bluuebunny/crossref_metadata_2025_split huggingface dataset:
A food web approach reveals the vulnerability of biocontrol services by birds and bats to landscape modification at regional scale
Authors: Herrera José M. , Silva Bruno , Jiménez-Navarro Gerardo , Barreiro Silvia , Melguizo-Ruiz Nereida , Moreira Francisco , Vasconcelos Sasha , Morgado Rui , Rodriguez-Pérez Javier 
Published: December 2021

AbstractPest control services provided by naturally occurring species (the so-called biocontrol services) are widely recognized to provide key incentives for biodiversity conservation. This is particularly relevant for vertebrate-mediated biocontrol services as many vertebrate species are of conservation concern, with most of their decline associated to landscape modification for agricultural purposes. Yet, we still lack rigorous approaches evaluating landscape-level correlates of biocontrol potential by vertebrates over broad spatial extents to better inform land-use and management decisions. We performed a spatially-explicit interaction-based assessment of potential biocontrol services in Portugal, using 1853 pairwise trophic interactions between 78 flying vertebrate species (birds and bats) and 53 insect pests associated to two widespread and economically valuable crops in the Euro-Mediterranean region, olive groves (Olea europaea subsp. europaea) and vineyards (Vitis vinifera subsp. vinifera). The study area was framed using 1004 square cells, each 10 × 10 km in size. Potential biocontrol services were determined at all those 10 × 10 km grid-cells in which each crop was present as the proportion of the realized out of all potential pairwise interactions between vertebrates and pests. Landscape correlates of biocontrol potential were also explored. Our work suggests that both birds and bats can effectively provide biocontrol services in olive groves and vineyards as they prey many insect pest species associated to both crops. Moreover, it demonstrates that these potential services are impacted by landscape-scale features and that this impact is consistent when evaluated over broad spatial extents. Thus, biocontrol potential by vertebrates significantly increases with increasing amount of natural area, while decreases with increasing area devoted to target crops, particularly olive groves. Overall, our study highlights the suitability of our interaction-based approach to perform spatially-explicit assessments of potential biocontrol services by vertebrates at local spatial scales and suggest its utility for integrating biodiversity and ecosystem services in conservation planning over broad spatial extents.
A comparative study of plant volatiles induced by insect and gastropod herbivory
Authors: Mann Leslie , Laplanche Diane , Turlings Ted C. J. , Desurmont Gaylord A. 
Published: December 2021

AbstractInsect and gastropod herbivores are major plant consumers and their importance in the evolution of plant defensive traits is broadly recognized. However, their respective effects on plant responses have rarely been compared. Here we focused on plant volatile emissions (VOCs) following herbivory and compared the effects of herbivory by caterpillars of the generalist insect Spodoptera littoralis and by generalist slugs of the genus Arion on the VOCs emissions of 14 cultivated plant species. Results revealed that plants consistently produced higher amounts of volatiles and responded more specifically to caterpillar than to slug herbivory. Specifically, plants released on average 6.0 times more VOCs (total), 8.9 times more green leaf volatiles, 4.2 times more terpenoids, 6.0 times more aromatic hydrocarbons, and 5.7 times more other VOCs in response to 1 cm2 of insect damage than to 1 cm2 of slug damage. Interestingly, four of the plant species tested produced a distinct blend of volatiles following insect damage but not slug damage. These findings may result from different chemical elicitors or from physical differences in herbivory by the two herbivores. This study is an important step toward a more inclusive view of plant responses to different types of herbivores.
The effect of eraser sampling for proteomic analysis on Palaeolithic bone surface microtopography
Authors: Sinet-Mathiot Virginie , Martisius Naomi L. , Schulz-Kornas Ellen , van Casteren Adam , Tsanova Tsenka R. , Sirakov Nikolay , Spasov Rosen , Welker Frido , Smith Geoff M. , Hublin Jean-Jacques 
Published: December 2021

AbstractBone surface modifications are crucial for understanding human subsistence and dietary behaviour, and can inform about the techniques employed in the production and use of bone tools. Permission to destructively sample such unique artefacts is not always granted. The recent development of non-destructive proteomic extraction techniques has provided some alternatives for the analysis of rare and culturally significant artefacts, including bone tools and personal ornaments. The Eraser Extraction Method (EEM), first developed for ZooMS analysis of parchment, has recently been applied to bone and ivory specimens. To test the potential impact of the EEM on ancient bone surfaces, we analyse six anthropogenically modified Palaeolithic bone specimens from Bacho Kiro Cave (Bulgaria) through a controlled sampling experiment using qualitative and 3D quantitative microscopy. Although the overall bone topography is generally preserved, our findings demonstrate a slight flattening of the microtopography alongside the formation of micro-striations associated with the use of the eraser for all bone specimens. Such modifications are similar to ancient use-wear traces. We therefore consider the EEM a destructive sampling approach for Palaeolithic bone surfaces. Together with low ZooMS success rates in some of the reported studies, the EEM might not be a suitable approach to taxonomically identify Pleistocene bone specimens.
Robust, fiducial-free drift correction for super-resolution imaging
Authors: Wester Michael J. , Schodt David J. , Mazloom-Farsibaf Hanieh , Fazel Mohamadreza , Pallikkuth Sandeep , Lidke Keith A. 
Published: December 2021

AbstractWe describe a robust, fiducial-free method of drift correction for use in single molecule localization-based super-resolution methods. The method combines periodic 3D registration of the sample using brightfield images with a fast post-processing algorithm that corrects residual registration errors and drift between registration events. The method is robust to low numbers of collected localizations, requires no specialized hardware, and provides stability and drift correction for an indefinite time period.
Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal
Authors: Ahouidi Ambroise D. , Rodgers Mary A. , Padane Abdou , Leye Nafissatou , Olivo Ana , Mbow Moustapha , Mboup Aminata , Diaw Papa Alassane , Dia Aminata , Harris Barbara , Padane Yacine Amet Dia , Lo Gora , Meyer Todd V. , Diedhiou Cyrille K. , Diagne Diabou , Kane Ndeye Coumba Toure , Cloherty Gavin , Mboup Souleymane 
Published: December 2021

AbstractThe emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that carry mutations in the spike gene are of concern for potential impact to treatment and prevention efforts. To monitor for new SARS-CoV-2 mutations, a panel of specimens were sequenced from both wave one (N = 96), and wave two (N = 117) of the pandemic in Senegal by whole genome next generation sequencing. Amongst these genomes, new combinations of SARS-CoV-2 spike mutations were identified, with E484K + N501T, L452R + N501Y, and L452M + S477N exclusively found in second wave specimens. These sequences are evidence of local diversification over the course of the pandemic and parallel evolution of escape mutations in different lineages.
Single-cell mapping of DNA G-quadruplex structures in human cancer cells
Authors: Hui Winnie W. I. , Simeone Angela , Zyner Katherine G. , Tannahill David , Balasubramanian Shankar 
Published: December 2021

AbstractG-quadruplexes (G4s) are four-stranded DNA secondary structures that form in guanine-rich regions of the genome. G4s have important roles in transcription and replication and have been implicated in genome instability and cancer. Thus far most work has profiled the G4 landscape in an ensemble of cell populations, therefore it is critical to explore the structure–function relationship of G4s in individual cells to enable detailed mechanistic insights into G4 function. With standard ChIP-seq methods it has not been possible to determine if G4 formation at a given genomic locus is variable between individual cells across a population. For the first time, we demonstrate the mapping of a DNA secondary structure at single-cell resolution. We have adapted single-nuclei (sn) CUT&Tag to allow the detection of G4s in single cells of human cancer cell lines. With snG4-CUT&Tag, we can distinguish cellular identity from a mixed cell-type population solely based on G4 features within individual cells. Our methodology now enables genomic investigations on cell-to-cell variation of a DNA secondary structure that were previously not possible.
Effects of endocannabinoids on feed intake, stress response and whole-body energy metabolism in dairy cows
Authors: van Ackern Isabel , Wulf Ramona , Dannenberger Dirk , Tuchscherer Armin , Kuhla Björn 
Published: December 2021

AbstractEndocannabinoids, particularly anandamide (AEA) and 2-arachidonoylglycerol (2-AG), are instrumental in regulating energy homeostasis and stress response. However, little is known about the endocannabinoid system (ECS) in ruminants, although EC could improve dairy health and productivity, at least by increasing feed intake. In this study, we report if intraperitoneal (i.p.) AEA and 2-AG administration affects feed intake, whole-body macronutrient metabolism, isolation and restraint stress, and whether diet composition modulates circulating endocannabinoid concentrations in cows. Twenty Simmental cows in late lactation were fed a grass silage and a corn silage based diet. On each diet, cows received daily i.p. injections with either AEA (5 µg/kg; n = 7), 2-AG (2.5 µg/kg; n = 6) or saline (n = 7) for 8 days. Endocannabinoid administration for 5 days under free-ranging (non-stressed) conditions had no effect on feed intake or energy balance, but attenuated the stress-induced suppression of feed intake when housing changed to individual tie-stalls without social or tactile interaction. Endocannabinoids increased whole-body carbohydrate oxidation, reduced fat oxidation, and affected plasma non-esterified fatty acid concentrations and fatty acid contents of total lipids. There was no effect of endocannabinoids on plasma triglyceride concentrations or hepatic lipogenesis. Plasma AEA concentrations were not affected by diet, however, plasma 2-AG concentrations tended to be lower on the corn silage based diet. In conclusion, endocannabinoids attenuate stress-induced hypophagia, increase short-term feed intake and whole-body carbohydrate oxidation and decrease whole-body fat oxidation in cows.
Intraoperative discrimination of native meningioma and dura mater by Raman spectroscopy
Authors: Jelke Finn , Mirizzi Giulia , Borgmann Felix Kleine , Husch Andreas , Slimani Rédouane , Klamminger Gilbert Georg , Klein Karoline , Mombaerts Laurent , Gérardy Jean-Jacques , Mittelbronn Michel , Hertel Frank 
Published: December 2021

AbstractMeningiomas are among the most frequent tumors of the central nervous system. For a total resection, shown to decrease recurrences, it is paramount to reliably discriminate tumor tissue from normal dura mater intraoperatively. Raman spectroscopy (RS) is a non-destructive, label-free method for vibrational analysis of biochemical molecules. On the microscopic level, RS was already used to differentiate meningioma from dura mater. In this study we test its suitability for intraoperative macroscopic meningioma diagnostics. RS is applied to surgical specimen of intracranial meningiomas. The main purpose is the differentiation of tumor from normal dura mater, in order to potentially accelerate the diagnostic workflow. The collected meningioma and dura mater samples (n = 223 tissue samples from a total of 59 patients) are analyzed under untreated conditions using a new partially robotized RS acquisition system. Spectra (n = 1273) are combined with the according histopathological analysis for each sample. Based on this, a classifier is trained via machine learning. Our trained classifier separates meningioma and dura mater with a sensitivity of 96.06 $$\pm $$
±
0.03% and a specificity of 95.44 $$\pm $$
±
0.02% for internal fivefold cross validation and 100% and 93.97% if validated with an external test set. RS is an efficient method to discriminate meningioma from healthy dura mater in fresh tissue samples without additional processing or histopathological imaging. It is a quick and reliable complementary diagnostic tool to the neuropathological workflow and has potential for guided surgery. RS offers a safe way to examine unfixed surgical specimens in a perioperative setting.
Cellular heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by single-cell RNA sequencing
Authors: Choi Sung Min , Park Hi Jung , Choi Eun A. , Jung Kyeong Cheon , Lee Jae Il 
Published: December 2021

AbstractCirculating CD4+CD8+ double-positive (DP) T cells are associated with a variety of disease states. However, unlike conventional T cells, the composition of this population is poorly understood. Here, we used single-cell RNA sequencing (scRNA-seq) to analyze the composition and characteristics of the DP T cell population circulating in the peripheral blood of cynomolgus monkeys. We found that circulating DP T cells not only contain a large number of naïve cells, but also comprise a heterogeneous population (CD4 CTL-, Eomes+ Tr1-, Th2-, Th17-, Tfh-, Treg-, CD8 CTL-, and innate-like cells) with multiple potential functions. Flow cytometry analysis revealed that a substantial number of the naïve DP T cells expressed CD8αβ, as well as CD8αα, along with high expression of CD31. Moreover, the CD4hiCD8lo and CD4hiCD8hi populations, which express high levels of the CD4 coreceptor, comprised subsets characterized by helper and regulatory functions, some of which also exhibited cytotoxic functions. By contrast, the CD4loCD8hi population with high CD8 coreceptor expression comprised a subset characterized by CD8 CTL- and innate-like properties. Taken together, the data show that scRNA-seq analysis identified a more diverse subset of the circulating DP cells than is currently known, despite this population being very small.
Macrophages expressing uncoupling protein 1 increase in adipose tissue in response to cold in humans
Authors: Finlin Brian S. , Memetimin Hasiyet , Confides Amy L. , Zhu Beibei , Westgate Philip M. , Dupont-Versteegden Esther E. , Kern Philip A. 
Published: December 2021

AbstractAcute cold induces beige adipocyte protein marker expression in human subcutaneous white adipose tissue (SC WAT) from both the cold treated and contralateral leg, and the immune system regulates SC WAT beiging in mice. Cold treatment significantly increased the gene expression of the macrophage markers CD68 and 86 in SC WAT. Therefore, we comprehensively investigated the involvement of macrophages in SC WAT beiging in lean and obese humans by immunohistochemistry. Cold treatment significantly increased CD163/CD68 macrophages in SC WAT from the cold treated and contralateral legs of lean and obese subjects, and had similar effects on CD206/CD68 macrophages, whereas the effects on CD86/CD68 macrophages were inconsistent between lean and obese. However, linear regression analysis did not find significant relationships between the change in macrophage numbers and the change in UCP1 protein abundance. A high percentage of CD163 macrophages in SC WAT expressed UCP1, and these UCP1 expressing CD163 macrophages were significantly increased by cold treatment in SC WAT of lean subjects. In conclusion, our results suggest that CD163 macrophages are involved in some aspect of the tissue remodeling that occurs during SC WAT beiging in humans after cold treatment, but they are likely not direct mediators of the beiging process.
Young people are not blameworthy: the generation’s awareness of COVID-19 and behavioral responses
Authors: Jun Seung-Pyo , Yoo Hyoung Sun , Lee Chul 
Published: December 2021

AbstractAt a time when the COVID-19 pandemic has been ongoing for more than a year, young people have been the subject of vigilant scrutiny and criticism regarding their active engagement in social activities. We posed the question of whether young people's response to COVID-19 was different from that of other generations and analyzed awareness and behavior to investigate this question. Specifically, we examined internet searches for information on COVID-19 and credit card consumption in South Korea among young people in their 20s and compared them to a reference group of people in their 50s. Our research has confirmed that there was no statistically significant difference between young people and the reference group in this regard. Furthermore, in the 25 sub-sectors of industry we examined, young people's consumption activities recovered significantly faster than the reference group in only three sub-sectors. This study demonstrated that young people showed stronger interest than the reference group in their response to COVID-19, and that they cooperated with the government’s social distancing policy by reducing their activities. Through this study, we presented a scientific approach for evaluating young people in regard to their response to COVID-19, offering useful implications for designing appropriate policies for public health.
Maximizing gerrymandering through ising model optimization
Authors: Okamoto Yasuharu 
Published: December 2021

AbstractBy using the Ising model formulation for combinatorial optimization with 0–1 binary variables, we investigated the extent to which partisan gerrymandering is possible from a random but even distribution of supporters. Assuming that an electoral district consists of square subareas and that each subarea shares at least one edge with other subareas in the district, it was possible to find the most tilted assignment of seats in most cases. However, in cases where supporters' distribution included many enclaves, the maximum tilted assignment was usually found to fail. We also discussed the proposed algorithm is applicable to other fields such as the redistribution of delivery destinations.
A nationwide cohort study on growth impairment by cleft lip with or without palate
Authors: Ryu Jeong Yeop , Park Tae Hyun , Lee Joon Seok , Yang Jung Dug , Chung Ho Yun , Cho Byung Chae , Choi Kang Young 
Published: December 2021

AbstractThere are very few nationwide studies discussing the height, weight, head circumference, and dental screening of children with cleft lip with or without palate (CL/P), with most reports on this subject based on a 1900s cohort. This study aimed to characterize CL/P children in the 2000s in terms of height, weight, head circumference, and dental screening. This nationwide population-based study evaluated the National Health Insurance Service-Infants and Children’s Health Screening (NHIS-INCHS), specifically the height, weight, and head circumference of millions of children. Dental screening data, including the status of each tooth and comprehensive dental judgment, were also evaluated. Syndromic and nonsyndromic CL/P children had lower height, weight, and head circumference than no CL/P children until the age of 66–71 months. Children with cleft palate only or both cleft lip and palate showed similar results. Regarding dental screening, the primary teeth of CL/P children erupted later and fell out faster than no CL/P children. Dental caries was also more common in CL/P children. Children with CL/P had inferior general growth, regardless of palatoplasty surgery. More aggressive dental treatment was required for CL/P children due to the instability of primary teeth and tendency for caries.
Tanshinone IIA suppresses the progression of lung adenocarcinoma through regulating CCNA2-CDK2 complex and AURKA/PLK1 pathway
Authors: Li Ziheng , Zhang Ying , Zhou Yuan , Wang Fuqian , Yin Chao , Ding Li , Zhang Shunbo 
Published: December 2021

AbstractLung adenocarcinoma (LUAD) belongs to a subgroup of non-small cell lung cancer (NSCLC) with an increasing incidence all over the world. Tanshinone IIA (TSA), an active compound of Salvia miltiorrhiza Bunge., has been found to have anti-tumor effects on many tumors, but its anti-LUAD effect and its mechanism have not been reported yet. In this study, bio-information analysis was applied to characterize the potential mechanism of TSA on LUA, biological experiments were used to verify the mechanisms involved. TCGA, Pubchem, SwissTargetPrediction, Venny2.1.0, STRING, DAVID, Cytoscape 3.7.2, Omicshare, GEPIA, RSCBPDB, Chem Draw, AutoDockTools, and PyMOL were utilized for analysis in the bio-information analysis and network pharmacology. Our experiments in vitro focused on the anti-LUAD effects and mechanisms of TSA on LUAD cells (A549 and NCI-H1975 cells) via MTT, plate cloning, Annexin V-FITC and PI dual staining, flow cytometry, and western blot assays. A total of 64 differentially expressed genes (DEGs) of TSA for treatment of LUAD were screened out. Gene ontology and pathway analysis revealed characteristic of the DEGs network. After GEPIA-based DEGs confirmation, 46 genes were considered having significant differences. Further, 10 key DEGs (BTK, HSD11B1, ADAM33, TNNC1, THRA, CCNA2, AURKA, MIF, PLK1, and SORD) were identified as the most likely relevant genes from overall survival analysis. Molecular Docking results showed that CCNA2, CDK2 and PLK1 had the lowest docking energy. MTT and plate cloning assays results showed that TSA inhibited the proliferation of LUAD cells in a concentration-dependent manner. Annexin V-FITC and PI dual staining and flow cytometry assays results told that TSA promoted the apoptosis of the two LUAD cells in different degrees, and induced cycle arrest in the G1/S phase. Western blot results showed that TSA significantly down-regulated the expression of CCNA2, CDK2, AURKA, PLK1, and p-ERK. In summary, TSA could suppress the progression of LUAD by inducing cell apoptosis and arresting cell cycle, and these were done by regulating CCNA2-CDK2 complex and AURKA/PLK1 pathway. These findings are the first to demonstrate the molecular mechanism of TSA in treatment of LUAD combination of network bio-information analysis and biological experiments in vitro.
Osteopontin levels are associated with late-time lower regional brain volumes in multiple sclerosis
Authors: Orsi Gergely , Hayden Zsofia , Cseh Tamas , Berki Timea , Illes Zsolt 
Published: December 2021

AbstractOsteopontin (OPN) is a proinflammatory marker produced by systemic immune and central nervous system (CNS) resident cells. We examined, if the level of OPN in the cerebrospinal fluid (CSF) and blood is associated with late-time regional brain volumes and white matter (WM) lesion load in MS. Concentrations of OPN in blood and CSF were related to MRI findings 10.1 ± 2.0 years later in 46 patients with MS. OPN concentration was measured by ELISA, while regional brain volumes and lesion load was assessed by magnetic resonance imaging (MRI) using 3D MPRAGE sequence and automated MR volumetry. OPN measured in the CSF was associated with several regional brain volumes and WM lesion load measured 10.1 ± 2.0 years later. CSF OPN concentration correlated with long-term enlargement of lateral- and inferior lateral ventricles and the elevation of gross CSF volume, in conjunction with the reduction of several cortical/subcortical gray matter and WM volumes. Serum OPN showed no long-term association with regional brain volumes. OPN measured from the CSF but not from the serum was associated with lower regional brain volumes measured a decade later, indicating the primary role of inflammation within the CNS in developing long-term brain related alterations.