bluuebunny/crossref_metadata_2025_split huggingface dataset:
Looking into the flora of Dutch Brazil: botanical identifications of seventeenth century plant illustrations in the Libri Picturati
Authors: Alcàntara-Rodríguez Mireia , Françozo Mariana , Van Andel Tinde 
Published: October 2021

AbstractThe Libri Picturati includes a collection of plant illustrations from seventeenth century Dutch Brazil that is kept in the Jagiellonian library in Krakow since World War II. While many studies focused on the artistic details and history of these images, we identified the flora depicted. We used contemporary textual sources (e.g., Historia Naturalis Brasiliae), monographs and taxonomist’ assessments. We checked origin, life form, domestication and conservation status and the plant parts that are represented. We identified 198 taxa, consisting mostly of wild, native rainforest trees and 35 introduced species. Fertile branches are the most represented, although some loose dry fruits and sterile material were also painted, which sheds light into the collection methods by naturalists in Dutch Brazil. Several species are no longer abundant or have become invasive due to anthropogenic influences since colonialism. Through this botanical iconography, we traced the first records of the sunflower and the Ethiopian pepper in Brazil, as well as the dispersion and assimilation of the flora encountered in the colony by Indigenous, African and European peoples. We emphasized the relevance of combining visual and textual sources when studying natural history collections and we highlighted how digitalization makes these artistic and scientific collections more accessible.
Particular matter influences the incidence of acute otitis media in children
Authors: Park Mina , Han Jiyeon , Park Jiwon , Jang Myoung-jin , Park Moo Kyun 
Published: October 2021

AbstractParticulate matter (PM) is the main component of air pollution. Children are vulnerable to PM and acute otitis media (AOM), which is one of the most common diseases in children. However, studies on the relationship between AOM in children and PM are rare and their results are inconsistent. The aim of this study is to investigate the effect of PM on AOM in children on the basis of the Korea National Health Insurance service (NHIS) claims data. NHIS claim data from 2008 to 2015 was used to identify outpatient visits, antibiotic use to treat AOM, and demographic data. This data was combined with the data on PM2.5 (≤ 2.5 μm) and PM10 (≤ 10 μm according to its aerodynamic diameter) level extracted from air pollution data from Korean National Institute of Environmental Research for 16 administrative regions. The children with AOM were divided into three age groups (< 2, 2–4, 5–10 years). Generalized linear Poisson regression model was used to estimate the association between AOM and PM using daily counts of AOM and daily mean PM concentrations. It was adjusted to temperature, wind, humidity, season, year, age, and region. With an increase in PM2.5 of 10 μg/m3, the relative risk of OM increased by 4.5% in children under 2 years of age. The effect of PM2.5 was strongest influence on the day of exposure. The exposure to PM10 was related to the incidence of AOM on the day of exposure and the following seven days in all three age groups. The PM concentrations did not strongly affect either AOM duration or the use of antibiotics to cure AOM. The RR in the each lag day after exposure to PM10 was diverse according to the age groups. Regardless of PM size and children’s age, the PM levels are positively related to the incidence of AOM. Both PM2.5 and PM10 have the most adverse effects on children under 2 years of age and on the day of exposure.
First direct determination of the 93Mo half-life
Authors: Kajan I. , Heinitz S. , Kossert K. , Sprung P. , Dressler R. , Schumann D. 
Published: October 2021

AbstractThis work presents the first direct measurement of the 93Mo half-life. The measurement is a combination of high-resolution mass spectrometry for the determination of the 93Mo concentration and liquid scintillation counting for determining the specific activity. A 93Mo sample of high purity was obtained from proton irradiated niobium by chemical separation of molybdenum with a decontamination factor larger than 1.6 × 1014 with respect to Nb. The half-life of 93Mo was deduced to be 4839(63) years, which is more than 20% longer than the currently adopted value, whereas the relative uncertainty could be reduced by a factor of 15. The probability that the 93Mo decays to the metastable state 93mNb was determined to be 95.7(16)%. This value is a factor of 8 more precise than previous estimations. Due to the man-made production of 93Mo in nuclear facilities, the result leads to significantly increased precision for modelling the low-level nuclear waste composition. The presented work demonstrates the importance of chemical separations in combination with state-of-the-art analysis techniques, which are inevitable for precise and accurate determinations of nuclear decay data.
Genomic epidemiology of rifampicin ADP-ribosyltransferase (Arr) in the Bacteria domain
Authors: Morgado Sergio , Fonseca Érica , Vicente Ana Carolina 
Published: October 2021

AbstractArr is an ADP-ribosyltransferase enzyme primarily reported in association with rifamycin resistance, which has been used to treat tuberculosis in addition to Gram-positive infections and, recently, pan-resistant Gram-negative bacteria. The arr gene was initially identified on the Mycolicibacterium smegmatis chromosome and later on Proteobacteria plasmids. This scenario raised concerns on the distribution and spread of arr, considering the Bacteria domain. Based on 198,082 bacterial genomes/metagenomes, we performed in silico analysis, including phylogenetic reconstruction of Arr in different genomic contexts. Besides, new arr alleles were evaluated by in vitro analysis to assess their association with rifampin resistance phenotype. The arr gene was prevalent in thousands of chromosomes and in hundreds of plasmids from environmental and clinical bacteria, mainly from the phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Furthermore, this gene was identified in other and new genomic contexts. Interestingly, Arr sequences associated with rifampin resistance were distributed across all phylogeny, indicating that, despite the diversity, their association with rifampin resistance phenotype were maintained. In fact, we found that the key residues were highly conserved. In addition, other analyzes have raised evidence of another Arr function, which is related to guanidine metabolism. Finally, this scenario as a whole also suggested the Actinobacteria phylum as a potential ancestral source of arr within the Bacteria domain.
Biosafety assessment of Acinetobacter strains isolated from the Three Gorges Reservoir region in nematode Caenorhabditis elegans
Authors: Deng Yunjia , Du Huihui , Tang Mingfeng , Wang Qilong , Huang Qian , He Ying , Cheng Fei , Zhao Feng , Wang Dayong , Xiao Guosheng 
Published: October 2021

AbstractAcinetobacter has been frequently detected in backwater areas of the Three Gorges Reservoir (TGR) region. We here employed Caenorhabditis elegans to perform biosafety assessment of Acinetobacter strains isolated from backwater area in the TGR region. Among 21 isolates and 5 reference strains of Acinetobacter, exposure to Acinetobacter strains of AC1, AC15, AC18, AC21, A. baumannii ATCC 19606T, A. junii NH88-14, and A. lwoffii DSM 2403T resulted in significant decrease in locomotion behavior and reduction in lifespan of Caenorhabditis elegans. In nematodes, exposure to Acinetobacter strains of AC1, AC15, AC18, AC21, A. baumannii, A. junii and A. lwoffii also resulted in significant reactive oxygen species (ROS) production. Moreover, exposure to Acinetobacter isolates of AC1, AC15, AC18, and AC21 led to significant increase in expressions of both SOD-3::GFP and some antimicrobial genes (lys-1, spp-12, lys-7, dod-6, spp-1, dod-22, lys-8, and/or F55G11.4) in nematodes. The Acinetobacter isolates of AC1, AC15, AC18, and AC21 had different morphological, biochemical, phylogenetical, and virulence gene properties. Our results suggested that exposure risk of some Acinetobacter strains isolated from the TGR region exists for environmental organisms and human health. In addition, C. elegans is useful to assess biosafety of Acinetobacter isolates from the environment.
Soluble PD-L1 is a predictive and prognostic biomarker in advanced cancer patients who receive immune checkpoint blockade treatment
Authors: Oh So Yeon , Kim Soyeon , Keam Bhumsuk , Kim Tae Min , Kim Dong-Wan , Heo Dae Seog 
Published: October 2021

AbstractCirculating soluble programmed death-1 ligand (sPD-L1) is measurable in the serum of cancer patients. This study aimed to investigate the significance of sPD-L1 in cancer patients receiving immune checkpoint inhibitor therapy. Blood samples were obtained before and after immune checkpoint inhibitor therapy (January 2015 to January 2019). The study cohort consisted of 128 patients who were diagnosed with non-small cell lung cancer (n = 50), melanoma (n = 31), small cell lung cancer (n = 14), urothelial carcinoma (n = 13), and other cancers (n = 20). Patients with a high level (> 11.0 pg/μL) of sPD-L1 were more likely to exhibit progressive disease compared with those with a low level (41.8% versus 20.7%, p = 0.013). High sPD-L1 was also associated with worse prognosis; the median PFS was 2.9 (95% confidence interval [CI] 2.1–3.7) months versus 6.3 (95% CI 3.0–9.6) months (p = 0.023), and the median OS was 7.4 (95% CI 6.3–8.5) months versus 13.3 (95% CI 9.2–17.4) months (p = 0.005). In the multivariate analyses, high sPD-L1 was an independent prognostic factor for both decreased PFS (HR 1.928, p = 0.038) and OS (HR 1.788, p = 0.004). sPD-L1 levels did not correlate with tissue PD-L1 expression. However, sPD-L1 levels were positively correlated with neutrophil to lymphocyte ratios and negatively correlated with both the proportion and the total number of lymphocytes. We found that high pretreatment sPD-L1 levels were associated with progressive disease and were an independent prognostic factor predicting lower PFS and OS in these patients.
Enhancing adoptive CD8 T cell therapy by systemic delivery of tumor associated antigens
Authors: Jæhger Ditte E. , Hübbe Mie L. , Kræmer Martin K. , Clergeaud Gael , Olsen André V. , Stavnsbjerg Camilla , Wiinholt Mette N. , Kjær Andreas , Henriksen Jonas R. , Hansen Anders E. , Andresen Thomas L. 
Published: October 2021

AbstractAdoptive T-cell transfer (ACT) offers a curative therapeutic option for subsets of melanoma and hematological cancer patients. To increase response rates and broaden the applicability of ACT, it is necessary to improve the post-infusion performance of the transferred T cells. The design of improved treatment strategies includes transfer of cells with a less differentiated phenotype. Such T cell subsets have high proliferative potential but require stimulatory signals in vivo to differentiate into tumor-reactive effector T cells. Thus, combination strategies are needed to support the therapeutic implementation of less differentiated T cells. Here we show that systemic delivery of tumor-associated antigens (TAAs) facilitates in vivo priming and expansion of previously non-activated T cells and enhance the cytotoxicity of activated T cells. To achieve this in vivo priming, we use flexible delivery vehicles of TAAs and a TLR7/8 agonist. Contrasting subcutaneous delivery systems, these vehicles accumulate TAAs in the spleen, thereby achieving close proximity to both cross-presenting dendritic cells and transferred T cells, resulting in robust T-cell expansion and anti-tumor reactivity. This TAA delivery platform offers a strategy to safely potentiate the post-infusion performance of T cells using low doses of antigen and TLR7/8 agonist, and thereby enhance the effect of ACT.
Ppia is the most stable housekeeping gene for qRT-PCR normalization in kidneys of three Pkd1-deficient mouse models
Authors: Muñoz Juan J. , Anauate Ana C. , Amaral Andressa G. , Ferreira Frederico M. , Watanabe Elieser H. , Meca Renata , Ormanji Milene S. , Boim Mirian A. , Onuchic Luiz F. , Heilberg Ita P. 
Published: October 2021

AbstractAutosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited renal disorder, characterized by renal cyst development leading to end-stage renal disease. Although the appropriate choice of suitable reference is critical for quantitative RNA analysis, no comparison of frequently used “housekeeping” genes is available. Here, we determined the validity of 7 candidate housekeeping genes (Actb, Actg1, B2m, Gapdh, Hprt, Pgam1 and Ppia) in kidney tissues from mouse models orthologous to ADPKD, including a cystic mice (CY) 10–12 weeks old (Pkd1flox/flox:Nestincre/Pkd1flox/−:Nestincre, n = 10) and non-cystic (NC) controls (Pkd1flox/flox/Pkd1flox/-, n = 10), Pkd1-haploinsufficient (HT) mice (Pkd1+/−, n = 6) and wild-type (WT) controls (Pkd1+/+, n = 6) and a severely cystic (SC) mice 15 days old (Pkd1V/V, n = 7) and their controls (CO, n = 5). Gene expression data were analyzed using six distinct statistical softwares. The estimation of the ideal number of genes suggested the use of Ppia alone as sufficient, although not ideal, to analyze groups altogether. Actb, Hprt and Ppia expression profiles were correlated in all samples. Ppia was identified as the most stable housekeeping gene, while Gapdh was the least stable for all kidney samples. Stat3 expression level was consistent with upregulation in SC compared to CO when normalized by Ppia expression. In conclusion, present findings identified Ppia as the best housekeeping gene for CY + NC and SC + CO groups, while Hprt was the best for the HT + WT group.
The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm
Authors: Matra Deden Derajat , Fathoni Muh Agust Nur , Majiidu Muhammad , Wicaksono Hanif , Sriyono Agung , Gunawan Gunawan , Susanti Hilda , Sari Rismita , Fitmawati Fitmawati , Siregar Iskandar Zulkarnaen , Widodo Winarso Drajad , Poerwanto Roedhy 
Published: October 2021

AbstractMangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi’s genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.
A prediction model using 2-propanol and 2-butanone in urine distinguishes breast cancer
Authors: Kure Shoko , Satoi Sera , Kitayama Toshihiko , Nagase Yuta , Nakano Nobuo , Yamada Marina , Uchiyama Noboru , Miyashita Satoshi , Iida Shinya , Takei Hiroyuki , Miyashita Masao 
Published: October 2021

AbstractSafe and noninvasive methods for breast cancer screening with improved accuracy are urgently needed. Volatile organic compounds (VOCs) in biological samples such as breath and blood have been investigated as noninvasive novel markers of cancer. We investigated volatile organic compounds in urine to assess their potential for the detection of breast cancer. One hundred and ten women with biopsy-proven breast cancer and 177 healthy volunteers were enrolled. The subjects were divided into two groups: a training set and an external validation set. Urine samples were collected and analyzed by gas chromatography and mass spectrometry. A predictive model was constructed by multivariate analysis, and the sensitivity and specificity of the model were confirmed using both a training set and an external set with reproducibility tests. The training set included 60 breast cancer patients (age 34–88 years, mean 60.3) and 60 healthy controls (age 34–81 years, mean 58.7). The external validation set included 50 breast cancer patients (age 35–85 years, mean 58.8) and 117 healthy controls (age 18–84 years, mean 51.2). One hundred and ninety-one compounds detected in at least 80% of the samples from the training set were used for further analysis. The predictive model that best-detected breast cancer at various clinical stages was constructed using a combination of two of the compounds, 2-propanol and 2-butanone. The sensitivity and specificity in the training set were 93.3% and 83.3%, respectively. Triplicated reproducibility tests were performed by randomly choosing ten samples from each group, and the results showed a matching rate of 100% for the breast cancer patient group and 90% for the healthy control group. Our prediction model using two VOCs is a useful complement to the current diagnostic tools. Further studies inclusive of benign tumors and non-breast malignancies are warranted.
Effect of AAV-mediated overexpression of ATF5 and downstream targets of an integrated stress response in murine skeletal muscle
Authors: Brearley-Sholto Madelaine C. , Loczenski-Brown David M. , Jones Sarah , Daniel Zoe C. T. R. , Ebling Francis J. P. , Parr Tim , Brameld John M. 
Published: October 2021

AbstractWe previously reported that growth promoter-induced skeletal muscle hypertrophy co-ordinately upregulated expression of genes associated with an integrated stress response (ISR), as well as potential ISR regulators. We therefore used Adeno-Associated Virus (AAV)-mediated overexpression of these genes, individually or in combination, in mouse skeletal muscle to test whether they induced muscle hypertrophy. AAV of each target gene was injected into mouse Tibialis anterior (TA) and effects on skeletal muscle growth determined 28 days later. Individually, AAV constructs for Arginase-2 (Arg2) and Activating transcription factor-5 (Atf5) reduced hindlimb muscle weights and upregulated expression of genes associated with an ISR. AAV-Atf5 also decreased Myosin heavy chain (MyHC)-IIB mRNA, but increased MyHC-IIA and isocitrate dehydrogenase-2 (Idh2) mRNA, suggesting ATF5 is a novel transcriptional regulator of Idh2. AAV-Atf5 reduced the size of both TA oxidative and glycolytic fibres, without affecting fibre-type proportions, whereas Atf5 combined with Cebpg (CCAAT enhancer binding protein-gamma) only reduced the size of glycolytic fibres and tended to increase the proportion of oxidative fibres. It is likely that persistent Atf5 overexpression maintains activation of the ISR, thereby reducing protein synthesis and/or increasing protein degradation and possibly apoptosis, resulting in inhibition of muscle growth, with overexpression of Arg2 having a similar effect.
Glacial lake outburst floods enhance benthic microbial productivity in perennially ice-covered Lake Untersee (East Antarctica)
Authors: Faucher Benoit , Lacelle Denis , Marsh Nicole Britney , Jasperse Liam , Clark Ian Douglas , Andersen Dale Thomas 
Published: October 2021

AbstractBenthic ecosystems of perennially ice-covered lakes in Antarctica are highly sensitive to climate-driven changes. Lake Untersee has been in hydrological steady-state for several hundred years with a high pH water column and extremely low levels of dissolved inorganic carbon. Here, we show that glacial lake outburst floods can replenish carbon dioxide-depleted lakes with carbon, enhancing phototrophic activity of the benthic ecosystem. In 2019, a glacial lake outburst flood brought 17.5 million m3 of water to Lake Untersee, the most substantial reported increase for any surface lake in Antarctica. High-resolution grain-size and carbon isotope analyses of microbial mats suggest that glacial lake outburst floods have occurred periodically over the Holocene and help explain the complex patterns of carbon cycling and sequestration observed in the lake. Our findings suggest that periodic flooding events may provide biological stimuli to other carbon dioxide-depleted Antarctic ecosystems and perhaps even icy lakes on early Mars.
Severe Acquired Primary Hypothyroidism in Children and its Influence
on Growth: A Retrospective Analysis of 43 Cases
Authors: Becker Marianne , Blankenstein Oliver , Lankes Erwin , Schnabel Dirk , Krude Heiko 
Published: October 2021

Abstract
Introduction Severe acquired hypothyroidism in childhood is a rare
condition, mostly caused by autoimmune thyroiditis. Scarce and inconsistent data
based on small patient numbers exist concerning its impact on growth in
height.
Methods Patient files at a single centre university hospital over 8 years
were retrospectively reviewed. We identified 43 patients (mean age 10.6 years,
3.3–15.25, 59% prepubertal, 88% females) in a cohort of
children older than 3 years with an initial TSH>30 mIU/l and
reduced T4 or fT4; congenital and drug-induced hypothyroidism were excluded.
Results All patients had signs of autoimmune thyroiditis (93%
positive autoantibodies, 95% typical ultrasonography, 63%
goiter). Median TSH was 100 mIU/l [0.3–4 mIU/l]), median
fT4 3.55 pg/ml [8–19 pg/ml], median T4
2.85 µg/dl
[5.3–11 µg/dl]. Presenting symptoms included
goiter (26%), tiredness (23%), weight gain (19%), and
growth retardation (19%). The diagnosis was made incidentally in
26% patients. In 75% growth was retarded (median height standard
deviation score (SDS)-0.55), in 17% height SDS was<-2 at
diagnosis. Midparental height SDS at diagnosis correlated significantly with T4
and fT4 (r=0.77, p=0.0012 and r=0.53, p=0.021
respectively). Catch-up growth under T4 substitution was significantly greater
in prepubertal than in pubertal children (p 0.049).
Conclusion This so far largest pediatric cohort with severe acquired
hypothyroidism confirms a serious impact on growth which, however in most cases,
showed a certain catch-up growth after adequate L-thyroxine therapy. The
pubertal state seems to be important for catch-up growth. A significant number
of patients were not diagnosed clinically, although affected by severe
hypothyroidism.