bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of sampling strategy and DNA extraction on human skin microbiome investigations
Authors: Bjerre Rie Dybboe , Hugerth Luisa Warchavchik , Boulund Fredrik , Seifert Maike , Johansen Jeanne Duus , Engstrand Lars 
Published: November 2019

AbstractThe human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.
Terminal fucose mediates progression of human cholangiocarcinoma through EGF/EGFR activation and the Akt/Erk signaling pathway
Authors: Indramanee Somsiri , Sawanyawisuth Kanlayanee , Silsirivanit Atit , Dana Paweena , Phoomak Chatchai , Kariya Ryusho , Klinhom-on Nathakan , Sorin Supannika , Wongkham Chaisiri , Okada Seiji , Wongkham Sopit 
Published: November 2019

AbstractAberrant glycosylation is recognized as a cancer hallmark that is associated with cancer development and progression. In this study, the clinical relevance and significance of terminal fucose (TFG), by fucosyltransferase-1 (FUT1) in carcinogenesis and progression of cholangiocarcinoma (CCA) were demonstrated. TFG expression in human and hamster CCA tissues were determined using Ulex europaeus agglutinin-I (UEA-I) histochemistry. Normal bile ducts rarely expressed TFG while 47% of CCA human tissues had high TFG expression and was correlated with shorter survival of patients. In the CCA-hamster model, TFG was elevated in hyperproliferative bile ducts and gradually increased until CCA was developed. This evidence indicates the involvement of TFG in carcinogenesis and progression of CCA. The mechanistic insight was performed in 2 CCA cell lines. Suppression of TFG expression using siFUT1 or neutralizing the surface TFG with UEA-I significantly reduced migration, invasion and adhesion of CCA cells in correlation with the reduction of Akt/Erk signaling and epithelial-mesenchymal transition. A short pulse of EGF could stimulate Akt/Erk signaling via activation of EGF-EGFR cascade, however, decreasing TFG using siFUT1 or UEA-I treatment reduced the EGF-EGFR activation and Akt/Erk signaling. This evidence provides important insight into the relevant role and molecular mechanism of TFG in progression of CCA.
Selecting Clinically Relevant Gait Characteristics for Classification of Early Parkinson’s Disease: A Comprehensive Machine Learning Approach
Authors: Rehman Rana Zia Ur , Del Din Silvia , Guan Yu , Yarnall Alison J. , Shi Jian Qing , Rochester Lynn 
Published: November 2019

AbstractParkinson’s disease (PD) is the second most common neurodegenerative disease; gait impairments are typical and are associated with increased fall risk and poor quality of life. Gait is potentially a useful biomarker to help discriminate PD at an early stage, however the optimal characteristics and combination are unclear. In this study, we used machine learning (ML) techniques to determine the optimal combination of gait characteristics to discriminate people with PD and healthy controls (HC). 303 participants (119 PD, 184 HC) walked continuously around a circuit for 2-minutes at a self-paced walk. Gait was quantified using an instrumented mat (GAITRite) from which 16 gait characteristics were derived and assessed. Gait characteristics were selected using different ML approaches to determine the optimal method (random forest with information gain and recursive features elimination (RFE) technique with support vector machine (SVM) and logistic regression). Five clinical gait characteristics were identified with RFE-SVM (mean step velocity, mean step length, step length variability, mean step width, and step width variability) that accurately classified PD. Model accuracy for classification of early PD ranged between 73–97% with 63–100% sensitivity and 79–94% specificity. In conclusion, we identified a subset of gait characteristics for accurate early classification of PD. These findings pave the way for a better understanding of the utility of ML techniques to support informed clinical decision-making.
In-situ study of oxygen exposure effect on spin-orbit torque in Pt/Co bilayers in ultrahigh vacuum
Authors: Xie Hang , Yuan Jiaren , Luo Ziyan , Yang Yumeng , Wu Yihong 
Published: November 2019

AbstractOxygen incorporation has been reported to increase the current-induced spin-orbit torque in ferromagnetic heterostructures, but the underlying mechanism is still under active debate. Here, we report on an in-situ study of the oxygen exposure effect on spin-orbit torque in Pt/Co bilayers via controlled oxygen exposure, Co and Mg deposition, and electrical measurements in ultrahigh vacuum. We show that the oxygen exposure on Pt/Co indeed leads to an increase of spin-orbit torque, but the enhancement is not as large as those reported previously. Similar enhancement of spin-orbit torque is also observed after the deposition of an MgO capping layer. The results of ab initio calculations on the Rashba splitting of Pt/Co and Pt/Co/O suggest that the enhancement is due to enhanced Rashba-Edelstein effect by surface-adsorbed oxygen. Our findings shed some light on the varying roles of oxygen in modifying the spin torque efficiency reported previously.
Targeted delivery of lysosomal enzymes to the endocytic compartment in human cells using engineered extracellular vesicles
Authors: Do Mai Anh , Levy Daniel , Brown Annie , Marriott Gerard , Lu Biao 
Published: November 2019

AbstractTargeted delivery of lysosomal enzymes to the endocytic compartment of human cells represents a transformative technology for treating a large family of lysosomal storage diseases (LSDs). Gaucher disease is one of the most common types of LSDs caused by mutations to the lysosomal β-glucocerebrosidase (GBA). Here, we describe a genetic strategy to produce engineered exosomes loaded with GBA in two different spatial configurations for targeted delivery to the endocytic compartment of recipient cells. By fusing human GBA to an exosome-anchoring protein: vesicular stomatitis virus glycoprotein (VSVG), we demonstrate that the chimeric proteins were successfully integrated into exosomes which were secreted as extracellular vesicles (EVs) by producer cells. Isolation and molecular characterization of EVs confirmed that the fusion proteins were loaded onto exosomes without altering their surface markers, particle size or distribution. Further, enzyme-loaded exosomes/EVs added to cultured medium were taken up by recipient cells. Further, the endocytosed exosomes/EVs targeted to endocytic compartments exhibited a significant increase in GBA activity. Together, we have developed a novel method for targeting and delivery of lysosomal enzymes to their natural location: the endocytic compartment of recipient cells. Since exosomes/EVs have an intrinsic ability to cross the blood-brain-barrier, our technology may provide a new approach to treat severe types of LSDs, including Gaucher disease with neurological complications.
Treatment with a new benzimidazole derivative bearing a pyrrolidine side chain overcomes sorafenib resistance in hepatocellular carcinoma
Authors: Suk Fat-Moon , Liu Chao-Lien , Hsu Ming-Hua , Chuang Yu-Ting , Wang Jack P. , Liao Yi-Jen 
Published: November 2019

AbstractHepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. Currently, sorafenib is the standard first-line drug for patients with advanced HCC. However, long-term exposure to sorafenib often results in reduced sensitivity of tumour cells to the drug, leading to acquired resistance. Therefore, developing new compounds to treat sorafenib resistance is urgently needed. Although benzimidazole and its derivatives have been reported to exert antimicrobial and antitumour effects, the anti-drug resistance potential of these molecules is still unknown. In this study, we established sorafenib-resistant (SR) cell lines and an acquired sorafenib resistance xenograft model. We showed that treatment with a benzimidazole derivative bearing a pyrrolidine side chain (compound 9a) inhibited the proliferation of SR cells by blocking the phosphorylation of AKT, p70S6 and the downstream molecule RPS6. In addition, caspase 3/PARP-dependent apoptotic signals were induced in 9a-treated cells. Regarding epithelial-mesenchymal transition (EMT) activities, 9a treatment significantly suppressed the migration of SR cells. In particular, the levels of EMT-related transcription factors (snail, slug and twist) and mesenchymal markers (vimentin and N-cadherin) were downregulated. In the acquired sorafenib resistance xenograft model, compound 9a administration decreased the growth of tumours with acquired sorafenib resistance and the expression of the HCC markers α-fetoprotein, glypican 3 and survivin. In conclusion, treatment with this compound may be a novel therapeutic strategy for patients with sorafenib resistance.
Core-shell nanowire arrays based on ZnO and CuxO for water stable photocatalysts
Authors: Florica Camelia , Costas Andreea , Preda Nicoleta , Beregoi Mihaela , Kuncser Andrei , Apostol Nicoleta , Popa Cristina , Socol Gabriel , Diculescu Victor , Enculescu Ionut 
Published: November 2019

AbstractStaggered gap radial heterojunctions based on ZnO-CuxO core-shell nanowires are used as water stable photocatalysts to harvest solar energy for pollutants removal. ZnO nanowires with a wurtzite crystalline structure and a band gap of approximately 3.3 eV are obtained by thermal oxidation in air. These are covered with an amorphous CuxO layer having a band gap of 1.74 eV and subsequently form core-shell heterojunctions. The electrical characterization of the ZnO pristine and ZnO-CuxO core-shell nanowires emphasizes the charge transfer phenomena at the junction and at the interface between the nanowires and water based solutions. The methylene blue degradation mechanism is discussed taking into consideration the dissolution of ZnO in water based solutions for ZnO nanowires and ZnO-CuxO core-shell nanowires with different shell thicknesses. An optimum thickness of the CuxO layer is used to obtain water stable photocatalysts, where the ZnO-CuxO radial heterojunction enhances the separation and transport of the photogenerated charge carriers when irradiating with UV-light, leading to swift pollutant degradation.
The effects of organic and inorganic phosphorus amendments on the biochemical attributes and active microbial population of agriculture podzols following silage corn cultivation in boreal climate
Authors: Ali Waqas , Nadeem Muhammad , Ashiq Waqar , Zaeem Muhammad , Gilani Syed Shah Mohioudin , Rajabi-Khamseh Sanaz , Pham Thu Huong , Kavanagh Vanessa , Thomas Raymond , Cheema Mumtaz 
Published: November 2019

AbstractPhosphorus (P) is the second most important macronutrient that limits the plant growth, development and productivity. Inorganic P fertilization in podzol soils predominantly bound with aluminum and iron, thereby reducing its availability to crop plants. Dairy manure (DM) amendment to agricultural soils can improve physiochemical properties, nutrient cycling through enhanced enzyme and soil microbial activities leading to improved P bioavailability to crops. We hypothesized that DM amendment in podzol soil will improve biochemical attributes and microbial community and abundance in silage corn cropping system under boreal climate. We evaluated the effects of organic and inorganic P amendments on soil biochemical attributes and abundance in podzol soil under boreal climate. Additionally, biochemical attributes and microbial population and abundance under short-term silage corn monocropping system was also investigated. Experimental treatments were [P0 (control); P1: DM with high P2O5; P2: DM with low P2O5; P3: inorganic P and five silage-corn genotypes (Fusion RR, Yukon R, A4177G3RIB, DKC 23-17RIB and DKC 26-28RIB) were laid out in a randomized complete block design in factorial settings with three replications. Results showed that P1 treatment increased acid phosphatase (AP-ase) activity (29% and 44%), and soil available P (SAP) (60% and 39%) compared to control treatment, during 2016 and 2017, respectively. Additionally, P1 treatments significantly increased total bacterial phospholipids fatty acids (ΣB-PLFA), total phospholipids fatty acids (ΣPLFA), fungi, and eukaryotes compared to control and inorganic P. Yukon R and DKC 26-28RIB genotypes exhibited higher total bacterial PLFA, fungi, and total PLFA in their rhizospheres compared to the other genotypes. Redundancy analyses showed promising association between P1 and P2 amendment, biochemical attributes and active microbial population and Yukon R and DKC 26-28RIB genotypes. Pearson correlation also demonstrated significant and positive correlation between AP-ase, SAP and gram negative bacteria (G−), fungi, ΣB-PLFA, and total PLFA. Study results demonstrated that P1 treatment enhanced biochemical attributes, active microbial community composition and abundance and forage production of silage corn. Results further demonstrated higher active microbial population and abundance in rhizosphere of Yukon R and DKC 26-28RIB genotypes. Therefore, we argue that dairy manure amendment with high P2O5 in podzol soils could be a sustainable nutrient source to enhance soil quality, health and forage production of silage corn. Yukon R and DKC 26-28RIB genotypes showed superior agronomic performance, therefore, could be good fit under boreal climatic conditions.
Transcriptional profiling reveals differentially expressed genes involved in lipid biosynthesis during cacao seed development
Authors: Li Fupeng , Wu Baoduo , Yan Lin , Hao Chaoyun , Qin Xiaowei , Lai Jianxiong , Song Yinghui 
Published: November 2019

AbstractTheobroma cacao is a plant of economic value due to the use of its seed lipid for chocolate, confectionery, and cosmetic industries. The seed lipid contains a stable ratio of saturated and unsaturated fatty acids, which determines its unique melting temperature. However, little is known about the molecular mechanism determining the fatty acid ratio and lipid content in cacao. To gain insight into the unique properties of lipid synthesis in cacao, biochemical and transcriptomic approaches were used to compare the lipid accumulation between high and low lipid content cacao accessions. Lipid accumulation rates and lipid content were different between the two accessions. Moreover, differentially expressed genes were detected between high and low lipid content cacao accessions. The data allowed the identification of distinct candidate genes and furthered our understanding of lipid accumulation, potentially explaining the differences in lipid content between various cacao accessions. The results might be used to develop molecular tools and engineer alternative pathways for cacao breeding with improved lipid production potentials.
Targeting bromodomain-containing proteins to prevent spontaneous preterm birth
Authors: Lim Ratana , Nguyen-Ngo Caitlyn , Lappas Martha 
Published: November 2019

Abstract
Preterm birth is a global healthcare challenge. Spontaneous preterm birth (sPTB) is commonly caused by inflammation, yet there are currently no effective therapies available. The Bromodomain and Extra-Terminal motif (BET) proteins, Bromodomain-containing protein (Brd) 2 (Brd2), Brd3 and Brd4 regulate inflammation in non-gestational tissues. The roles of Brd2–4 in human pregnancy are unknown.
Using human and mouse models, the present study has identified the Brd proteins part of the process by which inflammation induces parturition. Using human clinical samples, we demonstrate that labor and infection increase the expression of Brds in the uterus and fetal membranes. In primary human myometrial, amnion and decidual cells, we found that global Brd protein inhibition, as well as selective inhibition of Brds, suppressed inflammation-induced expression of mediators involved in myometrial contractions and rupture of fetal membranes. Importantly, studies in the mouse model demonstrate that the pan-Brd inhibitor JQ1 reduced intrauterine inflammation induced by bacterial endotoxin LPS as well as decreasing the effectiveness of LPS to induce parturition. These results implicate BET proteins as novel therapeutic targets for reducing inflammation associated with spontaneous preterm labor.
Crystallization of the outer crust of a non-accreting neutron star
Authors: Fantina A. F. , De Ridder S. , Chamel N. , Gulminelli F. 
Published: November 2019

Context. The interior of a neutron star is usually assumed to be made of cold catalyzed matter. However, the outer layers are unlikely to remain in full thermodynamic equilibrium during the formation of the star and its subsequent cooling, especially after crystallization occurs.
Aims. We study the cooling and the equilibrium composition of the outer layers of a non-accreting neutron star down to crystallization. Here the impurity parameter, generally taken as a free parameter in cooling simulations, is calculated self-consistently using a microscopic nuclear model for which a unified equation of state has recently been determined.
Methods. We follow the evolution of the nuclear distributions of the multi-component Coulomb liquid plasma fully self-consistently, adapting a general formalism originally developed for the description of supernova cores. We calculate the impurity parameter at the crystallization temperature as determined in the one-component plasma approximation.
Results. Our analysis shows that the sharp changes in composition obtained in the one-component plasma approximation are smoothed out when a full nuclear distribution is allowed. The Coulomb coupling parameter at melting is found to be reasonably close to the canonical value of 175, except for specific values of the pressure for which supercooling occurs in the one-component plasma approximation. Our multi-component treatment leads to non-monotonic variations of the impurity parameter with pressure. Its values can change by several orders of magnitude reaching about 50, suggesting that the crust may be composed of an alternation of pure (highly conductive) and impure (highly resistive) layers. The results presented here complement the recent unified equation of state obtained within the same nuclear model.
Conclusions. Our self-consistent approach to hot dense multi-component plasma shows that the presence of impurities in the outer crust of a neutron star is non-negligible and may have a sizeable impact on transport properties. In turn, this may have important implications not only for the cooling of neutron stars, but also for their magneto-rotational evolution.
Nicht-okklusive Mesenterialischämie bei diabetischem Koma
Authors: Hohmann Christian , Teuteberg Saskia , Aschenbrenner Ina , Kaag Norbert , Heizmann Oleg 
Published: November 2019

Zusammenfassung
Anamnese Eine 67-jährige Frau wurde entkleidet im Badezimmer vorgefunden. Es bestand eine Liegedauer von min. 12 Stunden. Wesentliche Vorerkrankungen waren ein insulinpflichtiger Diabetes mellitus Typ 2 und eine Nekrose-bedingte Coecalpolresektion.
Untersuchungen Die sarkopene Patientin war hypoton (60/40 mmHg) und hypotherm (29 °C), die Darmgeräusche spärlich. Es bestanden eine schwere metabolische Azidose (pH 6,7) sowie eine Hyperglykämie. Ketonkörper waren im Urin stark erhöht. Sonografische Luftreflexe im Leberparenchym veranlassten uns zum CT, hier zeigte sich eine akute Mesenterialischämie (AMI) mit Pneumatosis intestinalis und portal-venösem Gas.
Therapie und Verlauf In explorativer Laparotomie wurden infarzierter Dünndarm sowie Rest-Ileum und -Hemikolon rechts am Folgetag reseziert. Histopathologisch bestand kein Anhalt für eine okklusive Genese.
Folgerung Die Klinik der AMI ist mannigfaltig – mit meist letalen Folgen bei Diagnoseverzögerung. Serumparameter sind häufig überschätzt. In der Kasuistik war das diabetische Koma verantwortlich für die AMI. Wegweisend war die sonografische Darstellung von portal-venösem Gas, sodass zeitnah die lebensrettende Operation erfolgen konnte. Ein Ultraschall sollte daher Bestandteil der initialen Untersuchung von kritisch kranken Patienten sein.
Management of Status Epilepticus
Authors: Lamsal Ritesh , Bista Navindra R. 
Published: November 2019

AbstractStatus epilepticus (SE) is a life-threatening neurologic condition that requires immediate assessment and intervention. Over the past few decades, the duration of seizure required to define status epilepticus has shortened, reflecting the need to start therapy without the slightest delay. The focus of this review is on the management of convulsive and nonconvulsive status epilepticus in critically ill patients. Initial treatment of both forms of status epilepticus includes immediate assessment and stabilization, and administration of rapidly acting benzodiazepine therapy followed by nonbenzodiazepine antiepileptic drug. Refractory and super-refractory status epilepticus (RSE and SRSE) pose a lot of therapeutic problems, necessitating the administration of continuous infusion of high doses of anesthetic agents, and carry a high risk of debilitating morbidity as well as mortality.
Pre-Liver Transplantation Evaluation and Listing
Authors: Pan Alexander , Koppe Sean 
Published: November 2019

AbstractLiver transplantation provides a curative treatment option for patients with both acute and chronic liver disease, but the decision to list a patient for transplant should be an informed one to maximize post-transplantation benefit and survivability. Potential candidates meeting transplantation indications must undergo a comprehensive evaluation consisting of both physical, as well as psychiatric, assessment to be considered for transplantation. Once listed, a candidate's place on the liver transplant waiting list is determined predominantly by his or her Model for End-Stage Liver Disease (MELD)-Na score, which is a reliable tool to stratify short-term survival risk. The severity of certain conditions, however, is not accurately reflected by the MELD-Na score, and these particular diagnoses may be assigned MELD exception points. Herein, we discuss common indications for liver transplantation: the MELD system and its exceptions, the physical and psychosocial evaluation of potential transplant candidates, and some limitations of the current organ allocation system and efforts to reduce disparity in organ distribution.