bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief Bioinformatics characterization of Cotton bZIP transcription factors family from Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii
Authors: Khanale Vaishali , Bhattacharya Anjanabha , Satpute Rajendra , Char Bharat 
Published: April 2021

Abstract
Cotton is an important commodity in the world economy. In this study we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species G. hirsutum along with two sub-genome species of allotetraploid cotton, G. arboreum and G. raimondii. A total of 228 bZIP genes of G. hirsutum, 91 bZIP genes of G. arboreum and 86 bZIP genes of G. raimondii were identified from CottonGen database. Cotton bZIP genes were annotated in standard pattern according to their match with Arabidopsis bZIPs. Multiple genes with similar bZIP designations were observed in cotton, linked to the gene duplication. Cotton bZIPs are distributed across all 13 chromosomes with varied density. Phylogenetic characterization of all three cotton species bZIPs classified them into 12 subfamilies, namely A B, C, D, E, F, G, H, I, J, K and S and further into eight subgroups according to their predicted functional similarities, viz., A1, A2, A3, C1, C2, S1, S2 and S3. Subfamily A and S are having maximum number of bZIP genes, subfamily B, H, J and K are single member families. Cotton bZIP protein functions were predicted from identified motifs and orthologs from varied species. BRLZ domain analysis of G. raimondii bZIPs revealed the presence of conserved basic region motif N-X7-R/K in almost all subfamily members, variants are GrbZIP62 with N-X7-I motif and GrbZIP76 with K-X7-R motif. Leucine heptad repeats motif, are also present in variant numbers from two to nine with leucine or other hydrophobic amino acid at designated position among 12 subfamily members. STRING protein interaction network analysis of G. raimondii bZIPs observed strong interaction between A-D, B-K and C-S subfamily members.
Dementia Management Act and Death Toll by Dementia Drug
Authors: Lee Jong-hoon 
Published: April 2021

Abstract
The Dementia Management Act (DMA) came into effect on August 04, 2011, in South Korea. Medical data on the correlation between Alzheimer's disease (AD) and anti-AD drug (AAD) groups were observed from 2010 to 2019. This study investigated the increase and decrease in deaths and AAD used to treat AD. It is known that psychotropic medicines should not be administered for dementia patients because they increase all-cause mortality. This study demonstrated that acetylcholinesterase inhibitors and N-methyl-D-aspartate (NMDA) receptor antagonist also increase the death toll when used to treat dementia.
Genome-wide Survey of the GATA Gene Family in Camptothecin-producing Plant Ophiorrhiza Pumila
Authors: Huang Qikai , Shi Min , Wang Can , Hu Jiangning , Kai Guoyin 
Published: April 2021

Abstract
Background: Ophiorrhiza pumila (Rubiaceae) is capable of producing camptothecin (CPT), one monoterpene indole alkaloid extensively employed in the treatment of multiple cancers. Transcription factors (TF) GATA are a group of transcription regulators involved in plant development and metabolism, and show the feature of binding to the GATA motif within the promoters of target genes. However, GATA TFs have not been characterized in O. pumila. Result: In this study, a total of 18 GATA genes classified into four subfamilies were identified, which randomly distributed on 11 chromosomes of O. pumila. Gene replication and homology between O. pumila and other plant species such as Arabidopsis thaliana, Oryza sativa, Glycine max, Solanum lycopersicum, and Vitis vinifera genomes were analyzed. Tissue expression pattern revealed that OpGATA7, OpGATA12 and OpGATA13 with higher transcript in leaves, which was correlated with ASA, MK, DXS, CMS, and MECS. OpGATA7, OpGATA14 and OpGATA15 showed high expression in roots as most of the CPT biosynthetic pathway genes did, suggesting that these OpGATAs may be potential candidates regulating CPT biosynthesis in O. pumila.Conclusions: Genome-wide survey of the GATA gene family from Ophiorrhiza pumila provided insights into the involvement of GATA transcription factors in CPT biosynthesis
Acircularity and Circularity Indexes of the Foveal Avascular Zone in High Myopia
Authors: Piao Helong , Guo Yue , Zhang Haowei , Sung Mi Sun , Park Sang Woo 
Published: April 2021

Abstract
We explored the association between foveal avascular zone (FAZ) parameters and high myopia using optical coherence tomography angiography (OCTA). To evaluate the specific influence of high myopia on the FAZ, we divided 106 eyes of 106 patients into quartiles based on the axial length. The upper quartile was then defined as the high myopia group (n = 27), while the lower quartile was the non-high myopia group (n = 26). The FAZ parameters of these two groups were then retrospectively compared to investigate variations in FAZ size and morphology. The mean axial length and spherical equivalent were 23.96 ± 0.94 mm and -2.27 ± 1.58 diopters in the non-high myopia group and 27.42 ± 0.36 mm and -8.12 ± 2.14 diopters in the high myopia group, respectively. The areas of superficial and deep FAZ, perimeters of deep FAZ, major axis lengths of deep FAZ, minor axis lengths of superficial and deep FAZ were significantly larger in eyes with high myopia than in eyes with non-high myopia (P < 0.05). Linear regression analyses showed that no significant correlation was observed between FAZ areas and acircularity and circularity index of FAZ in non-high myopia group, conversely, FAZ areas strongly correlated with acircularity and circularity index of FAZ in high myopia group. We found that An increase in the FAZ area in highly myopic eyes was accompanied by a significant variation in FAZ acircularity and circularity indexes. Further research should address whether these findings are associated with future disease development in highly myopic eyes.
RNA Sequencing of LX-2 Cells Treated with TGF-β1 Identifies Genes Associated with Early Hepatic Stellate Cell Activation
Authors: Carson Jack , Robinson Mark W. , Ramm Grant A. , Gobert Geoffrey N. 
Published: April 2021

Abstract
Hepatic stellate cells (HSCs) are liver-resident myofibroblast precursors. In chronic liver disease, HSC-derived myofibroblasts are responsible for the production of collagen and, as such, are generally associated with diseases characterised by hepatic fibrosis. HSCs undergo a process of "activation" in response to tissue damage or pathogen invasion, thereby assuming roles in extracellular matrix synthesis, wound healing, and pathogen defence. The process of HSC activation and collagen production is most commonly driven by the cytokine transforming growth factor-β1 (TGF-β1). To investigate the transcriptional impact of TGF-β1 signalling on liver myofibroblasts, RNA sequencing was used to quantitate the biological changes observed in LX-2 cells, an activated human HSC line, following TGF-b1 treatment. In total, 5,258 genes were found to be significantly differentially expressed with a false discovery rate cut-off of < 0.1. The topmost deregulated of these genes included those with known roles in influencing HSC activity, as well as those involved in fibrotic responses in other cell lines and tissues. Interestingly, genes with no currently characterised role in either HSC activation or fibrotic processes were also identified, including CIITA and SERPINB2. Further in silico analysis revealed the prominent signalling pathways downstream of TGF-β1 in LX-2 cells, which will be useful for improving the understanding of how this cytokine influences broader signalling pathways in the activation of HSCs. This work may be of use in the identification of new markers of liver fibrosis and could provide insight into prospective genes or pathways that might be targeted for the amelioration of fibrotic liver disease in the future.
Accuracy of Low-Cost Alternative Facial Scanners: A Prospective Cohort Study.
Authors: Bartella Alexander K. , Laser Josefine , Kamal Mohammad , Halama Dirk , Neuhaus Michael , Pausch Niels C. , Zimmerer Rüdiger , Sander Anna K. , Lethaus Bernd 
Published: April 2021

Abstract
Introduction: Three-dimensional facial scan images have been showing an increasingly important role in peri-therapeutic management of oral and maxillofacial and head and neck surgery cases. Face scan images can be open using optical facial scanners utilizing line-laser, stereophotography, structured light modality, or from volumetric data obtained from cone beam computed tomography (CBCT). The aim of this study is to evaluate, if two low-cost procedures for creating a three-dimensional face scan images are able to produce a sufficient data set for clinical analysis. Materials and methods: 50 healthy volunteers were included in the study. Two test objects with defined dimensions were attached to the forehead and the left cheek. Anthropometric values were first measured manually, and consecutively, face scans were performed with a smart device and manual photogrammetry and compared to the manually measured data sets.Results: Anthropometric distances on average deviated 2.17 mm from the manual measurement (smart device scanning 3.01 mm vs. photogrammetry 1.34 mm), with 7 out of 8 deviations were statistically significant. Of a total of 32 angles, 19 values showed a significant difference to the original 90° angles. The average deviation was 6.5° (smart device scanning 10.1° vs. photogrammetry 2.8°).Conclusion: Manual photogrammetry with a regular photo-camera shows higher accuracy than scanning with smart device. However, the smart device was more intuitive in handling and further technical improvement of the cameras used should be watched carefully.
Genetic Association Analysis Between RNF213&nbsp;Common Variants and Symptomatic Intracranial Atherosclerotic Stenosis in a Chinese Population
Authors: Li Xi , Wang Junyan , Zhou Xiaoqing , Yu Fang , Feng Xianjing , Liu Zeyu , Huang Qin , Liao Di , Jin Xin , Xia Jian 
Published: April 2021

Abstract
Background: RNF213 is the gene involved in symptomatic intracranial atherosclerotic stenosis (sICAS). The rare variants of this gene have a significant association with the clinical phenotype of the disease in the East Asian populations. However, the association between the common variants of RNF213 and sICAS has remained unclear. This study investigated the possible association between the common variants of RNF213 and sICAS in the Chinese population. Result: A total of 39 common variants of the RNF213 gene were detected. The chi-squared test revealed two sites (rs8082521 and rs55996424) at which the genotype frequency and the allele frequency were significantly different between the sICAS group and the healthy control group (P-value < 0.05). The haplotype analysis demonstrated that rs55996424 does not have haploids with the other nine SNPs, including rs8082521. Conclusion: The T allele of the RNF213 common mutation rs55996424 increases the risk of sICAS. Compared to females, males are more likely to carry the pathogenic allele.
Primary synchronous ipsilateral renal fibrosarcoma and renal pelvic carcinoma: a case report and literature review
Authors: Jiang Hua , Liu Lulu , Li Ganhong 
Published: April 2021

Abstract
BackgroundRenal fibrosarcoma is a rare tumor, with only a few cases reported so far, and simultaneous occurrence of ipsilateral renal fibrosarcoma and renal pelvic carcinoma in a patient is extraordinarily rare.Case presentationA 66-year-old man admitted to our hospital with right renal percutaneous nephrostomy and recurrent fever. And the patient underwent laparoendoscopic nephrectomy and partial ureterectomy for pyonephrotic nonfunctioning kidneys. Postoperative pathology showed fibrosarcoma of right kidney and carcinoma of the renal pelvis.ConclusionsThis is the first case of simultaneous occurrence of ipsilateral renal fibrosarcoma and renal pelvic carcinoma in a patient. The diagnosis of fibrosarcoma is one of ultimate immunohistologic exclusion, because there are no specific immunologic markers for fibroblasts. The most common primary treatment for localized disease is radical surgery plus adjuvant chemotherapy.
High-parameter Cytometry Unmasks Microglial Cell Spatio-temporal Response Kinetics in Severe Neuroinflammatory Disease.
Authors: Spiteri Alanna Gabrielle , Terry Rachel Louise , Wishart Claire Leana , Ashhurst Thomas Myles , Campbell Iain Leslie , Hofer Markus Johannes , King Nicholas Jonathan Cole 
Published: April 2021

Abstract
Background:Differentiating infiltrating myeloid cells from resident microglia in neuroinflammatory disease is challenging, because bone marrow-derived inflammatory monocytes infiltrating the inflamed brain adopt a ‘microglia-like’ phenotype. This precludes the accurate identification of either cell type without genetic manipulation, which is important to understand their temporal contribution to disease and inform effective intervention in its pathogenesis. During West Nile virus (WNV) encephalitis, widespread neuronal infection drives substantial CNS infiltration of inflammatory monocytes, causing severe immunopathology and/or death, but the role of microglia in this remains unclear. Methods:Using high-parameter cytometry and dimensionality-reduction, we devised a simple, novel gating strategy to identify microglia and infiltrating myeloid cells under extreme inflammatory conditions. Validating our strategy we 1) blocked the entry of infiltrating myeloid populations from peripheral blood using monoclonal blocking antibodies, 2) adoptively transferred BM-derived monocytes and tracked their phenotypic changes after infiltration and 3) labelled peripheral leukocytes that infiltrate into the brain with an intravenous dye. We demonstrated that myeloid immigrants populated only the identified macrophage gates, while PLX5622 depletion reduced all 4 subsets defined by the microglial gates. Results:Using this novel gating approach, we identified four consistent microglia subsets in the homeostatic and WNV-infected brain. These were P2RY12hiCD86-, P2RY12hiCD86+, and P2RY12loCD86- P2RY12loCD86+. During infection, 2 further populations were identified as inflammatory and microglia-like macrophages, recruited from the bone marrow. Detailed kinetic analysis showed significant increases in the proportions of both P2RY12lo microglia subsets in all anatomical areas, largely at the expense of the P2RY12hiCD86- subset, with the latter undergoing compensatory proliferation, suggesting replenishment of, and differentiation from this subset in response to infection. Microglia altered their morphology early in infection, with all cells adopting temporal and regional disease-specific phenotypes. Late in disease, microglia produced IL-12, downregulated CX3CR1, F4/80 and TMEM119 and underwent apoptosis. Infiltrating macrophages expressed both TMEM119 and P2RY12 de novo, with the microglia-like subset notably exhibiting the highest proportional myeloid population death. Conclusions:Our approach enables detailed kinetic analysis of resident vs infiltrating myeloid cells in a wide range of neuroinflammatory models without non-physiological manipulation. This will more clearly inform potential therapeutic approaches that specifically modulate these cells.
A Mild Causal Relationship between Tea Consumption and Decreased Risk for Obesity in General Population: A Two-Sample Mendelian Randomization Study&nbsp;
Authors: Li Cancan , Niu Mingyun , Guo Zheng , Liu Pengcheng , Zheng Yulu , Liu Di , Yang Song , Wang Wei , Li Yuanmin , Hou Haifeng 
Published: April 2021

Abstract
Background

Tea consumption is considered as a protective factor for obesity. This study aimed to verify the casual association between tea consumption and obesity through a two-sample Mendelian randomization (MR) analysis in general population-based datasets.
Methods

The genetic instruments, single nucleotide polymorphisms (SNPs) associated with tea consumption habits, were obtained from genome-wide association studies (GWAS): UK Biobank, Nurses’ Health Study, Health Professionals Follow-up Study and Women’s Genome Health Study. The effect of the genetic instruments on obesity was analyzed using UK Biobank dataset (among ~ 500,000 participants). The causal relationship between tea consumption and obesity risk was analyzed by five methods of MR analyses: inverse variance weighted (IVW) method, MR-Egger regression method, weighted median estimator (WME), weighted mode and simple mode.
Results

Ninety-one SNPs were identified as genetic instruments in our study. A significant result was observed in IVW analysis (odds ratio [OR] = 0.998, 95% confidence interval [CI] = 0.996 to 1.000, P = 0.049]), which is the commonly used approach of two-sample MR analysis.
Conclusion

Our findings evidenced a mild causal relationship between tea consumption and the decreased risk for obesity. Further studies are needed to clarify the effects of tea consumption on obesity-related health problems in detail.
Imaging Generalized Wigner Crystal States in a WSe2/WS2 Moiré Superlattice
Authors: Wang Feng , Li Hongyuan , Li Shaowei , Regan Emma , Wang Danqing , Zhao Wenyu , Kahn Salman , Yumigeta Kentaro , Blei Mark , Taniguchi Takashi , Watanabe Kenji , Tongay Sefaattin , Zettl Alex , Crommie Michael 
Published: April 2021

Abstract
The Wigner crystal state, first predicted by Eugene Wigner in 19341, has fascinated condensed matter physicists for nearly 90 years2-10. Studies of two-dimensional (2D) electron gases first revealed signatures of the Wigner crystal in electrical transport measurements at high magnetic fields2-4. More recently optical spectroscopy has provided evidence of generalized Wigner crystal states in transition metal dichalcogenide (TMDC) moiré superlattices6-9. Direct observation of the 2D Wigner crystal lattice in real space, however, has remained an outstanding challenge. Scanning tunneling microscopy (STM) in principle has sufficient spatial resolution to image the Wigner crystal, but conventional STM measurements can potentially alter fragile Wigner crystal states in the process of measurement. Here we demonstrate real-space imaging of 2D Wigner crystals in WSe2/WS2 moiré heterostructures using a novel non-invasive STM spectroscopy technique. We employ a graphene sensing layer in close proximity to the WSe2/WS2 moiré superlattice for Wigner crystal imaging, where local STM tunneling current into the graphene sensing layer is modulated by the underlying electron lattice of the Wigner crystal in the WSe2/WS2 heterostructure. Our measurement directly visualizes different lattice configurations associated with Wigner crystal states at fractional electron fillings of n = 1/3, 1/2, and 2/3, where n is the electron number per site. The n=1/3 and n=2/3 Wigner crystals are observed to exhibit a triangle and a honeycomb lattice, respectively, in order to minimize nearest-neighbor occupations. The n = 1/2 state, on the other hand, spontaneously breaks the original C3 symmetry and forms a stripe structure in real space. Our study lays a solid foundation toward the fundamental understanding of rich Wigner crystal states in WSe2/WS2 moiré heterostructures. Furthermore, this new STM technique is generally applicable to imaging novel correlated electron lattices in different van der Waals moiré heterostructures.
Potential of High Dimensional Radiomic Features to Assess Flowing Blood Components in Non-contrast CT Scans
Authors: Mahmoudi Scherwin , Martin Simon S. , Ackermann Jörg , Zhdanovich Yauheniya , Koch Ina , Vogl Thomas J. , Albrecht Moritz H. , Lenga Lukas , Bernatz Simon 
Published: April 2021

Abstract
Background: To assess the potential of radiomic features to quantify components of flowing blood to non-invasively predict moderate-to-severe anemia in non-contrast enhanced CT scans. Methods: One hundred patients (median age, 69 years; range, 19–94 years) who received CT scans of the thoracolumbar spine and blood-testing for hemoglobin and hematocrit levels ± 24h between 08/2018 and 11/2019 were retrospectively included. Intraaortic blood was segmented using a spherical volume of interest with consecutive radiomic analysis. Feature selection was performed applying analysis of correlation and collinearity. The final feature set was obtained to differentiate moderate-to-severe anemia. Random forest machine learning was applied and predictive performance was assessed. A decision-tree was obtained to propose a cut-off value of CT Hounsfield units (HU).Results: High correlation with hemoglobin and hematocrit levels was shown for first-order radiomic features (p<0.001 to p=0.032). The top 3 features showed high correlation to hemoglobin values (p) and minimal collinearity (r) to the top ranked feature Median (p<0.001), Energy (p=0.002, r=0.387), Minimum (p=0.032, r=0.437). Median (p<0.001) and Minimum (p=0.003) differed in moderate-to-severe anemia compared to non-anemic state. Median yielded superiority to the combination of Median and Minimum (p(AUC)=0.015, p(precision)=0.017, p(accuracy)=0.612) in the predictive performance employing random forest analysis. A Median HU value ≤ 36.5 indicated moderate-to-severe anemia (accuracy=0.90, precision=0.80).Conclusions: First-order radiomic features correlate with hemoglobin levels and may be feasible for the prediction of moderate-to-severe anemia. High dimensional radiomic features did not inherit the potential to augment the data in our exemplary use case of flowing blood component assessment.Trial registration: Retrospectively registered.
Geochemical features of the distribution of major and trace elements in sediments and soils of the Zarafshon River Valley
Authors: Abdusamadzoda Daler , Abdushukurov Djamshed , Duliu Octavian , Zinicovscaia Inga , Nekhoroshkov Pavel 
Published: April 2021

Abstract
Purpose

The aim of this research was to estimate impact of the geochemical features to distribution of major and trace elements in soil and sediments, assess of anthropogenic and natural factors in terrestrial ecosystems of Zarafshon. As well as to answer the common criticism of the water, soil and sediment pollution in Zarafshon. In this way this research will be reasonable substantial information about distribution of major and trace elements in mountains and piedmont regions.
Materials and methods

In view of a planned detailed investigation, and to get more data concerning the geochemistry of sediments and soils along the Zarafshon Valley of Western Tajikistan, as well as to assess of the local environmental situation, the mass fraction of eight major, rock-forming elements together with other 38 trace elements were determined by Instrumental Neutron Activation Analysis. To accomplish this task 116 samples of sediment and an equal number of soils were collected around the Tajik sector of the Zarafshon catchment basin and its main tributaries.
Results and discussion

Both major and trace elements proved a significant similarity between soil and sediments including potentially contaminating elements As, Sb and Hg, whose mass fractions showed in some places to be significantly higher. An analysis of the distribution of major elements oxides as well as of incompatible trace elements Sc, Zr, REE, Th, and U suggested that the analysed soil and sediments have rather a felsic origin. A more careful examination revealed a reduced degree of recycling and for some location, a certain degree of weathering. All these peculiarities could be ascribed to a vast investigated area spread onto a significant diversity of geological formations.
Conclusion

The process of soil weathering of the studied area takes place relatively quick, but mainly it's has a natural character rather. The high content of accumulation of major and trace element in the sediment also related to rock source but only in rare cases is it of an anthropogenic nature. Based on these results, it can be predicted that the seriously environmental threat was not observed in the Zarafshon river valley. The activities of industrial facilities cover only a small part of this region and their impacts on the ecological state of the Zarafshon river valley is very small.