bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula
Authors: Trefault Nicole , De la Iglesia Rodrigo , Moreno-Pino Mario , Lopes dos Santos Adriana , Gérikas Ribeiro Catherine , Parada-Pozo Génesis , Cristi Antonia , Marie Dominique , Vaulot Daniel 
Published: January 2021

AbstractYear-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris, which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.
Memory-specific correlated neuronal activity in higher-order auditory regions of a parrot
Authors: Satoh Ryohei , Eda-Fujiwara Hiroko , Watanabe Aiko , Okamoto Yasuharu , Miyamoto Takenori , Zandbergen Matthijs A. , Bolhuis Johan J. 
Published: January 2021

AbstractMale budgerigars (Melopsittacus undulatus) are open-ended learners that can learn to produce new vocalisations as adults. We investigated neuronal activation in male budgerigars using the expression of the protein products of the immediate early geneszenkandc-fosin response to exposure to conspecific contact calls (CCs: that of the mate or an unfamiliar female) in three subregions (CMM, dNCM and vNCM) of the caudomedial pallium, a higher order auditory region. Significant positive correlations of Zenk expression were found between these subregions after exposure to mate CCs. In contrast, exposure to CCs of unfamiliar females produced no such correlations. These results suggest the presence of a CC-specific association among the subregions involved in auditory memory. The caudomedial pallium of the male budgerigar may have functional subdivisions that cooperate in the neuronal representation of auditory memory.
Reconstructing Late Pleistocene paleoclimate at the scale of human behavior: an example from the Neandertal occupation of La Ferrassie (France)
Authors: Pederzani Sarah , Aldeias Vera , Dibble Harold L. , Goldberg Paul , Hublin Jean-Jacques , Madelaine Stéphane , McPherron Shannon P. , Sandgathe Dennis , Steele Teresa E. , Turq Alain , Britton Kate 
Published: January 2021

AbstractExploring the role of changing climates in human evolution is currently impeded by a scarcity of climatic information at the same temporal scale as the human behaviors documented in archaeological sites. This is mainly caused by high uncertainties in the chronometric dates used to correlate long-term climatic records with archaeological deposits. One solution is to generate climatic data directly from archaeological materials representing human behavior. Here we use oxygen isotope measurements of Bos/Bison tooth enamel to reconstruct summer and winter temperatures in the Late Pleistocene when Neandertals were using the site of La Ferrassie. Our results indicate that, despite the generally cold conditions of the broader period and despite direct evidence for cold features in certain sediments at the site, Neandertals used the site predominantly when climatic conditions were mild, similar to conditions in modern day France. We suggest that due to millennial scale climate variability, the periods of human activity and their climatic characteristics may not be representative of average conditions inferred from chronological correlations with long-term climatic records. These results highlight the importance of using direct routes, such as the high-resolution archives in tooth enamel from anthropogenically accumulated faunal assemblages, to establish climatic conditions at a human scale.
Post-gel polymerisation shrinkage profiling of polymer biomaterials using a chirped fibre Bragg grating
Authors: Rajan Ginu , Wong Alex , Farrar Paul , Prusty Gangadhara B. 
Published: January 2021

AbstractA strain profile measurement technique using a chirped fibre Bragg grating (CFBG) sensor by implementing an integration of differences (IOD) method is reported in this paper. Using the IOD method the spatial distribution of strain along the length of the CFBG is extracted from its power reflectance spectra. As a proof of concept demonstration, the developed technique is applied to measure the polymerisation shrinkage strain profile of a photo-cured polymer dental composite which exhibits a non-uniform strain distribution attributed to the curing lamp characteristics. The result from the CFBG technique is compared with that of an FBG array embedded in the dental composite and is correlated with the degree of conversion of the material which also depends on the curing lamp intensity distribution. This technology will have significant impact and applications in a range of medical, materials and engineering areas where strain or temperature gradient profile measurement is required in smaller scales.
Myocyte-specific enhancer factor 2c triggers transdifferentiation of adipose tissue-derived stromal cells into spontaneously beating cardiomyocyte-like cells
Authors: Takashima Shinichiro , Usui Soichiro , Inoue Oto , Goten Chiaki , Yamaguchi Kosei , Takeda Yusuke , Cui Shihe , Sakai Yoshio , Hayashi Kenshi , Sakata Kenji , Kawashiri Masa-aki , Takamura Masayuki 
Published: January 2021

AbstractCardiomyocyte regeneration is limited in adults. The adipose tissue-derived stromal vascular fraction (Ad-SVF) contains pluripotent stem cells that rarely transdifferentiate into spontaneously beating cardiomyocyte-like cells (beating CMs). However, the characteristics of beating CMs and the factors that regulate the differentiation of Ad-SVF toward the cardiac lineage are unknown. We developed a simple culture protocol under which the adult murine inguinal Ad-SVF reproducibly transdifferentiates into beating CMs without induction. The beating CMs showed the striated ventricular phenotype of cardiomyocytes and synchronised oscillation of the intracellular calcium concentration among cells on day 28 of Ad-SVF primary culture. We also identified beating CM-fated progenitors (CFPs) and performed single-cell transcriptome analysis of these CFPs. Among 491 transcription factors that were differentially expressed (≥ 1.75-fold) in CFPs and the beating CMs, myocyte-specific enhancer 2c (Mef2c) was key. Transduction of Ad-SVF cells with Mef2c using a lentiviral vector yielded CFPs and beating CMs with ~ tenfold higher cardiac troponin T expression, which was abolished by silencing of Mef2c. Thus, we identified the master gene required for transdifferentiation of Ad-SVF into beating CMs. These findings will facilitate the development of novel cardiac regeneration therapies based on gene-modified, cardiac lineage-directed Ad-SVF cells.
Vasoactive intestinal polypeptide plasma levels associated with affective symptoms and brain structure and function in healthy females
Authors: Simon Rozalyn A. , Barazanji Nawroz , Jones Michael P. , Bednarska Olga , Icenhour Adriane , Engström Maria , Hamilton J. Paul , Keita Åsa V. , Walter Susanna 
Published: January 2021

AbstractVasoactive intestinal polypeptide (VIP) is a neuroendocrine peptide distributed throughout the human body, including the CNS, where it is particularly abundant in brain regions associated with anxiety and depression. Based on earlier studies indicating that peripheral VIP may cross through the blood–brain barrier, we hypothesized plasma VIP levels to be associated with symptoms of anxiety and depression, as well as brain volume and resting-state functional connectivity in the amygdala, hippocampus, parahippocampus, and orbitofrontal cortex. Plasma VIP concentrations and anxiety/depression symptoms were measured in 37 healthy females. Functional and structural magnetic resonance imaging were used to evaluate functional connectivity and brain volume respectively, and their associations with VIP concentrations within brain regions associated with anxiety and depression. Negative correlations were found between VIP levels and symptoms of anxiety (r = − 0.44,p = 0.002) and depression (r = − 0.50,p = 0.001). Functional connectivity demonstrated significant VIP-dependent positive associations between the amygdala seed region with both the right parahippocampus (t(33) = 3.1, pFDR = 0.02) and right lateral orbitofrontal cortex (OFC;t(33) = 2.9, pFDR = 0.02). Moreover, VIP concentrations were significantly, positively correlated with brain volume in the left amygdala (r = 0.28,p = 0.007) and left lateral OFC (r = 0.29,p = 0.004). The present findings highlight a potential role for VIP in the neurobiology of affective symptoms.
The role of Toll-like receptor 9 in a murine model of Cryptococcus gattii infection
Authors: da Silva-Junior Elias Barbosa , Firmino-Cruz Luan , Guimarães-de-Oliveira Joyce Cristina , De-Medeiros Juliana Valente Rodrigues , de Oliveira Nascimento Danielle , Freire-de-Lima Matheus , de Brito-Gitirana Lycia , Morrot Alexandre , Previato Jose Osvaldo , Mendonça-Previato Lucia , Decote-Ricardo Debora , de Matos Guedes Herbert Leonel , Freire-de-Lima Celio Geraldo 
Published: January 2021

AbstractToll-like receptor 9 (TLR9) is crucial to the host immune response against fungi, such as Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, but its importance in Cryptococcus gattii infection is unknown. Our study aimed to understand the role of TLR9 during the course of experimental C. gattii infection in vivo, considering that the cryptococcal DNA interaction with the receptor could contribute to host immunity even in an extremely susceptible model. We inoculated C57BL/6 (WT) and TLR9 knock-out (TLR9−/−) mice intratracheally with 104C. gattii yeast cells. TLR9−/− mice had a higher mortality rate compared to WT mice and more yeast cells that had abnormal size, known as titan cells, in the lungs. TLR9−/− mice also had a greater number of CFUs in the spleen and brain than WT mice, in addition to having lower levels of IFN-γ and IL-17 in the lung. With these markers of aggressive cryptococcosis, we can state that TLR9−/− mice are more susceptible to C. gattii, probably due to a mechanism associated with the decrease of a Th1 and Th17-type immune response that promotes the formation of titan cells in the lungs. Therefore, our results indicate the participation of TLR9 in murine resistance to C. gattii infection.
Multifocal acceptance score to evaluate vision: MAS-2EV
Authors: Barcala Xoana , Vinas Maria , Romero Mercedes , Gambra Enrique , Mendez-Gonzalez Juan Luis , Marcos Susana , Dorronsoro Carlos 
Published: January 2021

AbstractWe present a new metric (Multifocal Acceptance Score, MAS-2EV) to evaluate vision with presbyopic corrections. The MAS-2EV is based on a set of images representing natural visual scenes at day and night conditions projected in far and near displays, and a near stereo target. Subjects view and score the images through different binocular corrections (monofocal corrections at far; bifocal corrections; monovision and modified monovision) administered with soft contact lenses (in cyclopleged young subjects) or with a binocular simultaneous vision simulator (in presbyopic and cyclopleged young subjects). MAS-2EV scores are visually represented in the form of polygons, and quantified using different metrics: overall visual quality, visual degradation at far, visual benefit at near, near stereo benefit, visual imbalance near-far, overall visual imbalance and a combined overall performance metric. We have found that the MAS-2EV has sufficient repeatability and sensitivity to allow differentiation across corrections with only two repetitions, and the duration of the psychophysical task (3 min for subject/condition/correction) makes it useable in the clinic. We found that in most subjects binocular bifocal corrections produce the lowest visual imbalance, and the highest near stereo benefit. 46.67% of the subjects ranked binocular bifocal corrections first, and 46.67% of the subjects ranked monovision first. MAS-2EV, particularly in combination with visual simulators, can be applied to select prospective presbyopic corrections in patients prior to contact lens fitting or intraocular lens implantation.
Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins
Authors: Boeckaerts Dimitri , Stock Michiel , Criel Bjorn , Gerstmans Hans , De Baets Bernard , Briers Yves 
Published: January 2021

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.
Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission
Authors: Kombe Ivy K. , Agoti Charles N. , Munywoki Patrick K. , Baguelin Marc , Nokes D. James , Medley Graham F. 
Published: January 2021

AbstractRespiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; particularly infants. Prior to rolling out any vaccination program, identification of the source of infant infections could further guide vaccination strategies. We extended a dynamic model calibrated at the individual host level initially fit to social-temporal data on shedding patterns to include whole genome sequencing data available at a lower sampling intensity. The study population was 493 individuals (55 aged < 1 year) distributed across 47 households, observed through one RSV season in coastal Kenya. We found that 58/97 (60%) of RSV-A and 65/125 (52%) of RSV-B cases arose from infection probably occurring within the household. Nineteen (45%) infant infections appeared to be the result of infection by other household members, of which 13 (68%) were a result of transmission from a household co-occupant aged between 2 and 13 years. The applicability of genomic data in studies of transmission dynamics is highly context specific; influenced by the question, data collection protocols and pathogen under investigation. The results further highlight the importance of pre-school and school-aged children in RSV transmission, particularly the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group.
Symptoms of anxiety/depression is associated with more aggressive inflammatory bowel disease
Authors: Gao Xin , Tang Yu , Lei Na , Luo Ying , Chen Pingrun , Liang Chang , Duan Shihao , Zhang Yan 
Published: January 2021

AbstractStudies have demonstrated that inflammatory bowel disease (IBD) patients are at an increased risk of developing anxiety and/or depression. IBD patients with depression/anxiety have higher rates of hospitalization and increased disease severity than those without. So far, there is a paucity of data concerning the impact of anxiety/depression on Chinese IBD patients. The aim of this study was to find out the prevalence of symptoms of anxiety/depression in Chinese IBD population and its impact on IBD-related features. This is a cross-sectional study from the southwest China IBD referral center. Eligible participants were divided into those with symptoms of anxiety/depression and those without based on the Hospital Anxiety and Depression Scale (HADS). Demographic data and disease duration, IBD-related surgery, tobacco use, extra-intestinal manifestations, disease activity scores, endoscopic evaluation, laboratory data and current medication use were compared between two groups. A total of 341 IBD patients [221 Crohn’s disease (CD) and 120 ulcerative colitis (UC)] were included. The prevalence of symptoms of anxiety/depression in IBD was 33.1%. CD patients with symptoms of anxiety/depression tended to have higher scores of simple endoscopic scores for Crohn’s disease (SES-CD) (p = 0.0005). UC patients with symptoms of anxiety/depression had a significantly higher Mayo score (p = 0.0017) and ulcerative colitis endoscopic index of severity (UCEIS) (p < 0.0001) than their non-anxiety/depression counterparts. CD-related surgery (p = 0.012) and Crohn's disease activity index (CDAI) (p < 0.0001) were identified as independent risk factors for symptoms of anxiety/depression in CD, while corticosteroid use (p = 0.036) as an independent risk factor for symptoms of anxiety/depression in UC. This study helps our understanding of the prevalence of symptoms of anxiety/depression in IBD patients and its impact on IBD course and reminds us to pay more attention on IBD management with anxiety/depression.
Brain reactivity using fMRI to insomnia stimuli in insomnia patients with discrepancy between subjective and objective sleep
Authors: Kim Young-Bo , Kim Nambeom , Lee Jae Jun , Cho Seo-Eun , Na Kyoung-Sae , Kang Seung-Gul 
Published: January 2021

AbstractSubjective–objective discrepancy of sleep (SODS) might be related to the distorted perception of sleep deficit and hypersensitivity to insomnia-related stimuli. We investigated differences in brain activation to insomnia-related stimuli among insomnia patients with SODS (SODS group), insomnia patients without SODS (NOSODS group), and healthy controls (HC). Participants were evaluated for subjective and objective sleep using sleep diary and polysomnography. Functional magnetic resonance imaging was conducted during the presentation of insomnia-related (Ins), general anxiety-inducing (Gen), and neutral (Neu) stimuli. Brain reactivity to the contrast of Ins vs. Neu and Gen vs. Neu was compared among the SODS (n = 13), NOSODS (n = 15), and HC (n = 16) groups. In the SODS group compared to other groups, brain areas including the left fusiform, bilateral precuneus, right superior frontal gyrus, genu of corpus callosum, and bilateral anterior corona radiata showed significantly increased blood oxygen level dependent (BOLD) signal in the contrast of Ins vs. Neu. There was no brain region with significantly increased BOLD signal in the Gen vs. Neu contrast in the group comparisons. Increased brain activity to insomnia-related stimuli in several brain regions of the SODS group is likely due to these individuals being more sensitive to sleep-related threat and negative cognitive distortion toward insomnia.
The association between bowel resection and the risk of nontyphoidal salmonella infection: a nationwide propensity score-matched cohort study
Authors: Yang Kuang-Tsu , Juang Sin-Ei , Hung Yao-Min , Wei James Cheng-Chung , Yip Hei-Tung , Chang Renin 
Published: January 2021

AbstractNontyphoidal salmonella (NTS) infection has a high mortality rate. Bowel resections affect gut microbiota and immune function, and the association between bowel resection and NTS infection in human beings has not been addressed. We conducted a nationwide propensity score (PS)-matched cohort study to clarify this association. Data from the Longitudinal Health Insurance Database of Taiwan were used to establish a case-cohort with bowel resections from 2000 to 2013. Informed consent was waived by the Institutional Review Board of China Medical University Hospital (CMUH104-REC2-115) because all personal identifying information used had been de-identified. Each case was matched with one control without any bowel resection according to age, gender, index date, and propensity score (PS). Cumulative incidences of and hazard ratios (HRs) for NTS infection development were analyzed. The incidence of NTS infection was greater in patients with a bowel resection than in the control group (2.97 vs. 1.92 per 10,000 person-years), with an adjusted hazard ratio (aHR) of 1.64 (95% CI = 1.08–2.48). The incidence of NTS infection increased significantly for cases with small bowel resections and right hemicolectomies. Age (31–40 and > 50 years), hypertension, chronic kidney disease, chronic obstructive pulmonary disease, and autoimmune diseases were significant risk factors of NTS infection. Stratification analysis revealed that patients without comorbidities were prone to NTS infection after bowel resections. The increased risk of developing NTS infection could be related to the bowel resection. Specific age groups and comorbidities also contribute to increased risk of NTS infection.