bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients
Authors: Kwan Jennifer Yin Yee , Lin Liang-Tzung , Bell Rachel , Bruce Jeffrey P. , Richardson Christopher , Pugh Trevor J. , Liu Fei-Fei 
Published: February 2021

AbstractMultiple studies have reported a doubling in risk of Coronavirus Disease-2019 (COVID-19) among cancer patients. Here, we examine the potential biological rationale behind this recurrent epidemiological observation. By leveraging large-scale genome-wide transcriptional data of normal and malignant tissues from adults and children, we found evidence of increased expression of SARS-CoV-2 viral entry genes in the cancer state, particularly in respiratory, gastrointestinal, and genitourinary tract tissues, with decreased expression in pediatricvs. adult samples. Additionally, by interrogating the temporal effects of radiotherapy on human peripheral blood mononuclear and mucosal cells, we observed important treatment-related alterations in host innate immunity, specifically type I interferon responses. Overall, cancers enhance expression of critical viral entry genes, and innate viral defenses can be dysregulated transiently during radiation treatments. These factors may contribute to the observed increased susceptibility to SARS-CoV-2 entry and severity of COVID-19 in cancer patients.
Insecticide resistance and underlying targets-site and metabolic mechanisms in Aedes aegypti and Aedes albopictus from Lahore, Pakistan
Authors: Rahman Rafi Ur , Souza Barbara , Uddin Iftikhar , Carrara Luana , Brito Luiz Paulo , Costa Monique Melo , Mahmood Muhammad Asif , Khan Sozaina , Lima Jose Bento Pereira , Martins Ademir Jesus 
Published: February 2021

AbstractInsecticide resistant Aedes populations have recently been reported in Pakistan, imposing a threat to their control. We aimed to evaluate the susceptibility of Aedes aegypti and Aedes albopictus populations from Lahore to WHO-recommended insecticides and to investigate metabolic and target-site resistance mechanisms. For this purpose, we first carried out bioassays with the larvicides temephos and pyriproxyfen, and the adulticides malathion, permethrin, deltamethrin, alpha-cypermethrin, and etofenprox. We looked for Knockdown resistance mutations (kdr) by qPCR, High-Resolution Melt (HRM), and sequencing. In order to explore the role of detoxifying enzymes in resistance, we carried out synergist bioassay with both species and then checked the expression of CYP9M6, CYP9J10, CYP9J28, CYP6BB2, CCAe3a, and SAP2 genes in Ae. aegypti. Both species were susceptible to organophosphates and the insect growth regulator, however resistant to all pyrethroids. We are reporting the kdr haplotypes 1520Ile + 1534Cys and T1520 + 1534Cys in high frequencies in Ae. aegypti while Ae. albopictus only exhibited the alteration L882M. PBO increased the sensitivity to permethrin in Ae. aegypti, suggesting the participation of P450 genes in conferring resistance, and indeed, CYP928 was highly expressed. We presume that dengue vectors in Lahore city are resistant to pyrethroids, probably due to multiple mechanisms, such as kdr mutations and P450 overexpression.
Variation in wood physical properties and effects of climate for different geographic sources of Chinese fir in subtropical area of China
Authors: You Ren , Zhu Ninghua , Deng Xiangwen , Wang Jing , Liu Fei 
Published: February 2021

AbstractChinese fir is one of the most important commercial timber species in China, with many geographic sources. However, little is known of the variation in wood physical properties among them. To explore the differences in wood physical properties and their influencing factors, five geographic sources of Chinese fir were selected. The variance inflation factor, stepwise regression, and principle component analysis were used to reduce multicollinearity and dimensions of the 19 wood physical properties (including density, shrinkage, and mechanical properties). The results showed that the wood density differed significantly among five geographic sources. The tangential shrinkage rate and radial shrinkage rate reached maximum values in black-heart Chinese fir (HNYX-T) but accompanied by the lowest value for difference dry shrinkage. The wood density and mechanical properties of HNYX-T was exceeded to that of others geographic sources. Fast-growth Chinese fir (FJYK-P) had the lowest value for all mechanical properties. The precipitation and temperature had significant correlations with the wood physical properties of this five geographic sources. The temperature in summer was mainly positive correlated with physical properties, while precipitation was negatively correlated with them. HNYX-T had the highest comprehensive score of PCA, followed by JXCS-R, emerged as higher-quality geographic source, which is important for selecting and utilizing geographic sources in forest management.
A spatiotemporal analysis of opioid poisoning mortality in Ohio from 2010 to 2016
Authors: Park Chihyun , Clemenceau Jean R. , Seballos Anna , Crawford Sara , Lopez Rocio , Coy Tyler , Atluri Gowtham , Hwang Tae Hyun 
Published: February 2021

AbstractOpioid-related deaths have severely increased since 2000 in the United States. This crisis has been declared a public health emergency, and among the most affected states is Ohio. We used statewide vital statistic data from the Ohio Department of Health (ODH) and demographics data from the U.S. Census Bureau to analyze opioid-related mortality from 2010 to 2016. We focused on the characterization of the demographics from the population of opioid-related fatalities, spatiotemporal pattern analysis using Moran’s statistics at the census-tract level, and comorbidity analysis using frequent itemset mining and association rule mining. We found higher rates of opioid-related deaths in white males aged 25–54 compared to the rest of Ohioans. Deaths tended to increasingly cluster around Cleveland, Columbus and Cincinnati and away from rural regions as time progressed. We also found relatively high co-occurrence of cardiovascular disease, anxiety or drug abuse history, with opioid-related mortality. Our results demonstrate that state-wide spatiotemporal and comorbidity analysis of the opioid epidemic could provide novel insights into how the demographic characteristics, spatiotemporal factors, and/or health conditions may be associated with opioid-related deaths in the state of Ohio.
Microfluidic Overhauser DNP chip for signal-enhanced compact NMR
Authors: Kiss Sebastian Z. , MacKinnon Neil , Korvink Jan G. 
Published: February 2021

AbstractNuclear magnetic resonance at low field strength is an insensitive spectroscopic technique, precluding portable applications with small sample volumes, such as needed for biomarker detection in body fluids. Here we report a compact double resonant chip stack system that implements in situ dynamic nuclear polarisation of a 130 nL sample volume, achieving signal enhancements of up to − 60 w.r.t. the thermal equilibrium level at a microwave power level of 0.5 W. This work overcomes instrumental barriers to the use of NMR detection for point-of-care applications.
Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species
Authors: Jakob Lena , Vereshchagina Kseniya P. , Tillmann Anette , Rivarola-Duarte Lorena , Axenov-Gribanov Denis V. , Bedulina Daria S. , Gurkov Anton N. , Drozdova Polina , Timofeyev Maxim A. , Stadler Peter F. , Luckenbach Till , Pörtner Hans-Otto , Sartoris Franz J. , Lucassen Magnus 
Published: February 2021

AbstractLake Baikal is inhabited by more than 300 endemic amphipod species, which are narrowly adapted to certain thermal niches due to the high interspecific competition. In contrast, the surrounding freshwater fauna is commonly represented by species with large-scale distribution and high phenotypic thermal plasticity. Here, we investigated the thermal plasticity of the energy metabolism in two closely-related endemic amphipod species from Lake Baikal (Eulimnogammarus verrucosus; stenothermal andEulimnogammarus cyaneus; eurythermal) and the ubiquitous Holarctic amphipodGammarus lacustris(eurythermal) by exposure to a summer warming scenario (6–23.6 °C; 0.8 °C d−1). In concert with routine metabolic rates, activities of key metabolic enzymes increased strongly with temperature up to 15 °C inE. verrucosus, whereupon they leveled off (except for lactate dehydrogenase). In contrast, exponential increases were seen inE. cyaneusandG. lacustristhroughout the thermal trial (Q10-values: 1.6–3.7). Cytochrome-c-oxidase, lactate dehydrogenase, and 3-hydroxyacyl-CoA dehydrogenase activities were found to be higher inG. lacustristhan inE. cyaneus, especially at the highest experimental temperature (23.6 °C). Decreasing gene expression levels revealed some thermal compensation inE. cyaneusbut not inG. lacustris. In all species, shifts in enzyme activities favored glycolytic energy generation in the warmth. The congruent temperature-dependencies of enzyme activities and routine metabolism inE. verrucosusindicate a strong feedback-regulation of enzymatic activities by whole organism responses. The species-specific thermal reaction norms reflect the different ecological niches, including the spatial distribution, distinct thermal behavior such as temperature-dependent migration, movement activity, and mating season.
Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
Authors: Salabi Fatemeh , Jafari Hedieh , Navidpour Shahrokh , Sadr Ayeh Sadat 
Published: February 2021

AbstractThe potential function of long non-coding RNAs in regulating neighbor protein-coding genes has attracted scientists’ attention. Despite the important role of lncRNAs in biological processes, a limited number of studies focus on non-model animal lncRNAs. In this study, we used a stringent step-by-step filtering pipeline and machine learning-based tools to identify the specific Androctonus crassicauda lncRNAs and analyze the features of predicted scorpion lncRNAs. 13,401 lncRNAs were detected using pipeline in A. crassicauda transcriptome. The blast results indicated that the majority of these lncRNAs sequences (12,642) have no identifiable orthologs even in closely related species and those considered as novel lncRNAs. Compared to lncRNA prediction tools indicated that our pipeline is a helpful approach to distinguish protein-coding and non-coding transcripts from RNA sequencing data of species without reference genomes. Moreover, analyzing lncRNA characteristics in A. crassicauda uncovered that lower protein-coding potential, lower GC content, shorter transcript length, and less number of isoform per gene are outstanding features of A. crassicauda lncRNAs transcripts.
High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes
Authors: de Jager Deon , Glanzmann Brigitte , Möller Marlo , Hoal Eileen , van Helden Paul , Harper Cindy , Bloomer Paulette 
Published: February 2021

AbstractGenomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
Investigating the effect of a nap following experimental trauma on analogue PTSD symptoms
Authors: Wilhelm Ines , Azza Yasmine , Brennwald Karin , Ehrt-Schäfer Yamina , Seifritz Erich , Kleim Birgit 
Published: February 2021

AbstractCognitive models assume that the incomplete integration of a traumatic experience into the autobiographical memory results in typical symptoms associated with post-traumatic stress disorder (PTSD) such as intrusive re-experiencing. Sleep supports the integration of new experiences into existing memory networks through memory consolidation. In fifty-six females, we investigated whether a 90-min daytime nap (n = 33) compared to a wake period (n = 23) after being exposed to an experimental trauma (i.e. a trauma film) prevents PTSD analogue symptoms. Intrusive memories were recorded for seven days using a diary, overall PTSD symptoms were assessed using the Impact of Event Scale (IES-R) and affective response to trauma cues were measured one week after experimental trauma. The two groups did not differ in any of the analogue PTSD symptoms. However, participants obtaining rapid eye movement (REM) sleep in the nap experienced less distressing intrusive memories. Moreover, the duration of REM sleep and slow wave activity was negatively correlated with analogue PTSD symptoms. Our findings suggest that even a short sleep period after experimental trauma can play a protective role in trauma memory formation but only if the nap contains REM sleep. Our data provide additional evidence for a critical role of REM sleep in PTSD development.
Chimpanzees balance resources and risk in an anthropogenic landscape of fear
Authors: Bersacola Elena , Hill Catherine M. , Hockings Kimberley J. 
Published: February 2021

AbstractHuman-wildlife coexistence is possible when animals can meet their ecological requirements while managing human-induced risks. Understanding how wildlife balance these trade-offs in anthropogenic environments is crucial to develop effective strategies to reduce risks of negative interactions, including bi-directional aggression and disease transmission. For the first time, we use a landscape of fear framework with Bayesian spatiotemporal modelling to investigate anthropogenic risk-mitigation and optimal foraging trade-offs in Critically Endangered western chimpanzees (Pan troglodytes verus). Using 12 months of camera trap data (21 camera traps, 6722 camera trap days) and phenology on wild and cultivated plant species collected at Caiquene–Cadique, Cantanhez National Park (Guinea-Bissau), we show that humans and chimpanzees broadly overlapped in their use of forest and anthropogenic parts of the habitat including villages and cultivated areas. The spatiotemporal model showed that chimpanzee use of space was predicted by the availability of naturalised oil-palm fruit. Chimpanzees used areas away from villages and agriculture more intensively, but optimised their foraging strategies by increasing their use of village areas with cultivated fruits when wild fruits were scarce. Our modelling approach generates fine-resolution space–time output maps, which can be scaled-up to identify human-wildlife interaction hotspots at the landscape level, informing coexistence strategy.
Bio-inspired synthesis of palladium nanoparticles fabricated magnetic Fe3O4 nanocomposite over Fritillaria imperialis flower extract as an efficient recyclable catalyst for the reduction of nitroarenes
Authors: Veisi Hojat , Karmakar Bikash , Tamoradi Taiebeh , Tayebee Reza , Sajjadifar Sami , Lotfi Shahram , Maleki Behrooz , Hemmati Saba 
Published: February 2021

AbstractThis current research is based on a bio-inspired procedure for the synthesis of biomolecule functionalized hybrid magnetic nanocomposite with the Fe3O4 NPs at core and Pd NPs at outer shell. The central idea was the initial modification of magnetic NP by the phytochemicals from Fritillaria imperialis flower extract, which was further exploited in the green reduction of Pd2+ ions into Pd NPs, in situ. The flower extract also acted as a capping agent for the obtained Pd/Fe3O4 composite without the need of additional toxic reagents. The as-synthesized Fe3O4@Fritillaria/Pd nanocomposite was methodically characterized over different physicochemical measures like FT-IR, ICP-AES, FESEM, EDX, TEM, XPS and VSM analysis. Thereafter, its catalytic potential was evaluated in the reduction of various nitrobenzenes to arylamines applying hydrazine hydrate as reductant in ethanol/water (1:2) medium under mild conditions. Furthermore, the nanocatalyst was retrieved using a bar magnet and recycled several times without considerable leaching or loss of activity. This green, bio-inspired ligand-free protocol has remarkable advantages like environmental friendliness, high yields, easy workup and reusability of the catalyst.
Helicobacter pylori type 4 secretion systems as gastroduodenal disease markers
Authors: Phuc Bui Hoang , Tuan Vo Phuoc , Dung Ho Dang Quy , Binh Tran Thanh , Tung Pham Huu , Tri Tran Dinh , Thuan Ngo Phuong Minh , Van Khien Vu , Trang Tran Thi Huyen , Akada Junko , Matsumoto Takeshi , Yamaoka Yoshio 
Published: February 2021

AbstractAlthough the type 4 secretion system of the integrating and conjugative elements (tfs ICE) is common in Helicobacter pylori, its clinical association with the cag pathogenicity island (cagPAI) have not yet been well-investigated. In this study, Vietnamese patient H. pylori samples (46 duodenal ulcer (DU), 51 non-cardia gastric cancer (NCGC), 39 chronic gastritis (CG)) were fully sequenced using next-generation sequencing and assembled into contigs. tfs3, tfs4, and cagPAI genes were compared with the public database. Most (94%) H. pylori strains possessed a complete cagPAI, which was the greatest risk factor for clinical outcomes, while the prevalences of tfs3 and tfs4 were 45% and 77%, respectively. Complete tfs3 and tfs4 were found in 18.3% and 17.6% of strains, respectively. The prevalence of H. pylori strains with complete tfs3 ICE in DU patients was significantly higher than that in NCGC patients (30.4% vs 11.7%, P < 0.05). In addition, the prevalence of strains with complete tfs3 ICE and cagPAI was significantly higher in DU patients than that in NCGC (28.4% vs 9.8%, P = 0.038) and CG patients (28.2% vs 7.7%, P = 0.024). cagPAI and complete tfs3 increased the risk of DU compared to NCGC (OR = 3.56, 95%CI: 1.1–14.1, P = 0.038) and CG (OR = 4.64, 95%CI: 1.1–27.6, P = 0.024). A complete cluster of tfs3 ICE was associated with gastroduodenal diseases in Vietnam. However, there was a low prevalence of the dupA/complete dupA cluster (15.4%) in the Vietnam strains. The prevalence of cagPAI in Vietnam strains was significantly higher than in US (P = 0.01) and Indonesia (P < 0.0001); the prevalence of the dupA cluster was also higher in the Vietnam strains than in the Indonesian strains (P < 0.05). In addition, the prevalence of ctkA, an accessory gene of tfs3, was significantly different between Vietnam and US strains (28% vs 2%, P = 0.0002). In summary, the acquisition of tfs3/4 ICE was common in H. pylori strains in patients with gastroduodenal disease in Vietnam, and the complete cluster of tfs3 ICE was a reliable marker for the severity of disease in the H. pylori infected population.
Three-dimensional imaging of xylem at cell wall level through near field nano holotomography
Authors: Koddenberg Tim , Greving Imke , Hagemann Johannes , Flenner Silja , Krause Andreas , Laipple Daniel , Klein Kim C. , Schmitt Uwe , Schuster Max , Wolf Andreas , Seifert Maria , Ludwig Veronika , Funk Stefan , Militz Holger , Nopens Martin 
Published: February 2021

AbstractDetailed imaging of the three-dimensionally complex architecture of xylary plants is important for studying biological and mechanical functions of woody plants. Apart from common two-dimensional microscopy, X-ray micro-computed tomography has been established as a three-dimensional (3D) imaging method for studying the hydraulic function of wooden plants. However, this X-ray imaging method can barely reach the resolution needed to see the minute structures (e.g. pit membrane). To complement the xylem structure with 3D views at the nanoscale level, X-ray near-field nano-holotomography (NFH) was applied to analyze the wood speciesPinus sylvestrisandFagus sylvatica. The demanded small specimens required focused ion beam (FIB) application. The FIB milling, however, influenced the image quality through gallium implantation on the cell-wall surfaces. The measurements indicated that NFH is appropriate for imaging wood at nanometric resolution. With a 26 nm voxel pitch, the structure of the cell-wall surface inPinus sylvestriscould be visualized in genuine detail. In wood ofFagus sylvatica, the structure of a pit pair, including the pit membrane, between two neighboring fibrous cells could be traced tomographically.
Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer
Authors: Golovinas Edvardas , Rutkauskas Danielis , Manakova Elena , Jankunec Marija , Silanskas Arunas , Sasnauskas Giedrius , Zaremba Mindaugas 
Published: February 2021

AbstractArgonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos), which are the core of RNA interference. The best understood prokaryotic Ago (pAgo) proteins are full-length pAgos. They are composed of four major structural/functional domains (N, PAZ, MID, and PIWI) and thereby closely resemble eAgos. It was demonstrated that full-length pAgos function as prokaryotic antiviral systems, with the PIWI domain performing cleavage of invading nucleic acids. However, the majority of identified pAgos are shorter and catalytically inactive (encode just MID and inactive PIWI domains), thus their action mechanism and function remain unknown. In this work we focus on AfAgo, a short pAgo protein encoded by an archaeon Archaeoglobus fulgidus. We find that in all previously solved AfAgo structures, its two monomers form substantial dimerization interfaces involving the C-terminal β-sheets. Led by this finding, we have employed various biochemical and biophysical assays, including SEC-MALS, SAXS, single-molecule FRET, and AFM, to show that AfAgo is indeed a homodimer in solution, which is capable of simultaneous interaction with two DNA molecules. This finding underscores the diversity of prokaryotic Agos and broadens the range of currently known Argonaute-nucleic acid interaction mechanisms.