint of Croatia, Hungary, and Serbia, being located basically at the centre of the middle Danube River basin. Therefore, it can be easily affected by airborne pollution from various locations in the Middle Europe and beyond. The goal of our research was to assess whether the Park could serve as a location where any new radioactive contamination could be sensitively detected, which implied a necessity for low activity concentrations at the present time. Our gamma-ray spectrometry revealed the presence of only one anthropogenic gamma emitter, that is,137Cs. Its activity concentration in the mosses ranged from 0.7 to 13.1 Bq kg−1, being low indeed. Another radionuclide in our focus was210Pb. Generally, its elevated concentrations may signify ecologically undesirable human activities that involve naturally occurring radioactive matter. The activity concentration of210Pb in the mosses was in the range from 183 to 690 Bq kg−1. This did not depart from the results of other similar studies and was again low enough for a detection of possible excess amounts of this radionuclide in the future.
Association between organochlorine pesticides and nonalcoholic fatty liver disease in the National Health and Nutrition Examination Survey 2003–2004
Authors: Sang Hyunji , Lee Kyu-Na , Jung Chang Hee , Han Kyungdo , Koh Eun Hee 
Published: July 2022

AbstractWhile endocrine disruptors are emerging as a cause of nonalcoholic fatty liver disease (NAFLD), little is known about the link between NAFLD and organochlorine pesticides (OCPs), one of the endocrine disruptors. We retrospectively analyzed the U.S. National Health and Nutrition Examination Survey 2003–2004 and compared the baseline demographics in individuals according to the presence of NAFLD (fatty liver index [FLI] ≥ 60). Logistic regression analysis was performed to determine whether OCP concentration affected NAFLD prevalence and subgroup analyses regarding NAFLD-related variables and advanced hepatic fibrosis (FIB-4 ≥ 2.67) were performed. Of the 1515 individuals, 579 (38.2%) had NAFLD. Oxychlordane showed concentration-dependent risk for NAFLD (OR 3.471 in fourth quartile [Q4]; 95% CI 1.865–6.458; P = 0.007). p,p′-DDE and trans-nonachlor showed similar trends without statistical significance. Conversely, mirex showed the lowest risk for NAFLD in the highest concentration quartile (OR 0.29 in Q4; 95% CI 0.175–0.483; P < 0.001). Oxychlordane showed the most pronounced association with the levels of each component of FLI and liver enzymes. None of the OCPs were significantly associated with advanced fibrosis. In conclusion, among OCPs, exposure to oxychlordane showed the most prominent impact associated with NAFLD.
Biofabrication of ZnO/Malachite nanocomposite and its coating with chitosan to heal infectious wounds
Authors: Rajabloo Zahra , Farahpour Mohammad Reza , Saffarian Parvaneh , Jafarirad Saeed 
Published: July 2022

AbstractRecently, nanocomposites produced from clays and metals coated with chitosan have shown wound healing activity. This study aimed to synthesize the zinc oxide/malachite nanocomposite (ZnO/Mlt-NC) and its coating form with chitosan (ZnO/Mlt/Chsn-NC). Physicochemical characterization of the produced nanocomposites was investigated. Biomedical effects of nanocomposites, such as in vivo and in vitro antibacterial activity, antioxidant properties, cytotoxicity, and modulation in the gene expressions of interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-10 (IL-10), and transforming growth factor-β (TGF-β) and histopathological parameters, were also investigated. Expression intensities of basic fibroblast growth factor (bFGF) and tumor necrosis factor alpha (TNF-α) were also investigated by immunofluorescence staining. To investigate biomedical effects under in vivo conditions, infected wounds were induced and inoculated with Staphylococcus aureus (ATCC 25923), and Pseudomonas aeruginosa (ATCC 27853). The results indicated spherical ZnO nanoparticles on the surface of malachite and strong antibacterial activity and antioxidant properties. The ointments produced from the nanocomposites also exhibited wound healing activity. The administration of the ointments prepared from ZnO/Mlt, and ZnO/Mlt/Chsn NCs decreased the expressions of IL-1β, IL-6, and TNF-α, while it increased the expressions of IL-10, TGF-β and bFGF. In sum, the nanocomposites produced from ZnO, malachite, and chitosan had better biological activity than ZnO/Malachite nanocomposites. We suggest applying ZnO/Mlt/Chsn nanocomposites in the structure of ointments to treat infected wounds after future clinical studies.
Effect of physiotherapy on the promotion of bone mineralization in preterm infants: a randomized controlled trial
Authors: Torró-Ferrero Galaad , Fernández-Rego Francisco Javier , Agüera-Arenas Juan José , Gomez-Conesa Antonia 
Published: July 2022

AbstractPreterm infants have a low level of bone mineralization compared to those born at term. The purpose of the present study was to investigate the effect of reflex locomotion therapy (RLT) on bone mineralization and growth in preterm infants and compare its effect to other physiotherapy procedures. Forty-six preterm infants born at 29–34 weeks were randomized into three groups: one group received RLT (n = 17); the other group received passive movements with gentle joint compression (n = 14); and the control group received massages (n = 15). All the treatments were performed at the neonatal unit for one month. The main outcome measure was bone mineralization, which was measured using the tibial speed of sound (Tibial-SOS). All the groups were similar in terms of gestational age (31.8 ± 1.18), birth weight (1,583.41 ± 311.9), and Tibia-SOS (1,604.7 ± 27.9) at the beginning of the intervention. At the end of the study, significant differences were found among the groups in the Tibial-SOS [F(4,86) = 2.77, p = 0.049, ηp2 = 0.114] in terms of the benefit to the RLT group. In conclusion, RLT has been effective at improving Tibial-SOS levels and has been more effective than other physical therapy modalities; therefore, it could be considered an effective physiotherapeutic modality for the prevention and treatment of osteopenia from prematurity.