bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the underlying mechanism of Xianlinggubao capsule against osteoporosis by network pharmacology
Authors: Bao Hangsheng , Guo Huizhi , Feng Zongquan , Li Xin 
Published: July 2020

Abstract
Background
Xianlinggubao formula (XLGB), a Chinese State Food and Drug Administration-permitted traditional Chinese herbal medicine, has been extensively used to treat osteoporosis. Although XLGB was shown to improve bone mass in ovariectomized rats and clinically alleviate osteoporosis symptoms, its pharmacological mechanisms remain unclear.

Methods
In this study, we used a network pharmacological approach to explore the potential mechanism of XLGB in treating osteoporosis. We obtained XLGB compounds from the TCMSP and TCMID databases and identified potential targets of these compounds through target fishing based on the TCMSP and Swiss Target Prediction databases. Next, we identified the osteoporosis targets by using the CTD, TTD, GeneCards, OMIM and PharmGKB databases. Then, the overlapping genes between the XLGB potential targets and the osteoporosis targets were used to establish a protein-protein interaction (PPI) network and to analyze their interactions and identify the major hub genes in this network. Subsequently, the Metascape database was utilized to conduct the enrichment of Gene Ontology biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.

Results
There were 104 active compounds and 295 related targets identified overall. After the Metascape enrichment analysis, we identified the top 25 cellular biological processes and top 15 pathways based on the logP value and found that the XLGB-mediated anti-osteoporosis effect was mainly associated with reactive oxygen species, organonitrogen compound response and cell migration. Furthermore, 36 hub genes of XLGB, such as EGF, EGFR, MTOR, MAPK14 and NFKB1, were considered potential therapeutic targets, suggesting the underlying mechanisms of XLGB acting on osteoporosis.

Conclusion
We investigated the possible therapeutic mechanisms of XLGB from a systemic perspective. These key targets and pathways provide promising directions for future research to reveal the exact regulatory mechanisms of XLGB.
Composite CDE: modeling composite relationships between common data elements for representing complex clinical data
Authors: Kim Hye Hyeon , Park Yu Rang , Lee Suehyun , Kim Ju Han 
Published: July 2020

Abstract
Background
Semantic interoperability is essential for improving data quality and sharing. The ISO/IEC 11179 Metadata Registry (MDR) standard has been highlighted as a solution for standardizing and registering clinical data elements (DEs). However, the standard model has both structural and semantic limitations, and the number of DEs continues to increase due to poor term reusability. Semantic types and constraints are lacking for comprehensively describing and evaluating DEs on real-world clinical documents.

Methods
We addressed these limitations by defining three new types of semantic relationship (dependency, composite, and variable) in our previous studies. The present study created new and further extended existing semantic types (hybrid atomic and repeated and dictionary composite common data elements [CDEs]) with four constraints: ordered, operated, required, and dependent. For evaluation, we extracted all atomic and composite CDEs from five major clinical documents from five teaching hospitals in Korea, 14 Fast Healthcare Interoperability Resources (FHIR) resources from FHIR bulk sample data, and MIMIC-III (Medical Information Mart for Intensive Care) demo dataset. Metadata reusability and semantic interoperability in real clinical settings were comprehensively evaluated by applying the CDEs with our extended semantic types and constraints.

Results
All of the CDEs (n = 1142) extracted from the 25 clinical documents were successfully integrated with a very high CDE reuse ratio (46.9%) into 586 CDEs (259 atomic and 20 unique composite CDEs), and all of CDEs (n = 238) extracted from the 14 FHIR resources of FHIR bulk sample data were successfully integrated with high CDE reuse ration (59.7%) into 96 CDEs (21 atomic and 28 unique composite CDEs), which improved the semantic integrity and interoperability without any semantic loss. Moreover, the most complex data structures from two CDE projects were successfully encoded with rich semantics and semantic integrity.

Conclusion
MDR-based extended semantic types and constraints can facilitate comprehensive representation of clinical documents with rich semantics, and improved semantic interoperability without semantic loss.
Post-transplant cyclophosphamide versus antithymocyte globulin in patients with acute myeloid leukemia in first complete remission undergoing allogeneic stem cell transplantation from 10/10 HLA-matched unrelated donors
Authors: Brissot Eolia , Labopin Myriam , Moiseev Ian , Cornelissen J. J. , Meijer Ellen , Van Gorkom Gwendolyn , Rovira Montserrat , Ciceri Fabio , Griskevicius Laimonas , Blaise Didier , Forcade Edouard , Mistrik Martin , Mielke Stephan , Bulabois Claude Eric , Niittyvuopio Riitta , Deconinck Eric , Ruggeri Annalisa , Sanz Jaime , Spyridonidis Alexandros , Savani Bipin , Giebel Sebastian , Nagler Arnon , Mohty Mohamad 
Published: July 2020

AbstractBackgroundGraft-versus-host disease (GVHD) remains a major contributor to mortality and morbidity after allogeneic stem-cell transplantation (allo-HSCT). The updated recommendations suggest that rabbit antithymocyte globulin or anti-T-lymphocyte globulin (ATG) should be used for GVHD prophylaxis in patients undergoing matched-unrelated donor (MUD) allo-HSCT. More recently, using post-transplant cyclophosphamide (PTCY) in the haploidentical setting has resulted in low incidences of both acute (aGVHD) and chronic GVHD (cGVHD). Therefore, the aim of our study was to compare GVHD prophylaxis using either PTCY or ATG in patients with acute myeloid leukemia (AML) who underwent allo-HSCT in first remission (CR1) from a 10/10 HLA-MUD.MethodsOverall, 174 and 1452 patients from the EBMT registry receiving PTCY and ATG were included. Cumulative incidence of aGVHD and cGVHD, leukemia-free survival, overall survival, non-relapse mortality, cumulative incidence of relapse, and refined GVHD-free, relapse-free survival were compared between the 2 groups. Propensity score matching was also performed in order to confirm the results of the main analysisResultsNo statistical difference between the PTCY and ATG groups was observed for the incidence of grade II–IV aGVHD. The same held true for the incidence of cGVHD and for extensive cGVHD. In univariate and multivariate analyses, no statistical differences were observed for all other transplant outcomes. These results were also confirmed using matched-pair analysis.ConclusionThese results highlight that, in the10/10 HLA-MUD setting, the use of PTCY for GVHD prophylaxis may provide similar outcomes to those obtained with ATG in patients with AML in CR1.
Cloning and promoter analysis of palladin 90-kDa, 140-kDa, and 200-kDa isoforms involved in skeletal muscle cell maturation
Authors: Ouali Boimpoundi Eunice Flavie , Liu Tzu-Yu , Lu Chun-Yen , Cheng Pei-Yuan , Huang Chao-Li , Li Chun-Chun , Chiang Yu-Chung , Wang Hao-Ven 
Published: July 2020

Abstract
Objective
Palladin is a ubiquitous phosphoprotein expressed in vertebrate cells that works as a scaffolding protein. Several isoforms deriving from alternative splicing are originated from the palladin gene and involved in mesenchymal and muscle cells formation, maturation, migration, and contraction. Recent studies have linked palladin to the invasive spread of cancer and myogenesis. However, since its discovery, the promoter region of the palladin gene has never been studied. The objective of this study was to predict, identify, and measure the activity of the promoter regions of palladin gene.

Results
By using promoter prediction programs, we successfully identified the transcription start sites for the Palld isoforms and revealed the presence of a variety of transcriptional regulatory elements including TATA box, GATA, MyoD, myogenin, MEF, Nkx2-5, and Tcf3 upstream promoter regions. The transcriptome profiling approach confirmed the active role of predicted transcription factors in the mouse genome. This study complements the missing piece in the characterization of palladin gene and certainly contributes to understanding the complexity and enrollment of palladin regulatory factors in gene transcription.
Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector
Authors: Yokomi Raymond , Rattner Rachel , Osman Fatima , Maheshwari Yogita , Selvaraj Vijayanandraj , Pagliaccia Deborah , Chen Jianchi , Vidalakis Georgios 
Published: July 2020

Abstract
Objectives
Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution.

Data description
The whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4–25.6%. Characterization of extrachromosomal DNAs resulted in identification of one or two plasmids, with a G + C content of 23.3 to 27.6%, from plant hosts; and eight or nine plasmids, with a G + C content of 21.65 to 29.19%, from N. tenellus. Total genome size ranged from 1,611,714 to 1,832,173 bp from plants and 1,968,976 to 2,155,613 bp from the leafhopper. All sequence data has been deposited in DDBJ/ENA/GenBank under the accession numbers CP046368-CP046373 and CP047426-CP047446.
Facial erythema after the treatment of dupilumab in SLE patient
Authors: Jang Dong Hyek , Lee Jae In , Bae Joo Yoon , Jung Hye Jung , Park Mi Yeon , Ahn Jiyoung 
Published: July 2020

Abstract
Background
Dupilumab is a receptor antagonist binding to the alpha subunit of the interleukin-4 receptor. Through binding to it, dupilumab inhibits signaling of both IL-4 and IL-13, the representative Th2 biomarkers. Recently, in addition to the treatment effects for atopic dermatitis (AD), there is an emerging adverse event as facial erythema.

Case presentation
A twenty-seven-year-old female patient developed erythema and desquamation on the face and neck after dupilumab administration. She had AD on her arms, legs, and trunk before the treatment but there was no atopic clinical feature in her face and neck. With the treatment of dupilumab, her skin lesions of the body have improved from the beginning of the treatment. In the patch test, including dupilumab, there was no specific finding other than the 1+ response to neomycin on day 2. In the intradermal test to dupilumab, a positive result was observed 15 min later, but negative both days 1 and 2. The blood examination showed an elevation of both ANA as 1:80 and anti-phospholipid antibodies (Anti-cardiolipin IgM, IgG, and Anti- beta 2 GPI IgG). She was diagnosed with Systemic lupus erythematosus (SLE) based on diagnostic criteria by a rheumatologist.

Conclusion
Dupilumab is an emerging therapeutic agent for AD, and treatment cases are increasing in Korea. However, there are several adverse events during the treatment of dupilumab. Herein, we report the unexpected adverse event during the treatment of dupilumab in SLE patients.
Impaired autophagy triggered by HDAC9 in mesenchymal stem cells accelerates bone mass loss
Authors: Zhang Liqiang , Qi Meng , Chen Ji , Zhao Jiangdong , Li Liya , Hu Jiachen , Jin Yan , Liu Wenjia 
Published: July 2020

Abstract
Background
Bone mass loss in aging is linked with imbalanced lineage differentiation of bone marrow mesenchymal stem cells (BMMSCs). Recent studies have proved that histone deacetylases (HDACs) are regarded as key regulators of bone remodeling. However, HDACs involve in regulating BMMSC bio-behaviors remain elusive. Here, we investigated the ability of HDAC9 on modulation of autophagy and its significance in lineage differentiation of BMMSCs.

Methods
The effects of HDAC9 on lineage differentiation of BMMSCs and autophagic signaling were assessed by various biochemical (western blot and ChIP assay), morphological (TEM and confocal microscopy), and micro-CT assays.

Results
Sixteen-month mice manifested obvious bone mass loss and marrow fat increase, accompanied with decreased osteogenic differentiation and increased adipogenic differentiation of BMMSCs. Further, the expression of HDAC9 elevated in bone and BMMSCs. Importantly, HDAC9 inhibitors recovered the lineage differentiation abnormality of 16-month BMMSCs and reduced p53 expression. Mechanistically, we revealed that HDAC9 regulated the autophagy of BMMSCs by controlling H3K9 acetylation in the promoters of the autophagic genes, ATG7, BECN1, and LC3a/b, which subsequently affected their lineage differentiation. Finally, HDAC9 inhibition improved endogenous BMMSC properties and promoted the bone mass recovery of 16-month mice.

Conclusions
Our data demonstrate that HDAC9 is a key regulator in a variety of bone mass by regulating autophagic activity in BMMSCs and thus a potential target of age-related bone loss treatment.
Sulforaphane alter the microbiota and mitigate colitis severity on mice ulcerative colitis induced by DSS
Authors: Zhang Yan , Tan Luxuan , Li Chao , Wu Han , Ran Dan , Zhang Zhenyu 
Published: July 2020

AbstractSulforaphane (SFN) is a kind of natural isothiocyanate, which exists in cruciferous plants. Only few studies were about the anti-inflammatory effects of sulforaphane in ulcerative colitis. In this study, our purpose is to explore the effects of sulforaphane on the intestinal microbial community of UC mice. The severity of mice colitis were measured by colon length, survial rate, body weight and disease activity index (DAI) score. Histological and morphological evaluation of colon tissues were performed by HE. 16S rRNA gene amplicon pyrosequencing was used to analyza the changes of mouse flora. The variety of flora expression were explored using quantitative PCR. Sulforaphane treated mice had larger body weight and longer colon length than DSS-induced mice. The colon tissues of DSS group showed congestion and edema. Meanwhile, treatment with sulforaphane effectively reducted the damage scores and MPO activity. Sulforaphane reversed DSS-induced gut dysbiosis. Sulforaphane would shift the balance to Butyricicoccus on inflammation. The possible anti-inflammatory mechanism of sulforaphane is to coordinate with the probiotics such as Butyricicoccus. In summary, these findings proved that sulforaphane might be a useful content and serve as a potential therapy in the treatment of UC.
Estimate of the energy value of soybean meal relative to corn based on growth performance of nursery pigs
Authors: Cemin Henrique S. , Williams Hayden E. , Tokach Mike D. , Dritz Steve S. , Woodworth Jason C. , DeRouchey Joel M. , Goodband Robert D. , Coble Kyle F. , Carrender Brittany A. , Gerhart Mandy J. 
Published: July 2020

AbstractBackgroundTwo experiments were conducted to determine the effects of increasing amounts of soybean meal (SBM) in swine diets and estimate the energy value of SBM.MethodsA total of 2233 pigs (PIC 337 × 1050, Hendersonville, TN) and 3796 pigs (PIC 359 × C40), initially 11.0 kg and 17.6 kg body weight (BW), were used in Exp. 1 and 2, respectively. In Exp. 1, pigs were placed in 92 pens each containing 20 to 27 pigs. In Exp. 2, pigs were placed in 84 pens each containing 37 to 43 pigs. Treatments were assigned in a randomized complete block design with BW as the blocking factor. Dietary treatments consisted of 21%, 27%, 33%, or 39% SBM in Exp. 1 and 17.5%, 22%, 26.5%, 31%, 35.5%, or 40% SBM in Exp. 2, obtained by changing the inclusion rate of feed-grade amino acids and corn grain. For Exp. 1, representative samples of corn grain, SBM, and distillers dried grains with solubles were analyzed for total AA content prior to diet formulation. For Exp. 2, diets were formulated using NRC (2012) nutrient loadings. Treatment diets were fed for 21 and 22 d (Exp. 1 and 2) and there were 23 replicates in Exp. 1 and 14 replicates in Exp. 2. Pigs were weighed and feed disappearance measured weekly to calculate average daily gain (ADG), average daily feed intake (ADFI), gain-to-feed ratio (G:F), and caloric efficiency (CE). Data were analyzed with block as a random effect and treatment as a fixed effect, and contrasts were constructed to test the linear and quadratic effects of increasing SBM.ResultsIn Exp. 1, there was a tendency (linear,P = 0.092) for a decrease in ADFI as SBM increased. There was a tendency (P = 0.090) for a quadratic response for ADG, with a decrease in ADG observed with 39% SBM inclusion. Pigs fed diets with increasing SBM had a tendency (quadratic,P = 0.069) for an increase in G:F up to 33% SBM and an improvement (linear,P = 0.001; quadratic,P = 0.063) in CE with increasing SBM. Using CE to estimate the energy of SBM relative to corn, a value of 105.4% of corn energy or 2816 kcal/kg NE was determined using all data points. When removing the CE value of the 39% SBM treatment due to the quadratic tendency, SBM was estimated to have 121.1% of corn energy or 3236 kcal/kg NE. In Exp. 2, there was a decrease (linear,P = 0.001) in ADFI. Pigs fed increasing SBM had a tendency (linear,P = 0.065) for reduced ADG but an improvement (linear,P = 0.001) in G:F and CE as SBM increased. The energy value of SBM was estimated as 124.7% of corn energy or 3332 kcal/kg NE.ConclusionsThe results suggest that feeding increasing levels of SBM improves G:F and CE. The energy value of SBM was estimated to be between 105% and 125% of corn, which is much greater than the NRC (2012) would indicate.
Role of A Novel Angiogenesis FKBPL-CD44 Pathway in Preeclampsia Risk Stratification and Mesenchymal Stem Cell Treatment
Authors: Todd Naomi , McNally Ross , Alqudah Abdelrahim , Jerotic Djurdja , Suvakov Sonja , Obradovic Danilo , Hoch Denise , Hombrebueno Jose R , Campos Guillermo Lopez , Watson Chris J , Gojnic-Dugalic Miroslava , Simic Tatjana P , Krasnodembskaya Anna , Desoye Gernot , Eastwood Kelly-Ann , Hunter Alyson J , Holmes Valerie A , McCance David R , Young Ian S , Grieve David J , Kenny Louise C , Garovic Vesna D , Robson Tracy , McClements Lana 
Published: July 2020

Abstract

Context
Preeclampsia is a leading cardiovascular complication in pregnancy lacking effective diagnostic and treatment strategies.

Objective
To investigate the diagnostic and therapeutic target potential of the angiogenesis proteins, FK506-binding protein like (FKBPL) and CD44.

Design and Intervention
FKBPL and CD44 plasma concentration or placental expression were determined in women pre- or postdiagnosis of preeclampsia. Trophoblast and endothelial cell function was assessed following mesenchymal stem cell (MSC) treatment and in the context of FKBPL signaling.

Settings and Participants
Human samples prediagnosis (15 and 20 weeks of gestation; n ≥ 57), or postdiagnosis (n = 18 for plasma; n = 4 for placenta) of preeclampsia were used to determine FKBPL and CD44 levels, compared to healthy controls. Trophoblast or endothelial cells were exposed to low/high oxygen, and treated with MSC-conditioned media (MSC-CM) or a FKBPL overexpression plasmid.

Main Outcome Measures
Preeclampsia risk stratification and diagnostic potential of FKBPL and CD44 were investigated. MSC treatment effects and FKBPL-CD44 signaling in trophoblast and endothelial cells were assessed.

Results
The CD44/FKBPL ratio was reduced in placenta and plasma following clinical diagnosis of preeclampsia. At 20 weeks of gestation, a high plasma CD44/FKBPL ratio was independently associated with the 2.3-fold increased risk of preeclampsia (odds ratio = 2.3, 95% confidence interval [CI] 1.03-5.23, P = 0.04). In combination with high mean arterial blood pressure (&gt;82.5 mmHg), the risk further increased to 3.9-fold (95% CI 1.30-11.84, P = 0.016). Both hypoxia and MSC-based therapy inhibited FKBPL-CD44 signaling, enhancing cell angiogenesis.

Conclusions
The FKBPL-CD44 pathway appears to have a central role in the pathogenesis of preeclampsia, showing promising utilities for early diagnostic and therapeutic purposes.
In vitro efficacy of a copper iodine complex PPE disinfectant for SARS-CoV-2 inactivation
Authors: Mantlo Emily , Rhodes Tanya , Boutros Jenny , Patterson-Fortin Laura , Evans Alex , Paessler Slobodan 
Published: July 2020

Background: The ability to protect workers and healthcare professionals from infection by SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is of great concern. Hospitals, nursing homes and employers are adopting infection control strategies based on guidance from leading public health organizations such as the CDC, OSHA, FDA, and other government bodies. Certain hard surface disinfectants are effective against SARS-CoV-2 but are not suitable for use on skin or personal protective equipment (PPE) that comes into contact with skin. Furthermore, near-ubiquitous alcohol-based hand sanitizers are acceptable for use on skin, but they are not suitable for use on PPE. PPE, especially masks, are also commonly being used for longer durations than normal. There is a need for new products and techniques that can effectively disinfect PPE during wear time without having detrimental effects on surrounding skin. Clyraguard spray is a novel copper iodine complex designed to be used on non-critical PPE. Methods: In this study, the Clyraguard copper iodine complex was tested for its ability to inactivate SARS-CoV-2 in solution. Results: These data indicate the product to be effective in reducing SARS-CoV-2 titers in a time-dependent manner, with the virus being reduced below the detection limits within 30 minutes. Conclusions: These results suggest that Clyraguard may be an effective tool for mitigating cross-contamination of non-critical PPE that may come into contact with SARS-CoV-2.
Cosmetic stature lengthening
Authors: Marwan Yousef , Cohen Dan , Alotaibi Mohammed , Addar Abdullah , Bernstein Mitchell , Hamdy Reggie 
Published: July 2020

Aims To systematically review the outcomes and complications of cosmetic stature lengthening. Methods PubMed and Embase were searched on 10 November 2019 by three reviewers independently, and all relevant studies in English published up to that date were considered based on predetermined inclusion/exclusion criteria. The search was done using “cosmetic lengthening” and “stature lengthening” as key terms. The Preferred Reporting Item for Systematic Reviews and Meta-Analyses statement was used to screen the articles. Results A total of 11 studies including 795 patients were included. The techniques used in the majority of the patients were classic 3- or 4-ring Ilizarov fixator (267 patients; 33.6%) and lengthening over nail (LON) (253 patients; 31.8%), while implantable lengthening nail (ILN) was used in the smallest number of patients (63 patients; 7.9%). Mean end lengthening achieved was 6.7 cm (SD 0.6; 1.5 to 13.0), and the mean follow-up duration was 4.9 years (SD 2.1; 41 days to 7 years). Overall, the mean number of problems, obstacles, and complications per patient was 0.78 (SD 0.5), 0.94 (SD 1.0), and 0.15 (SD 0.2), respectively. The most common problem and obstacle was ankle equinus deformity, while the most common complications were deformation of the regenerate after end of treatment and subtalar joint stiffness/deformity. Conclusion Cosmetic stature lengthening provides favourable height gain, patient satisfaction, and functional outcomes, with low rate of major complications. Clear indications, contraindications, and guidelines for cosmetic stature lengthening are needed. Cite this article: Bone Joint Res 2020;9(7):341–350.