bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification
Authors: Wu Hoi-Yan , Chan Kwun-Tin , But Grace Wing-Chiu , Shaw Pang-Chui 
Published: February 2021

AbstractDNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.
North Pacific warming shifts the juvenile range of a marine apex predator
Authors: Tanaka Kisei R. , Van Houtan Kyle S. , Mailander Eric , Dias Beatriz S. , Galginaitis Carol , O’Sullivan John , Lowe Christopher G. , Jorgensen Salvador J. 
Published: February 2021

AbstractDuring the 2014–2016 North Pacific marine heatwave, unprecedented sightings of juvenile white sharks (Carcharodon carcharias) emerged in central California. These records contradicted the species established life history, where juveniles remain in warmer waters in the southern California Current. This spatial shift is significant as it creates potential conflicts with commercial fisheries, protected species conservation, and public safety concerns. Here, we integrate community science, photogrammetry, biologging, and mesoscale climate data to describe and explain this phenomenon. We find a dramatic increase in white sharks from 2014 to 2019 in Monterey Bay that was overwhelmingly comprised of juvenile sharks < 2.5 m in total body length. Next, we derived thermal preferences from 22 million tag measurements of 14 juvenile sharks and use this to map the cold limit of their range. Consistent with historical records, the position of this cold edge averaged 34° N from 1982 to 2013 but jumped to 38.5° during the 2014–2016 marine heat wave. In addition to a poleward shift, thermally suitable habitat for juvenile sharks declined 223.2 km2 year−1 from 1982 to 2019 and was lowest in 2015 at the peak of the heatwave. In addition to advancing the adaptive management of this apex marine predator, we discuss this opportunity to engage public on climate change through marine megafauna.
Purification of anti-glycoconjugate monoclonal antibodies using newly developed porous zirconia particles
Authors: Okuda Tetsuya , Kato Katsuya , Kitamura Masahiro , Kasahara Shinjiro 
Published: February 2021

AbstractHere, we describe porous zirconia particles (PZPs) optimized for the purification of immunoglobulins. PZPs, with a pore size of approximately 10 nm, were designed to specifically interact with antibodies via surface modification with a phosphate functional group. A simple PZP purification method based on precipitation enabled efficient purification of mouse anti-glycosphingolipid globoside/Gb4Cer monoclonal IgM (κ-light chains) from hybridoma culture supernatants. Over 99% of contaminating proteins were removed by the PZP purification process, and approximately 50% of the IgM was recovered in the purified fraction after eluting the PZP-adsorbed antibodies with 100 mM phosphate buffer. Other IgG3 and IgM monoclonal antibodies that react with Gb4Cer or α2,6-sialyl LacNAc-modified glycoproteins could also be purified using PZPs and elution buffer at concentrations of 100–500 mM. All of the purified antibodies retained their antigen reactivity and specificity, indicating that PZP purification does not affect antibody function. As PZP purification is also suitable for purification of IgM consisting of λ-light chains and IgG derived from other mammalian species, it is expected to be applied to the purification of a variety of antibodies, including anti-glycoconjugate IgMs.
Identification of potential salivary biomarker panels for oral squamous cell carcinoma
Authors: Jain Anu , Kotimoole Chinmaya Narayana , Ghoshal Sushmita , Bakshi Jaimanti , Chatterjee Aditi , Prasad Thottethodi Subrahmanya Keshava , Pal Arnab 
Published: February 2021

AbstractOral squamous cell carcinoma (OSCC) is one of the most prevalent cancers worldwide with the maximum number of incidences and deaths reported from India. One of the major causes of poor survival rate associated with OSCC has been attributed to late presentation due to non-availability of a biomarker. Identification of early diagnostic biomarker will help in reducing the disease morbidity and mortality. We validated 12 salivary proteins using targeted proteomics, identified initially by relative quantification of salivary proteins on LC–MS, in OSCC patients and controls. Salivary AHSG (p = 0.0041**) and KRT6C (p = 0.002**) were upregulated in OSCC cases and AZGP1 (p ≤ 0.0001***), KLK1 (p = 0.006**) and BPIFB2 (p = 0.0061**) were downregulated. Regression modelling resulted in a significant risk prediction model (p < 0.0001***) consisting of AZGP1, AHSG and KRT6C for which ROC curve had AUC, sensitivity and specificity of 82.4%, 78% and 73.5% respectively for all OSCC cases and 87.9%, 87.5% and 73.5% respectively for late stage (T3/T4) OSCC. AZGP1, AHSG, KRT6C and BPIFB2 together resulted in ROC curve (p < 0.0001***) with AUC, sensitivity and specificity of 94%, 100% and 77.6% respectively for N0 cases while KRT6C and AZGP1 for N+ cases with ROC curve (p < 0.0001***) having AUC sensitivity and specificity of 76.8%, 73% and 69.4%. Our data aids in the identification of biomarker panels for the diagnosis of OSCC cases with a differential diagnosis between early and late-stage cases.
Enhanced light extraction efficiency and viewing angle characteristics of microcavity OLEDs by using a diffusion layer
Authors: Park Cheol Hwee , Kang Shin Woo , Jung Sun-Gyu , Lee Dong Jun , Park Young Wook , Ju Byeong-Kwon 
Published: February 2021

AbstractThe viewing angle characteristics and light extraction efficiency of organic light-emitting diodes (OLEDs) with a micro-cavity structure were enhanced. This was accomplished by inserting a diffusion layer composed of nano-sized structures of a transparent polymer poly(methyl methacrylate) (PMMA) combined with a zinc oxide (ZnO) semi-planarization layer with a high refractive index (n = 2.1) into the devices. The PMMA nanostructures were fabricated by employing a reactive ion etching (RIE) process. The height and density of the PMMA nanostructures were controlled by varying the speed at which the PMMA was spin-coated onto the substrate. The insertion of the diffusion layer into the micro-cavity OLEDs (MC-OLEDs) improved the external quantum efficiency (EQE) by as much as 17% when compared to that of a MC-OLED without a diffusion layer. Furthermore, adjustment of the viewing angle from 0° to 60° halved the peak shift distance of the electroluminescence (EL) spectra from 42 to 20 nm. Additionally, changing the viewing angle from 0° to 60° changed the color coordinate movement distance of the MC-OLED with the diffusion layer to 0.078, less than half of the distance of the MC-OLED without the diffusion layer (0.165).
Past landscape structure drives the functional assemblages of plants and birds
Authors: Lecoq Lucie , Ernoult Aude , Mony Cendrine 
Published: February 2021

AbstractLandscape structure is a major driver of biodiversity in agricultural landscapes. However, the response of biodiversity can be delayed after landscape changes. This study aimed to determine the effect of current and past landscape structure on plant and bird assemblages. We used a trait-based approach to understand their responses to landscape simplification and habitat fragmentation. We quantified landscape structure at three different years (1963, 1985, 2000) and sampled current plant and bird assemblages in twenty 1 km2landscape windows located along the Seine Valley (France). For each window, we calculated plant and bird species richness, Community Weighted Variance (CWV), and Community Weighted Mean (CWM) of five functional traits related to dispersal capacity, reproduction, and life-cycle. We detected non-random patterns of traits for both taxa. Plant and bird species richness was lower in simple landscapes. The functional variance of plant traits was higher in landscapes simple in configuration. Both plant and bird assemblages strongly responded to past landscapes, especially their traits related to reproduction and life-cycle. It suggests that landscapes of the Seine valley will face a functional extinction debt. Further research is needed to better predict the delayed response of biodiversity expected to occur after landscape structure changes.
Effects of ambient particulate matter on a reconstructed human corneal epithelium model
Authors: Ko Ryota , Hayashi Masahiko , Tanaka Miho , Okuda Tomoaki , Nishita-Hara Chiharu , Ozaki Hiroaki , Uchio Eiichi 
Published: February 2021

AbstractWe evaluated the effects of ambient particulate matter (PM) on the corneal epithelium using a reconstructed human corneal epithelium (HCE) model. We collected two PM size fractions [aerodynamic diameter smaller than 2.4 µm: PM0.3–2.4 and larger than 2.4 µm: PM>2.4] and exposed these tissues to PM concentrations of 1, 10, and 100 µg/mL for 24 h. After exposure, cell viability and interleukin (IL) IL-6 and IL-8 levels were determined, and haematoxylin and eosin and immunofluorescence staining of the zonula occludens-1 (ZO-1) were performed on tissue sections. In addition, the effects of a certified reference material of urban aerosols (UA; 100 µg/mL) were also examined as a reference. The viability of cells exposed to 100 μg/mL UA and PM>2.4 decreased to 76.2% ± 7.4 and 75.4% ± 16.1, respectively, whereas PM0.3–2.4 exposure had a limited effect on cell viability. These particles did not increase IL-6 and IL-8 levels significantly even though cell viability was decreased in 100 μg/mL UA and PM>2.4. ZO-1 expression was reduced in a dose-dependent manner in all groups. Reconstructed HCE could be used as an in vitro model to study the effects of environmental PM exposure on ocular surface cell viability and inflammation.
CXCR7 ameliorates myocardial infarction as a β-arrestin-biased receptor
Authors: Ishizuka Masato , Harada Mutsuo , Nomura Seitaro , Ko Toshiyuki , Ikeda Yuichi , Guo Jiaxi , Bujo Satoshi , Yanagisawa-Murakami Haruka , Satoh Masahiro , Yamada Shintaro , Kumagai Hidetoshi , Motozawa Yoshihiro , Hara Hironori , Fujiwara Takayuki , Sato Tatsuyuki , Takeda Norifumi , Takeda Norihiko , Otsu Kinya , Morita Hiroyuki , Toko Haruhiro , Komuro Issei 
Published: February 2021

AbstractMost seven transmembrane receptors (7TMRs) are G protein-coupled receptors; however, some 7TMRs evoke intracellular signals through β-arrestin as a biased receptor. As several β-arrestin-biased agonists have been reported to be cardioprotective, we examined the role of the chemokine receptor CXCR7 as a β-arrestin-biased receptor in the heart. Among 510 7TMR genes examined, Cxcr7 was the most abundantly expressed in the murine heart. Single-cell RNA-sequencing analysis revealed that Cxcr7 was abundantly expressed in cardiomyocytes and fibroblasts. Cardiomyocyte-specific Cxcr7 null mice showed more prominent cardiac dilatation and dysfunction than control mice 4 weeks after myocardial infarction. In contrast, there was no difference in cardiac phenotypes between fibroblast-specific Cxcr7-knockout mice and control mice even after myocardial infarction. TC14012, a specific agonist of CXCR7, significantly recruited β-arrestin to CXCR7 in CXCR7-expressing cells and activated extracellular signal-regulated kinase (ERK) in neonatal rat cardiomyocytes. Cxcr7 expression was significantly increased and ERK was activated in the border zone of the heart in control, but not Cxcr7 null mice. These results indicate that the abundantly expressed CXCR7 in cardiomyocytes may play a protective role in the heart as a β-arrestin-biased receptor and that CXCR7 may be a novel therapeutic target for myocardial infarction.
Sea surface temperature variability and ischemic heart disease outcomes among older adults
Authors: Majeed Haris , Moineddin Rahim , Booth Gillian L. 
Published: February 2021

AbstractIschemic heart disease (IHD) is one of the leading causes of death worldwide. While extreme summer surface air temperatures are thought to be a risk factor for IHD, it is unclear whether large-scale climate patterns also influence this risk. This multi-national population-based study investigated the association between summer Pacific and Atlantic sea surface temperature (SST) variability and annual acute myocardial infarction (AMI) or IHD event rates among older adults residing in North America and the United Kingdom. Overall, a shift from cool to warm phase of the El Niño Southern Oscillation (ENSO) was associated with reduced AMI admissions in western Canada (adjusted rate ratio [RR] 0.89; 95% CI, 0.80–0.99), where this climate pattern predominatly forces below-normal cloud cover and precipitation during summertime, and increased AMI deaths in western United States (RR 1.09; 95% CI, 1.04–1.15), where it forces increased cloud cover and precipitation. Whereas, the Atlantic Multidecadal Oscillation (AMO) during a strong positive phase was associated with reduced AMI admissions in eastern Canada (RR 0.93; 95% CI, 0.87–0.98) and increased IHD mortality during summer months in the United Kingdom (RR 1.08; 95% CI, 1.03–1.14). These findings suggest that SST variability can be used to predict changes in cardiovascular event rates in regions that are susceptible.
Correlations between glycolysis with clinical traits and immune function in bladder urothelial carcinoma
Authors: Che Kai , Han Wenkai , Li Danxia , Cui Shuxia , Zhang Mingxin , Yang Xiaokun , Niu Haitao 
Published: February 2021

Abstract
Background: Glycolysis was a representative hallmark in the tumor microenvironment (TME), and we aimed to explore the correlations between glycolysis with immune activity and clinical traits in bladder urothelial carcinoma (BLCA).
Methods: Our study obtained glycolysis scores for each BLCA samples from TCGA by a single-sample gene set enrichment analysis (ssGSEA) algorithm, based on a glycolytic gene set. The relationship between glycolysis with prognosis, clinical characteristics, and immune function were investigated subsequently.
Results: We found that enhanced glycolysis was associated with poor prognosis and metastasis in BLCA. Moreover, glycolysis had a close correlation with immune function, and enhanced glycolysis increased immune activities. In other words, glycolysis had a positive correlation with immune activities. Immune checkpoints such as IDO1, CD274, were up-regulated in high-glycolysis group as well.
Conclusion: We speculated that in BLCA, elevated glycolysis enhanced immune function, which caused tumor cells to overexpress immune checkpoints to evade immune surveillance. Inhibition of glycolysis might be a promising assistant for immunotherapy in bladder cancer.
Dexmedetomidine attenuates lipopolysaccharide-induced acute liver injury in rats by inhibiting caveolin-1 downstream signaling pathway
Authors: Tong Fei , Shen Wenchao , Song Pengtao , Song Jiafeng , Hu Yonghe , Liu Feifan , Meng Zhipeng , Liu Jing 
Published: February 2021

AbstractObjective: The aim of the present study is to investigate the anti-injury and anti-inflammatory effects of dexmedetomidine (Dex) in acute liver injury induced by lipopolysaccharide (LPS) in Sprague–Dawley rats and its possible mechanism.Methods: The acute liver injury model of male rats was established by injecting LPS into tail vein. The mean arterial pressure (MAP) of rats was recorded at 0–7 h, and lactic acid was detected at different time points. Wet/dry weight ratio (W/D) was calculated. Pathological changes of rat liver were observed by HE staining. ALT and AST levels in serum were detected. The activities of myeloperoxidase (MPO) and superoxide dismutase (SOD) in liver tissue homogenate and the levels of IL-1β and IL-18 in serum were detected by ELISA. Protein levels of Caveolin-1 (Cav-1), TLR-4 and NLRP3 in liver tissue were tested by immunohistochemistry method. The expression of Cav-1, TLR-4 and NLRP3 mRNA in liver tissue was detected by quantitative polymerase chain reaction (qPCR) to explore its related mechanism.Results: Compared with NS group, serum lactic acid, W/D of liver tissue, MPO, SOD, IL-1β and IL-18 were significantly increased and MAP decreased significantly in LPS group and D+L group. However, compared with NS group, D group showed no significant difference in various indicators. Compared with LPS group, MPO, SOD, IL-1β and IL-18 were significantly decreased and MAP was significantly increased in D+L group. D+L group could significantly increase the level of Cav-1 protein and decrease the level of TLR-4 and NLRP3 protein in liver tissue caused by sepsis. The expression of Cav-1 mRNA was significantly up-regulated and the expression of TLR-4 and NLRP3 mRNA was inhibited in D+L group.Conclusion: Dex pretreatment protects against LPS-induced actue liver injury via inhibiting the activation of the NLRP3 signaling pathway by up-regulating the expression of Cav-1 by sepsis.
Acute and Long-Term Services for Elementary and Middle School Children With Early Childhood Brain Injury
Authors: Salley Jessica , Crook Libby , Iske Taylor , Ciccia Angela , Lundine Jennifer P. 
Published: February 2021

Purpose
The purpose of this study was to investigate the rates of referral to and receipt of acute and long-term services and identify factors that could impact these rates for children who experienced an acquired brain injury (ABI) during early childhood who are now in elementary and middle school.

Method
This was a retrospective chart review and prospective phone survey of 29 caregivers of children with ABIs.

Results
Acutely, two thirds of this sample received hospital-based rehabilitation services, but only 44.8% of families reported receiving ABI-specific education or a referral to educational or rehabilitation services at the time of discharge. At an average of 8.5 years postinjury, children in this sample were largely reported to be performing positively in school. While special education rates did not change significantly over time, 20.7% of the sample reported having unmet educational needs. Additionally, service receipt decreased over time. Various injury and educational factors influenced rates of long-term special education and service receipt.

Conclusions
This study contributes to the emerging literature focusing on long-term outcomes of children with ABI. The results reinforce that children who experience an ABI in early childhood are unlikely to receive ABI-specific education or referrals to educational and rehabilitation services during their acute-care stay and, in the chronic stages of recovery, present with educational and therapy needs that can go unmet. To improve long-term service access for children who experience an early ABI, pathways need to be established within the acute-care setting for education and referrals that connect the child and family to treatment within early intervention and educational systems. Maintaining these pathways long term, particularly for potential social-behavioral and cognitive-communication concerns, could increase access to appropriate services and, thus, decrease unmet needs for children with ABI.
Novel Adjective Processing in Preschool Children: Evidence From Event-Related Brain Potentials
Authors: Gerwin Katelyn L. , Leonard Laurence B. , Schumaker Jennifer , Deevy Patricia , Haebig Eileen , Weber Christine 
Published: February 2021

Purpose
Recent findings in preschool children indicated novel adjective recall was enhanced when learned using repeated retrieval with contextual reinstatement (RRCR) compared to repeated study (RS). Recall was similar for learned pictures used during training and new (generalized) pictures with the same adjective features. The current study compared the effects of learning method and learned/generalized pictures on the neural processes mediating the recognition of novel adjectives.

Method
Twenty typically developing children aged 4;6–5;11 (years;months) learned four novel adjectives, two using RRCR and two using RS. Five-minute and 1-week tests assessed adjective recall using learned and generalized pictures. Also, at the 1-week visit, event-related potentials (ERPs) were recorded to assess children's processing of learned/generalized pictures, followed by naturally spoken novel adjectives in a match–mismatch paradigm.

Results
Naming recall and match–mismatch judgment accuracy were similar for the RS and RRCR conditions and across learned/generalized pictures. However, ERPs revealed more reliable condition effects in the phonological mapping negativity, indexing phonological expectations, and the late positive component, indexing semantic reanalysis, for the adjectives learned in the RRCR relative to the RS condition. Unfamiliar pictures (generalized) elicited larger amplitude N300 and N400 components relative to learned pictures.

Conclusions
Although behavioral accuracy measures suggest similar effects of the RS and RRCR learning conditions, subtle differences in the ERPs underlying novel adjective processing indicate advantages of RRCR for phonological processing and semantic reanalysis. While children readily generalized the novel adjectives, ERPs revealed greater cognitive resources for processing unfamiliar compared to learned pictures of the novel adjective characteristics.

Supplemental Material

https://doi.org/10.23641/asha.13683214