bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-bodied birds are over-represented in unstructured citizen science data
Authors: Callaghan Corey T. , Poore Alistair G. B. , Hofmann Max , Roberts Christopher J. , Pereira Henrique M. 
Published: September 2021

AbstractCitizen science platforms are quickly accumulating hundreds of millions of biodiversity observations around the world annually. Quantifying and correcting for the biases in citizen science datasets remains an important first step before these data are used to address ecological questions and monitor biodiversity. One source of potential bias among datasets is the difference between those citizen science programs that have unstructured protocols and those that have semi-structured or structured protocols for submitting observations. To quantify biases in an unstructured citizen science platform, we contrasted bird observations from the unstructured iNaturalist platform with that from a semi-structured citizen science platform—eBird—for the continental United States. We tested whether four traits of species (body size, commonness, flock size, and color) predicted if a species was under- or over-represented in the unstructured dataset compared with the semi-structured dataset. We found strong evidence that large-bodied birds were over-represented in the unstructured citizen science dataset; moderate evidence that common species were over-represented in the unstructured dataset; strong evidence that species in large groups were over-represented; and no evidence that colorful species were over-represented in unstructured citizen science data. Our results suggest that biases exist in unstructured citizen science data when compared with semi-structured data, likely as a result of the detectability of a species and the inherent recording process. Importantly, in programs like iNaturalist the detectability process is two-fold—first, an individual organism needs to be detected, and second, it needs to be photographed, which is likely easier for many large-bodied species. Our results indicate that caution is warranted when using unstructured citizen science data in ecological modelling, and highlight body size as a fundamental trait that can be used as a covariate for modelling opportunistic species occurrence records, representing the detectability or identifiability in unstructured citizen science datasets. Future research in this space should continue to focus on quantifying and documenting biases in citizen science data, and expand our research by including structured citizen science data to understand how biases differ among unstructured, semi-structured, and structured citizen science platforms.
GABAB receptor signaling in the caudate putamen is involved in binge-like consumption during a high fat diet in mice
Authors: Sun Runan , Tsunekawa Taku , Hirose Tomonori , Yaginuma Hiroshi , Taki Keigo , Mizoguchi Akira , Miyata Takashi , Kobayashi Tomoko , Sugiyama Mariko , Onoue Takeshi , Takagi Hiroshi , Hagiwara Daisuke , Ito Yoshihiro , Iwama Shintaro , Suga Hidetaka , Banno Ryoichi , Bettler Bernhard , Arima Hiroshi 
Published: September 2021

AbstractPrevious studies suggest that signaling by the gamma-aminobutyric acid (GABA) type B receptor (GABABR) is involved in the regulation of binge eating, a disorder which might contribute to the development of obesity. Here, we show that intermittent access to a high fat diet (HFD) induced binge-like eating behavior with activation of dopamine receptor d1 (drd1)-expressing neurons in the caudate putamen (CPu) and nucleus accumbens (NAc) in wild-type (WT) mice. The activation of drd1-expressing neurons during binge-like eating was substantially increased in the CPu, but not in the NAc, in corticostriatal neuron-specific GABABR-deficient knockout (KO) mice compared to WT mice. Treatment with the GABABR agonist, baclofen, suppressed binge-like eating behavior in WT mice, but not in KO mice, as reported previously. Baclofen also suppressed the activation of drd1-expressing neurons in the CPu, but not in the NAc, during binge-like eating in WT mice. Thus, our data suggest that GABABR signaling in CPu neurons expressing drd1 suppresses binge-like consumption during a HFD in mice.
Real-time polarization microscopy of fibrillar collagen in histopathology
Authors: Keikhosravi Adib , Shribak Michael , Conklin Matthew W. , Liu Yuming , Li Bin , Loeffler Agnes , Levenson Richard M. , Eliceiri Kevin W. 
Published: September 2021

AbstractOver the past two decades, fibrillar collagen reorganization parameters such as the amount of collagen deposition, fiber angle and alignment have been widely explored in numerous studies. These parameters are now widely accepted as stromal biomarkers and linked to disease progression and survival time in several cancer types. Despite all these advances, there has not been a significant effort to make it possible for clinicians to explore these biomarkers without adding steps to the clinical workflow or by requiring high-cost imaging systems. In this paper, we evaluate previously described polychromatic polarization microscope (PPM) to visualize collagen fibers with an optically generated color representation of fiber orientation and alignment when inspecting the sample by a regular microscope with minor modifications. This system does not require stained slides, but is compatible with histological stains such as H&E. Consequently, it can be easily accommodated as part of regular pathology review of tissue slides, while providing clinically useful insight into stromal composition.
TYROBP, TLR4 and ITGAM regulated macrophages polarization and immune checkpoints expression in osteosarcoma
Authors: Liang Tuo , Chen Jiarui , Xu GuoYong , Zhang Zide , Xue Jiang , Zeng Haopeng , Jiang Jie , Chen Tianyou , Qin Zhaojie , Li Hao , Ye Zhen , Nie Yunfeng , Liu Chong , Zhan Xinli 
Published: September 2021

AbstractWe established a relationship among the immune-related genes, tumor-infiltrating immune cells (TIICs), and immune checkpoints in patients with osteosarcoma. The gene expression data for osteosarcoma were downloaded from UCSC Xena and GEO database. Immune-related differentially expressed genes (DEGs) were detected to calculate the risk score. “Estimate” was used for immune infiltrating estimation and “xCell” was used to obtain 64 immune cell subtypes. Furthermore, the relationship among the risk scores, immune cell subtypes, and immune checkpoints was evaluated. The three immune-related genes (TYROBP, TLR4, and ITGAM) were selected to establish a risk scoring system based on their integrated prognostic relevance. The GSEA results for the Hallmark and KEGG pathways revealed that the low-risk score group exhibited the most gene sets that were related to immune-related pathways. The risk score significantly correlated with the xCell score of macrophages, M1 macrophages, and M2 macrophages, which significantly affected the prognosis of osteosarcoma. Thus, patients with low-risk scores showed better results with the immune checkpoints inhibitor therapy. A three immune-related, gene-based risk model can regulate macrophage activation and predict the treatment outcomes the survival rate in osteosarcoma.
Effects of hypoxia and nanocarrier size on pH-responsive nano-delivery system to solid tumors
Authors: Soltani M. , Souri Mohammad , Moradi Kashkooli Farshad 
Published: September 2021

AbstractOne of the special features of solid tumors is the acidity of the tumor microenvironment, which is mainly due to the presence of hypoxic regions. Therefore, pH-responsive drug delivery systems have recently been highly welcomed. In the present study, a comprehensive mathematical model is presented based on extravascular drug release paradigm. Accordingly, drug delivery system using pH-responsive nanocarriers is taken into account to examine the impacts of hypoxic regions as well as the size of nanocarriers for cancerous cell-death. The extent of hypoxic regions is controlled by vascular density. This means that regions with very low vascular density represent regions of hypoxia. Using this mathematical model, it is possible to simulate the extracellular and intracellular concentrations of drug by considering the association/disassociation of the free drug to the cell-surface receptors and cellular uptake. Results show that nanocarriers with smaller sizes are more effective due to higher accumulation in the tumor tissue interstitium. The small size of the nanocarriers also allows them to penetrate deeper, so they can expose a larger portion of the tumor to the drug. Additionally, the presence of hypoxic regions in tumor reduces the fraction of killed cancer cells due to reduced penetration depth. The proposed model can be considered for optimizing and developing pH-sensitive delivery systems to reduce both cost and time of the process.
Mouse lipidomics reveals inherent flexibility of a mammalian lipidome
Authors: Surma Michał A. , Gerl Mathias J. , Herzog Ronny , Helppi Jussi , Simons Kai , Klose Christian 
Published: September 2021

AbstractLipidomics has become an indispensable method for the quantitative assessment of lipid metabolism in basic, clinical, and pharmaceutical research. It allows for the generation of information-dense datasets in a large variety of experimental setups and model organisms. Previous studies, mostly conducted in mice (Mus musculus), have shown a remarkable specificity of the lipid compositions of different cell types, tissues, and organs. However, a systematic analysis of the overall variation of the mouse lipidome is lacking. To fill this gap, in the present study, the effect of diet, sex, and genotype on the lipidomes of mouse tissues, organs, and bodily fluids has been investigated. Baseline quantitative lipidomes consisting of 796 individual lipid molecules belonging to 24 lipid classes are provided for 10 different sample types. Furthermore, the susceptibility of lipidomes to the tested parameters is assessed, providing insights into the organ-specific lipidomic plasticity and flexibility. This dataset provides a valuable resource for basic and pharmaceutical researchers working with murine models and complements existing proteomic and transcriptomic datasets. It will inform experimental design and facilitate interpretation of lipidomic datasets.
Melting of micro/nanoparticles considering anisotropy of surface energy
Authors: Yang C. M. , Chen M. W. , Zheng G. J. , Wang Z. D. 
Published: September 2021

AbstractThe effect of surface energy on the melting of micro/nanoparticles is studied using the asymptotic method. The asymptotic solution of the dynamic model for micro/nanoparticle melting reveals the dependence of the particle melting temperature on the particle size and the anisotropy of surface energy. Specifically, as the particle radius decreases, the isotropic surface energy reduces the melting temperature and accelerates the interface melting of the particle. Along certain crystal orientations, the anisotropy of surface energy enhances the melting temperature of the micro/nanoparticles, whereas depresses the melting temperature of the micro/nanoparticle along other crystal orientations. The anisotropy of surface energy enhances the melting speed of the micro/nanoparticles along certain crystal orientations, whereas reduces the melting speed of the micro/nanoparticles along other crystal orientations. The result of the asymptotic solution is in good agreement with the experimental data.
Assessing effectiveness of Komagataeibacter strains for producing surface-microstructured cellulose via guided assembly-based biolithography
Authors: Brugnoli Marcello , Robotti Francesco , La China Salvatore , Anguluri Kavitha , Haghighi Hossein , Bottan Simone , Ferrari Aldo , Gullo Maria 
Published: September 2021

AbstractIn this study, a medical device made of surface microstructured bacterial cellulose was produced using cellulose-producing acetic acid bacteria wild-type strains in combination with guided assembly-based biolithography. The medical device aims at interfering with the cell's focal adhesion establishment and maturation around implantable devices placed in soft tissues by the symmetrical array on its surface. A total of 25 Komagataeibacter strains was evaluated over a three-step selection. In the first step, the ability of strains to produce a suitable bacterial cellulose layer with high production yield was examined, then nine strains, with a uniform and smooth layer of bacterial cellulose, were cultured in a custom-made silicone bioreactor and finally the characteristics of the symmetrical array of topographic features on the surface were analysed. Selected strains showed high inter and intra species variability in bacterial cellulose production. The devices obtained by K2G30, K1G4, DSM 46590 (Komagataeibacter xylinus), K2A8 (Komagataeibacter sp.) and DSM 15973T (Komagataeibacter sucrofermentas) strains were pouched-formed with hexagonal surface pattern required for reducing the formation of fibrotic tissue around devices, once they are implanted in soft tissues. Our findings revealed the effectiveness of the selected Komagataeibacter wild-type strains in producing surface microstructured bacterial cellulose pouches for making biomedical devices.
Novel attempt at discrimination of a bullet-shaped siphonophore (Family Diphyidae) using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-ToF MS)
Authors: Park Nayeon , Yeom Jisu , Jeong Raehyuk , Lee Wonchoel 
Published: September 2021

AbstractOne major difficulty in identifying the gelatinous bodied bullet-shaped Siphonophore, Diphyids, is that their shape is deformed following ethanol fixation. Ethanol often is preferred over other fixatives, since samples fixed in ethanol can be used for molecular studies that can supplement morphological findings. To overcome this problem, we obtained protein mass spectra of ten species of Diphyidae found in the waters of the Kuroshio Current (Northwest Pacific and South Coast of South Korea) to test whether MALDI-ToF MS could be used as a methodology for species identification. In addition, a number of morphological characteristics that can be used with ethanol-treated samples was summarized. Concatenated phylogenetic analysis was also performed to determine the phylogenetic relationship by obtaining partial sequences of four genes (mtCOI, 16S rRNA, 18S rRNA, and ITS regions). Based on our integrative analysis, MALDI-ToF MS was evaluated as a potentially fast, inexpensive, and accurate tool for species identification along with conventional morphological and DNA barcoding for Diphyidae.
Necro-inflammatory activity grading in chronic viral hepatitis with three-dimensional multifrequency MR elastography
Authors: Garteiser Philippe , Pagé Gwenaël , d’Assignies Gaspard , Leitao Helena S. , Vilgrain Valérie , Sinkus Ralph , Van Beers Bernard E. 
Published: September 2021

AbstractThe purpose of this study was to assess the diagnostic value of multifrequency MR elastography for grading necro-inflammation in the liver. Fifty participants with chronic hepatitis B or C were recruited for this institutional review board-approved study. Their liver was examined with multifrequency MR elastography. The storage, shear and loss moduli, and the damping ratio were measured at 56 Hz. The multifrequency wave dispersion coefficient of the shear modulus was calculated. The measurements were compared to reference markers of necro-inflammation and fibrosis with Spearman correlations and multiple regression analysis. Diagnostic accuracy was assessed. At multiple regression analysis, necro-inflammation was the only determinant of the multifrequency dispersion coefficient, whereas fibrosis was the only determinant of the storage, loss and shear moduli. The multifrequency dispersion coefficient had the largest AUC for necro-inflammatory activity A ≥ 2 [0.84 (0.71–0.93) vs. storage modulus AUC: 0.65 (0.50–0.79), p = 0.03], whereas the storage modulus had the largest AUC for fibrosis F ≥ 2 [AUC (95% confidence intervals) 0.91 (0.79–0.98)] and cirrhosis F4 [0.97 (0.88–1.00)]. The measurement of the multifrequency dispersion coefficient at three-dimensional MR elastography has the potential to grade liver necro-inflammation in patients with chronic vial hepatitis.
A pilot study of 3D tissue-engineered bone marrow culture as a tool to predict patient response to therapy in multiple myeloma
Authors: Alhallak Kinan , Jeske Amanda , de la Puente Pilar , Sun Jennifer , Fiala Mark , Azab Feda , Muz Barbara , Sahin Ilyas , Vij Ravi , DiPersio John F. , Azab Abdel Kareem 
Published: September 2021

AbstractCancer patients undergo detrimental toxicities and ineffective treatments especially in the relapsed setting, due to failed treatment attempts. The development of a tool that predicts the clinical response of individual patients to therapy is greatly desired. We have developed a novel patient-derived 3D tissue engineered bone marrow (3DTEBM) technology that closely recapitulate the pathophysiological conditions in the bone marrow and allows ex vivo proliferation of tumor cells of hematologic malignancies. In this study, we used the 3DTEBM to predict the clinical response of individual multiple myeloma (MM) patients to different therapeutic regimens. We found that while no correlation was observed between in vitro efficacy in classic 2D culture systems of drugs used for MM with their clinical efficacious concentration, the efficacious concentration in the 3DTEBM were directly correlated. Furthermore, the 3DTEBM model retrospectively predicted the clinical response to different treatment regimens in 89% of the MM patient cohort. These results demonstrated that the 3DTEBM is a feasible platform which can predict MM clinical responses with high accuracy and within a clinically actionable time frame. Utilization of this technology to predict drug efficacy and the likelihood of treatment failure could significantly improve patient care and treatment in many ways, particularly in the relapsed and refractory setting. Future studies are needed to validate the 3DTEBM model as a tool for predicting clinical efficacy.
Predictors for depressive symptoms by four types of disability
Authors: Jung Sun Wook , Yoon Jin-Ha , Lee Wanhyung 
Published: September 2021

AbstractThis study aimed to examine the longitudinal relationship between disability and depressive symptoms, by comparing four types of disability in community-dwelling individuals with disabilities in South Korea. A total of 3347 South Koreans with disabilities from the second wave of the Panel Survey of Employment for the Disabled was utilized. Depressive symptomatology was assessed by whether the participant had experienced depressive symptoms for more than two weeks during the past year. A multivariate logistic regression model was used to calculate the odds ratio (OR) for depressive symptoms, and a Cox proportional hazards model to calculate the hazard ratio (HR) for two-year survival analysis. Persons who acquired mental disability from accident or industrial disaster and persons with congenital physical-internal disability were at higher risk for depressive symptoms. Maintaining employment was found to be an effective way to decrease the risk of depressive symptoms in persons with physical-external disability, sensory/speech disability, or mental disability. In contrast, in physical-internal disability, retaining normal ability to work seemed to be the key to reduce the risk of depressive symptoms. Predictors of depressive symptoms were found to differ depending on the type of disability. Such differences should be reflected in clinical and policy-level interventions to address the specific psychiatric needs of persons with different disabilities.
Establishment of appropriate glaucoma models using dexamethasone or TGFβ2 treated three-dimension (3D) cultured human trabecular meshwork (HTM) cells
Authors: Watanabe Megumi , Ida Yosuke , Ohguro Hiroshi , Ota Chiaki , Hikage Fumihito 
Published: September 2021

AbstractTo establish appropriate ex vivo models for a glaucomatous trabecular meshwork (TM), two-dimensional (2D) and three-dimensional (3D) cultures of human trabecular meshwork cells (HTM) were prepared in the presence of 250 nM dexamethasone (DEX) or 5 ng/mL TGFβ2, and characterized by the following analyses; transendothelial electrical resistance (TEER) measurements, FITC dextran permeability, scanning electron microscopy and the expression of the extracellular matrix (ECM) including collagen (COL)1, 4 and 6, and fibronectin (FN), α-smooth muscle actin (α-SMA), tissue inhibitor of metalloproteinase (TIMP)1–4, and matrix metalloproteinase (MMP)2, 9 and 14. DEX and TGFβ2 both caused a significant increase or decrease in the TEER values and FITC dextran permeability. During the 3D spheroid culture, DEX or TGFβ2 induced a mild and significant down-sizing and an increase in stiffness, respectively. TGFβ2 induced a significant up-regulation of COL1 and 4, FN, α-SMA, and MMP 2 and 14 (2D) or COL1 and 6, and TIMP2 and 3 (3D), and DEX induced a significant up-regulation of FN (3D) and TIMP4 (2D and 3D). The findings presented herein indicate that DEX or TGFβ2 resulted in mild and severe down-sized and stiff 3D HTM spheroids, respectively, thus making them viable in vitro HTM models for steroid-induced and primary open angle glaucoma.
Combination of FIB-4 with ultrasound surface nodularity or elastography as predictors of histologic advanced liver fibrosis in chronic liver disease
Authors: Moini Maryam , Onofrio Fernanda , Hansen Bettina E. , Adeyi Oyedele , Khalili Korosh , Patel Keyur 
Published: September 2021

AbstractReliable and available non-invasive methods for hepatic fibrosis assessment are important in chronic liver disease (CLD). Our aim was to compare stepwise algorithms combining standard ultrasound with serum markers and transient elastography (TE) for detecting advanced fibrosis (F3-4) and cirrhosis. Retrospective single center study between 2012 and 2018 of CLD patients with biopsy, TE, blood tests, and liver ultrasound parameters of surface nodularity (SN), lobar redistribution, and hepatic vein nodularity. Our cohort included 157 patients (51.6% males), mean age 47.6 years, predominantly non-alcoholic fatty liver disease and viral hepatitis (61%), with F3-4 prevalence of 60.5%. Area under the curve for F3-4 was 0.89 for TE ≥ 9.6 kPa and 0.80 for FIB-4 > 3.25. In multivariate modeling, TE ≥ 9.6 kPa (OR 21.78) and SN (OR 3.81) had independent association with F3-4; SN (OR 5.89) and TE ≥ 10.2 kPa (OR 15.73) were independently associated with cirrhosis. Two stepwise approaches included FIB-4 followed by SN or TE; sensitivity and specificity of stepwise SN were 0.65 and 1.00, and 0.89 and 0.33 for TE ≥ 9.6 kPa, respectively. Ultrasound SN and TE were independently predictive of F3-4 and cirrhosis in our cohort. FIB-4 followed by SN had high specificity for F3-4.