bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Amazon River plume, a barrier to animal dispersal in the Western Tropical Atlantic
Authors: Giachini Tosetto Everton , Bertrand Arnaud , Neumann-Leitão Sigrid , Nogueira Júnior Miodeli 
Published: January 2022

AbstractThe dispersal of marine organisms can be restricted by a set of isolation mechanisms including hard barriers or hydrological features. In the Western Atlantic Ocean, the Amazon River discharge has been shown to act as a biogeographical barrier responsible for the differences in reef fish communities between Caribbean Sea and Northeast Brazil continental shelves. Here, we compare the diversity of all Animalia phyla from biogeographic ecoregions along the Tropical Western Atlantic continental shelf to test the hypothesis that the Amazon River plume spatially structures species diversity. For that, we used beta diversity estimators and multivariate ecological analysis on a database of species occurrence of the whole animal kingdom including 175,477 occurrences of 8,375 species from six ecoregions along the Western Tropical Atlantic. Results of the whole animal kingdom and the richest phyla showed that the Caribbean Sea and Tropical Brazil ecoregions are isolated by the Amazon River Plume, broadening and confirming the hypothesis that it acts as a soft barrier to animal dispersal in the Western Tropical Atlantic. Species sharing is larger northwestwards, in direction of the Caribbean than the opposite direction. Beyond species isolation due to local characteristics such as low salinity and high turbidity, our results suggest the dominant northwestward currents probably play a major role in animal dispersion: it enhances the flux of larvae and other planktonic organisms with reduced mobility from Brazil to Caribbean and hinders their contrary movement. Thus, the Amazon area is a strong barrier for taxa with reduced dispersal capacity, while species of pelagic taxa with active swimming may transpose it more easily.
Hybrid systems using residual modeling for sea surface temperature forecasting
Authors: de Mattos Neto Paulo S. G. , Cavalcanti George D. C. , de O. Santos Júnior Domingos S. , Silva Eraylson G. 
Published: January 2022

AbstractThe sea surface temperature (SST) is an environmental indicator closely related to climate, weather, and atmospheric events worldwide. Its forecasting is essential for supporting the decision of governments and environmental organizations. Literature has shown that single machine learning (ML) models are generally more accurate than traditional statistical models for SST time series modeling. However, the parameters tuning of these ML models is a challenging task, mainly when complex phenomena, such as SST forecasting, are addressed. Issues related to misspecification, overfitting, or underfitting of the ML models can lead to underperforming forecasts. This work proposes using hybrid systems (HS) that combine (ML) models using residual forecasting as an alternative to enhance the performance of SST forecasting. In this context, two types of combinations are evaluated using two ML models: support vector regression (SVR) and long short-term memory (LSTM). The experimental evaluation was performed on three datasets from different regions of the Atlantic Ocean using three well-known measures: mean square error (MSE), mean absolute percentage error (MAPE), and mean absolute error (MAE). The best HS based on SVR improved the MSE value for each analyzed series by $$82.26\%$$

82.26
%

, $$98.93\%$$

98.93
%

, and $$65.03\%$$

65.03
%

compared to its respective single model. The HS employing the LSTM improved $$92.15\%$$

92.15
%

, $$98.69\%$$

98.69
%

, and $$32.41\%$$

32.41
%

concerning the single LSTM model. Compared to literature approaches, at least one version of HS attained higher accuracy than statistical and ML models in all study cases. In particular, the nonlinear combination of the ML models obtained the best performance among the proposed HS versions.
The incidence of COVID-19 infection following emergency use authorization of BBIBP-CORV inactivated vaccine in frontline workers in the United Arab Emirates
Authors: Al Kaabi Nawal , Oulhaj Abderrahim , Al Hosani Farida Ismail , Al Mazrouei Shamma , Najim Omer , Hussein Salah Eldin , Abdalla Jehad Saleh , Fasihuddin Mohammed Saifuddin , Hassan Afnan Abdellatif , Elghazali Gehad , Al Rumaithi Ahmed , Al Azazi Jumana , Weber Stefan , Beiram Rami , Parekh Khatija A. , Sheek-Hussein Mohamud , Yang Yunkai , Xiaoming Yang , Quliang Jenny , Eltantawy Islam , Mahmoud Sally , Koshy Ashish , Xiao Peng , Ganesan Subhashini , Elamin Wael , Zaher Walid 
Published: January 2022

AbstractBased on the findings from the Phase III clinical trials of inactivated SARS COV-2 Vaccine, (BBIBP-CORV) emergency use authorization (EUA) was granted for the vaccine to frontline workers in the UAE. A prospective cohort study was conducted among frontline workers to estimate the incidence rate and risk of symptomatic COVID-19 infection 14 days after the second dose of inoculation with BBIBP-CORV inactivated vaccine. Those who received two doses of the BBIBP-CORV vaccine in the period from 14th of September 2020 (first dose) to 21st of December 2020 (second dose) were followed up for COVID-19 infections. 11,322 individuals who received the two-dose BBIBP-CORV vaccine were included and were followed up post the second dose plus fourteen days. The incidence rate of symptomatic infection was 0.08 per 1000-person days (95% CI 0.07, 0.10). The estimated absolute risk of developing symptomatic infection was 0.97% (95% CI 0.77%, 1.17%). The confirmed seroconversion rate was 92.8%. There were no serious adverse events reported and no individuals suffered from severe disease. Our findings show that vaccinated individuals are likely to remain protected against symptomatic infection or becoming PCR positive for SARS COV 2 following the second dose of the vaccination.
Rapid video-based deep learning of cognate versus non-cognate T cell-dendritic cell interactions
Authors: Anandakumaran Priya N. , Ayers Abigail G. , Muranski Pawel , Creusot Remi J. , Sia Samuel K. 
Published: January 2022

AbstractIdentification of cognate interactions between antigen-specific T cells and dendritic cells (DCs) is essential to understanding immunity and tolerance, and for developing therapies for cancer and autoimmune diseases. Conventional techniques for selecting antigen-specific T cells are time-consuming and limited to pre-defined antigenic peptide sequences. Here, we demonstrate the ability to use deep learning to rapidly classify videos of antigen-specific CD8+ T cells. The trained model distinguishes distinct interaction dynamics (in motility and morphology) between cognate and non-cognate T cells and DCs over 20 to 80 min. The model classified high affinity antigen-specific CD8+ T cells from OT-I mice with an area under the curve (AUC) of 0.91, and generalized well to other types of high and low affinity CD8+ T cells. The classification accuracy achieved by the model was consistently higher than simple image analysis techniques, and conventional metrics used to differentiate between cognate and non-cognate T cells, such as speed. Also, we demonstrated that experimental addition of anti-CD40 antibodies improved model prediction. Overall, this method demonstrates the potential of video-based deep learning to rapidly classify cognate T cell-DC interactions, which may also be potentially integrated into high-throughput methods for selecting antigen-specific T cells in the future.
Effects of insertion torque values on the marginal bone loss of dental implants installed in sheep mandibles
Authors: Gehrke Sergio Alexandre , Júnior Jaime Aramburú , Treichel Tiago Luis Eirles , do Prado Tales Dias , Dedavid Berenice Anina , de Aza Piedad N. 
Published: January 2022

AbstractThe aim of the present in vivo study was to analyze and compare the effects on the crestal bone healing of two different implant macrogeometries installed in fresh socket areas and in normal bone areas with different insertion torque values. Two implant macrogeometries were used in the present study, DuoCone implant (DC) and Maestro implant (MAE), forming four groups: group DCws, in which the implants were installed in healing bone (without a socket); group DCfs, in which the implants were installed in post-extraction areas (fresh sockets); group MAEws, in which the implants were installed in healing bone (without a socket); group MAEfs, in which the implants were installed in post-extraction areas (fresh sockets). After 30 and 90 days of implantations in the bilateral mandibles of 10 sheep, eighty implants were evaluated through digital X-ray images and histologic slices. The crestal bone position in relation to the implant platform shoulder was measured and compared. The measured insertion torque was 47.2 ± 4.69 Ncm for the DCws group, 43.4 ± 4.87 Ncm for the DCfs group, 29.3 ± 3.16 Ncm for the MAEws group, and 27.7 ± 4.41 Ncm for the MAEfs group. The radiographic mesio-distal and histological bucco-lingual analyses showed significantly greater vertical bone loss in the implants installed with high torque (DC groups) in comparison to the implants installed with a low torque (MAE groups) (p < 0.05), at both evaluation times. In general, low insertion torque values (Maestro implants) showed better results of MBL when compared to implants installed with higher torque values (Duo Cone implants). Moreover, our results showed that the implants installed in the sites without sockets showed a less MBL in comparison with the implants installed in sites of fresh sockets.
Investigating the impact of emotion on temporal orientation in a deep multitask setting
Authors: Kamila Sabyasachi , Hasanuzzaman Mohammad , Ekbal Asif , Bhattacharyya Pushpak 
Published: January 2022

AbstractTemporal orientation is an important aspect of human cognition which shows how an individual emphasizes past, present, and future. Theoretical research in psychology shows that one’s emotional state can influence his/her temporal orientation. We hypothesize that measuring human temporal orientation can benefit from concurrent learning of emotion. To test this hypothesis, we propose a deep learning-based multi-task framework where we concurrently learn a unified model for temporal orientation (our primary task) and emotion analysis (secondary task) using tweets. Our multi-task framework takes users’ tweets as input and produces three temporal orientation labels (past, present or future) and four emotion labels (joy, sadness, anger, or fear) with intensity values as outputs. The classified tweets are then grouped for each user to obtain the user-level temporal orientation and emotion. Finally, we investigate the associations between the users’ temporal orientation and their emotional state. Our analysis reveals that joy and anger are correlated to future orientation while sadness and fear are correlated to the past orientation.
Transcriptional alterations in bladder epithelial cells in response to infection with different morphological states of uropathogenic Escherichia coli
Authors: Persson Katarina , Petersson Ulrika , Johansson Charlotte , Demirel Isak , Kruse Robert 
Published: January 2022

AbstractUropathogenic Escherichia coli (UPEC) may undergo a cyclic cascade of morphological alterations that are believed to enhance the potential of UPEC to evade host responses and re-infect host cell. However, knowledge on the pathogenic potential and host activation properties of UPEC during the morphological switch is limited. Microarray analysis was performed on mRNA isolated from human bladder epithelial cells (HBEP) after exposure to three different morphological states of UPEC (normal coliform, filamentous form and reverted form). Cells stimulated with filamentous bacteria showed the lowest number of significant gene alterations, although the number of enriched gene ontology classes was high suggesting diverse effects on many different classes of host genes. The normal coliform was in general superior in stimulating transcriptional activity in HBEP cells compared to the filamentous and reverted form. Top-scored gene entities activated by all three morphological states included IL17C, TNFAIP6, TNF, IL20, CXCL2, CXCL3, IL6 and CXCL8. The number of significantly changed canonical pathways was lower in HBEP cells stimulated with the reverted form (32 pathways), than in cells stimulated with the coliform (83 pathways) or filamentous bacteria (138 pathways). A host cell invasion assay showed that filamentous bacteria were unable to invade bladder cells, and that the number of intracellular bacteria was markedly lower in cells infected with the reverted form compared to the coliform. In conclusion, the morphological state of UPEC has major impact on the host bladder response both when evaluating the number and the identity of altered host genes and pathways.
KIBRA, MTNR1B, and FKBP5 genotypes are associated with decreased odds of incident delirium in elderly post-surgical patients
Authors: Terrelonge Mark , LaHue Sara C. , Tang Christopher , Movsesyan Irina , Pullinger Clive R. , Dubal Dena B. , Leung Jacqueline , Douglas Vanja C. 
Published: January 2022

AbstractDespite the association between cognitive impairment and delirium, little is known about whether genetic differences that confer cognitive resilience also confer resistance to delirium. To investigate whether older adults without postoperative delirium, compared with those with postoperative delirium, are more likely to have specific single nucleotide polymorphisms (SNPs) in the FKBP5, KIBRA, KLOTHO, MTNR1B, and SIRT1 genes known to be associated with cognition or delirium. This prospective nested matched exploratory case–control study included 94 older adults who underwent orthopedic surgery and screened for postoperative delirium. Forty-seven subjects had incident delirium, and 47 age-matched controls were not delirious. The primary study outcome was genotype frequency for the five SNPs. Compared with participants with delirium, those without delirium had higher adjusted odds of KIBRA SNP rs17070145 CT/TT [vs. CC; adjusted odds ratio (aOR) 2.80, 95% confidence interval (CI) 1.03, 7.54; p = 0.04] and MTNR1B SNP rs10830963 CG/GG (vs. CC; aOR 4.14, 95% CI 1.36, 12.59; p = 0.01). FKBP5 SNP rs1360780 CT/TT (vs. CC) demonstrated borderline increased adjusted odds of not developing delirium (aOR 2.51, 95% CI 1.00, 7.34; p = 0.05). Our results highlight the relevance of KIBRA, MTNR1B, and FKBP5 in understanding the complex relationship between delirium, cognition, and sleep, which warrant further study in larger, more diverse populations.
3D nanomechanical mapping of subcellular and sub-nuclear structures of living cells by multi-harmonic AFM with long-tip microcantilevers
Authors: Efremov Yuri M. , Suter Daniel M. , Timashev Peter S. , Raman Arvind 
Published: January 2022

AbstractRecent developments such as multi-harmonic Atomic Force Microscopy (AFM) techniques have enabled fast, quantitative mapping of nanomechanical properties of living cells. Due to their high spatiotemporal resolution, these methods provide new insights into changes of mechanical properties of subcellular structures due to disease or drug response. Here, we propose three new improvements to significantly improve the resolution, identification, and mechanical property quantification of sub-cellular and sub-nuclear structures using multi-harmonic AFM on living cells. First, microcantilever tips are streamlined using long-carbon tips to minimize long-range hydrodynamic interactions with the cell surface, to enhance the spatial resolution of nanomechanical maps and minimize hydrodynamic artifacts. Second, simultaneous Spinning Disk Confocal Microscopy (SDC) with live-cell fluorescent markers enables the unambiguous correlation between observed heterogeneities in nanomechanical maps with subcellular structures. Third, computational approaches are then used to estimate the mechanical properties of sub-nuclear structures. Results are demonstrated on living NIH 3T3 fibroblasts and breast cancer MDA-MB-231 cells, where properties of nucleoli, a deep intracellular structure, were assessed. The integrated approach opens the door to study the mechanobiology of sub-cellular structures during disease or drug response.
Genetic diversity and mate selection in a reintroduced population of gray wolves
Authors: Ausband David E. 
Published: January 2022

AbstractThe genetic composition of an individual can markedly affect its survival, reproduction, and ultimately fitness. As some wildlife populations become smaller, conserving genetic diversity will be a conservation challenge. Many imperiled species are already supported through population augmentation efforts and we often do not know if or how genetic diversity is maintained in translocated species. As a case study for understanding the maintenance of genetic diversity in augmented populations, I wanted to know if genetic diversity (i.e., observed heterozygosity) remained high in a population of gray wolves in the Rocky Mountains of the U.S. > 20 years after reintroduction. Additionally, I wanted to know if a potential mechanism for such diversity was individuals with below average genetic diversity choosing mates with above average diversity. I also asked whether there was a preference for mating with unrelated individuals. Finally, I hypothesized that mated pairs with above average heterozygosity would have increased survival of young. Ultimately, I found that females with below average heterozygosity did not choose mates with above average heterozygosity and wolves chose mates randomly with respect to genetic relatedness. Pup survival was not higher for mated pairs with above average heterozygosity in my models. The dominant variables predicting pup survival were harvest rate during their first year of life and years pairs were mated. Ultimately, genetic diversity was relatively unchanged > 20 years after reintroduction. The mechanism for maintaining such diversity does not appear related to individuals preferentially choosing more genetically diverse mates. Inbreeding avoidance, however, appears to be at least one mechanism maintaining genetic diversity in this population.
Endoplasmic reticulum stress and the unfolded protein response in skeletal muscle of subjects suffering from peritoneal sepsis
Authors: Metzing Uta Barbara , von Loeffelholz Christian , Steidl Ricardo , Romeike Bernd , Winkler René , Rauchfuß Falk , Settmacher Utz , Stoppe Christian , Coldewey Sina M. , Weinmann Claudia , Weickert Martin O. , Claus Ralf A. , Birkenfeld Andreas L. , Kosan Christian , Horn Paul 
Published: January 2022

AbstractWe provide a descriptive characterization of the unfolded protein response (UPR) in skeletal muscle of human patients with peritoneal sepsis and a sepsis model of C57BL/6J mice. Patients undergoing open surgery were included in a cross-sectional study and blood and skeletal muscle samples were taken. Key markers of the UPR and cluster of differentiation 68 (CD68) as surrogate of inflammatory injury were evaluated by real-time PCR and histochemical staining. CD68 mRNA increased with sepsis in skeletal muscle of patients and animals (p < 0.05). Mainly the inositol-requiring enzyme 1α branch of the UPR was upregulated as shown by elevated X-box binding-protein 1 (XBP1u) and its spliced isoform (XBP1s) mRNA (p < 0.05, respectively). Increased expression of Gadd34 indicated activation of PRKR-Like Endoplasmic Reticulum Kinase (PERK) branch of the UPR, and was only observed in mice (p < 0.001) but not human study subjects. Selected cell death signals were upregulated in human and murine muscle, demonstrated by increased bcl-2 associated X protein mRNA and TUNEL staining (p < 0.05). In conclusion we provide a first characterization of the UPR in skeletal muscle in human sepsis.
Insights into cell robustness against lignocellulosic inhibitors and insoluble solids in bioethanol production processes
Authors: Moreno Antonio D. , González-Fernández Cristina , Tomás-Pejó Elia 
Published: January 2022

AbstractIncreasing yeast robustness against lignocellulosic-derived inhibitors and insoluble solids in bioethanol production is essential for the transition to a bio-based economy. This work evaluates the effect exerted by insoluble solids on yeast tolerance to inhibitory compounds, which is crucial in high gravity processes. Adaptive laboratory evolution (ALE) was applied on a xylose-fermentingSaccharomyces cerevisiaestrain to simultaneously increase the tolerance to lignocellulosic inhibitors and insoluble solids. The evolved strain gave rise to a fivefold increase in bioethanol yield in fermentation experiments with high concentration of inhibitors and 10% (w/v) of water insoluble solids. This strain also produced 5% (P > 0.01) more ethanol than the parental in simultaneous saccharification and fermentation of steam-exploded wheat straw, mainly due to an increased xylose consumption. In response to the stress conditions (solids and inhibitors) imposed in ALE, cells induced the expression of genes related to cell wall integrity (SRL1,CWP2,WSC2andWSC4) and general stress response (e.g.,CDC5,DUN1,CTT1,GRE1), simultaneously repressing genes related to protein synthesis and iron transport and homeostasis (e.g.,FTR1,ARN1,FRE1), ultimately leading to the improved phenotype. These results contribute towards understanding molecular mechanisms that cells might use to convert lignocellulosic substrates effectively.
Do the total mercury concentrations detected in fish from Czech ponds represent a risk for consumers?
Authors: Pavla Sehonova , Danka Harustiakova , Premysl Mikula , Denisa Medkova , Kristyna Malacova , Zdenka Svobodova 
Published: January 2022

AbstractMercury is one of the important pollutants of the environment. Therefore, it’s necessary to monitor quantity of mercury especially in aquatic ecosystems. The main goal of the presented study was to compare the content of total mercury in tissues of fish coming from the Czech Republic, an important carp exporter, with focus on comparison of mercury content between 3 different ponds, its comparison between different fish species and between different tissues of the same species, and estimation whether the mercury content in tissues meets the limit given in the Commission Regulation (EC) No. 1881/2006 or not. Total mercury concentration was measured in 90 fish specimen sampled from three ponds (Velky Kocelovicky, Mysliv and Zehunsky) in autumn 2018. The values of total mercury in fish tissues was measured by atomic absorption spectrometry. The content of total mercury in the tissues decreased as follows: muscle > liver > gonads > scales. The highest average content of total mercury in muscle was 0.1517 ± 0.0176 mg/kg coming from pike caught in Velky Kocelovicky pond. In contrast, the lowest average content of total mercury in muscle 0.0036 ± 0.0003 mg/kg was found in carp tissue coming from the locality of Zehunsky pond. We confirmed that the predatory fish are more exposed to mercury than non-predatory fish. None of the monitored localities exceeded the set regulatory limit. Thus, our study shows that fish coming from these ponds are safe in terms of total mercury content.