bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning
Authors: Wang Daqi , Zhang Chengdong , Wang Bei , Li Bin , Wang Qiang , Liu Dong , Wang Hongyan , Zhou Yan , Shi Leming , Lan Feng , Wang Yongming 
Published: September 2019

AbstractHighly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/.
Src inhibition attenuates polyglutamine-mediated neuromuscular degeneration in spinal and bulbar muscular atrophy
Authors: Iida Madoka , Sahashi Kentaro , Kondo Naohide , Nakatsuji Hideaki , Tohnai Genki , Tsutsumi Yutaka , Noda Seiya , Murakami Ayuka , Onodera Kazunari , Okada Yohei , Nakatochi Masahiro , Tsukagoshi Okabe Yuka , Shimizu Shinobu , Mizuno Masaaki , Adachi Hiroaki , Okano Hideyuki , Sobue Gen , Katsuno Masahisa 
Published: September 2019

AbstractSpinal and bulbar muscular atrophy (SBMA) is a neuromuscular disease caused by an expanded CAG repeat in the androgen receptor (AR) gene. Here, we perform a comprehensive analysis of signaling pathways in a mouse model of SBMA (AR-97Q mice) utilizing a phosphoprotein assay. We measure the levels of 17 phosphorylated proteins in spinal cord and skeletal muscle of AR-97Q mice at three stages. The level of phosphorylated Src (p-Src) is markedly increased in the spinal cords and skeletal muscles of AR-97Q mice prior to the onset. Intraperitoneal administration of a Src kinase inhibitor improves the behavioral and histopathological phenotypes of the transgenic mice. We identify p130Cas as an effector molecule of Src and show that the phosphorylated p130Cas is elevated in murine and cellular models of SBMA. These results suggest that Src kinase inhibition is a potential therapy for SBMA.
Expert-level Automated Biomarker Identification in Optical Coherence Tomography Scans
Authors: Kurmann Thomas , Yu Siqing , Márquez-Neila Pablo , Ebneter Andreas , Zinkernagel Martin , Munk Marion R. , Wolf Sebastian , Sznitman Raphael 
Published: September 2019

AbstractIn ophthalmology, retinal biological markers, or biomarkers, play a critical role in the management of chronic eye conditions and in the development of new therapeutics. While many imaging technologies used today can visualize these, Optical Coherence Tomography (OCT) is often the tool of choice due to its ability to image retinal structures in three dimensions at micrometer resolution. But with widespread use in clinical routine, and growing prevalence in chronic retinal conditions, the quantity of scans acquired worldwide is surpassing the capacity of retinal specialists to inspect these in meaningful ways. Instead, automated analysis of scans using machine learning algorithms provide a cost effective and reliable alternative to assist ophthalmologists in clinical routine and research. We present a machine learning method capable of consistently identifying a wide range of common retinal biomarkers from OCT scans. Our approach avoids the need for costly segmentation annotations and allows scans to be characterized by biomarker distributions. These can then be used to classify scans based on their underlying pathology in a device-independent way.
Disease control efficacy of 32,33-didehydroroflamycoin produced by Streptomyces rectiviolaceus strain DY46 against gray mold of tomato fruit
Authors: Kim Jeong Do , Park Min Young , Jeon Byeong Jun , Kim Beom Seok 
Published: September 2019

AbstractDespite the efficacy of synthetic fungicides in controlling postharvest diseases, public concerns regarding chemical residues in food and an increase in drug-resistant strains of pathogens have led to a need for new agents to control postharvest diseases. The current study was performed to find control agents of microbial origin that are effective on gray mold of tomato fruits. We recently isolated Streptomyces rectiviolaceus DY46, which has antagonistic activity against various plant pathogenic fungi. The incidence of gray mold of tomato fruits was markedly reduced by 80.0% in tomatoes treated with the cell extract of Streptomyces rectiviolaceus DY46 compared with the control tomatoes. The active ingredient was purified from the cell extract of DY46 and identified to be 32,33-didehydroroflamycoin (DDHR). DDHR displayed MICs (minimal inhibitory concentrations) against the mycelial growth of various plant pathogenic fungi at concentrations of 8–64 mg L−1. The incidence of gray mold in tomato fruits inoculated with conidial suspension (104 conidia mL−1) of Botrytis cinerea was markedly reduced by 88.9% in tomatoes treated with DDHR (100 mg L−1) compared with the control. The DDHR residue in tomato fruit was significantly diminished 2 d after treatment. These results show that DDHR would be relatively safe for use as a postharvest fungicide.
The importance of coastal gorgonians in the blue carbon budget
Authors: Coppari Martina , Zanella Chiara , Rossi Sergio 
Published: September 2019

AbstractTerrestrial (trees, shrubs) and marine (seaweeds and seagrasses) organisms act as carbon (C) sinks, but the role of benthic suspension feeders in this regard has been largely neglected so far. Gorgonians are one of the most conspicuous inhabitants of marine animal forests (mainly composed of sessile filter feeders); their seston capture rates influence benthic-pelagic coupling processes and they act as C sinks immobilizing carbon in their long-living structures. Three gorgonian species (Paramuricea clavata, Eunicella singularis and Leptogorgia sarmentosa) were studied coupling data of population size structure, biomass and spatial distribution in a NW Mediterranean area (Cap de Creus, Spain) with feeding, respiration and growth rates. In the study area, we calculated that P. clavata sequestered 0.73 ± 0.71 g C m−2 year−1, E. singularis 0.73 ± 0.89 g C m−2 year−1 and L. sarmentosa 0.03 ± 0.02 g C m−2 year−1. To our knowledge, this is the first attempt to calculate the importance as C sinks of gorgonian species that we consider as a starting point to estimate the importance of marine animal forests in C sequestration, and to ensure appropriate management and protection especially in areas and at depths where they are concentrated.
Statin use and the risk of colorectal cancer in a population-based electronic health records study
Authors: Ibáñez-Sanz Gemma , Guinó Elisabet , Pontes Caridad , Quijada-Manuitt Mª Ángeles , de la Peña-Negro Luisa C , Aragón María , Domínguez Marga , Rodríguez-Alonso Lorena , Blasco Alex , García-Rodríguez Ana , Morros Rosa , Moreno Victor 
Published: September 2019

AbstractThere is extensive debate regarding the protective effect of 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors (statins) on colorectal cancer (CRC). We aimed to assess the association between CRC risk and exposure to statins using a large cohort with prescription data. We carried out a case-control study in Catalonia using the System for Development of Primary Care Research (SIDIAP) database that recorded patient diseases history and linked data on reimbursed medication. The study included 25 811 cases with an incident diagnosis of CRC between 2010 and 2015 and 129 117 frequency-matched controls. Subjects were classified as exposed to statins if they had ever been dispensed statins. Analysis considering mean daily defined dose, cumulative duration and type of statin were performed. Overall, 66 372 subjects (43%) were exposed to statins. There was no significant decrease of CRC risk associated to any statin exposure (OR = 0.98; 95% CI: 0.95–1.01). Only in the stratified analysis by location a reduction of risk for rectal cancer was observed associated to statin exposure (OR = 0.87; 95% CI: 0.81–0.92). This study does not support an overall protective effect of statins in CRC, but a protective association with rectal cancer merits further research.
Random transposon insertion in the Mycoplasma hominis minimal genome
Authors: Rideau Fabien , Le Roy Chloé , Sagné Eveline , Renaudin Hélène , Pereyre Sabine , Henrich Birgit , Dordet-Frisoni Emilie , Citti Christine , Lartigue Carole , Bébéar Cécile 
Published: September 2019

AbstractMycoplasma hominis is an opportunistic human pathogen associated with genital and neonatal infections. Until this study, the lack of a reliable transformation method for the genetic manipulation of M. hominis hindered the investigation of the pathogenicity and the peculiar arginine-based metabolism of this bacterium. A genomic analysis of 20 different M. hominis strains revealed a number of putative restriction-modification systems in this species. Despite the presence of these systems, a reproducible polyethylene glycol (PEG)-mediated transformation protocol was successfully developed in this study for three different strains: two clinical isolates and the M132 reference strain. Transformants were generated by transposon mutagenesis with an efficiency of approximately 10−9 transformants/cell/µg plasmid and were shown to carry single or multiple mini-transposons randomly inserted within their genomes. One M132-mutant was observed to carry a single-copy transposon inserted within the gene encoding P75, a protein potentially involved in adhesion. However, no difference in adhesion was observed in cell-assays between this mutant and the M132 parent strain. Whole genome sequencing of mutants carrying multiple copies of the transposon further revealed the occurrence of genomic rearrangements. Overall, this is the first time that genetically modified strains of M. hominis have been obtained by random mutagenesis using a mini-transposon conferring resistance to tetracycline.
Fruit fly identification, population dynamics and fruit damage during fruiting seasons of sweet oranges in Rusitu Valley, Zimbabwe
Authors: Musasa Stephen T. , Mashingaidze Arnold B. , Musundire Robert , Aguiar Ana A. R. M. , Vieira Jorge , Vieira Cristina P. 
Published: September 2019

AbstractIn 2003, the pest speciesBactrocera dorsalis(Hendel) was reported for the first time in Kenya, Africa, and subsequently on many other African countries. In this work, 20 locations along the Rusitu Valley (Zimbabwe) were sampled in 2014 during the sweet oranges fruiting seasons, to verify the fruit fly taxonomy, invasion source, population dynamics, and fruit damage. The trapped fruit flies were identified using morphological traits and molecular techniques, asB. dorsalis. The haplotype network analysis revealed that ZimbabweCOIsequences were identical to other AfricanB. dorsalissequences. Fruit fly trappings per day varied during the year, although it remained always high. The same applies to fruit damage, most likely due to the permanent availability of cultivated and wild fruit varieties during the year. Rusitu Valley was invaded byB. dorsalis, most likely from neighbouring countries. Ten years after the first report in Kenya, the complete or near complete invasion of Africa has been achieved byB. dorsalis. In northern Africa the distribution is clearly limited by the Sahara desert. The large population size, the polyphagous nature of the species, and the continuous availability of suitable host fruit species during the year complicates the eradication of this species.
18F-Labeled Cyclized α-Melanocyte-Stimulating Hormone Derivatives for Imaging Human Melanoma Xenograft with Positron Emission Tomography
Authors: Zhang Chengcheng , Zhang Zhengxing , Merkens Helen , Zeisler Jutta , Colpo Nadine , Hundal-Jabal Navjit , Perrin David M. , Lin Kuo-Shyan , Bénard François 
Published: September 2019

AbstractSince metastatic melanoma is deadly, early diagnosis thereof is crucial for managing the disease. We recently developed α-melanocyte-stimulating hormone (αMSH) derivatives, [68Ga]Ga-CCZ01048 and [18F]CCZ01064, that target the melanocortin 1 receptor (MC1R) for mouse melanoma imaging. In this study, we aim to evaluate [18F]CCZ01064 as well as a novel dual-ammoniomethyl-trifluoroborate (AmBF3) derivative, [18F]CCZ01096, for targeting human melanoma xenograft using μPET imaging. The peptides were synthesized on solid phase using Fmoc chemistry. Radiolabeling was achieved in a one-step 18F-19F isotope-exchange reaction. μPET imaging and biodistribution studies were performed in NSG mice bearing SK-MEL-1 melanoma xenografts. The MC1R density on the SK-MEL-1 cell line was determined to be 972 ± 154 receptors/cell (n = 4) via saturation assays. Using [18F]CCZ01064, moderate tumor uptake (3.05 ± 0.47%ID/g) and image contrast were observed at 2 h post-injection. Molar activity was determined to play a key role. CCZ01096 with two AmBF3 motifs showed comparable sub-nanomolar binding affinity to MC1R and much higher molar activity. This resulted in improved tumor uptake (6.46 ± 1.42%ID/g) and image contrast (tumor-to-blood and tumor-to-muscle ratios were 30.6 ± 5.7 and 85.7 ± 11.3, respectively) at 2 h post-injection. [18F]CCZ01096 represents a promising αMSH-based μPET imaging agent for human melanoma and warrants further investigation for potential clinical translation.
Amyloid β-Induced Upregulation of Nav1.6 Underlies Neuronal Hyperactivity in Tg2576 Alzheimer’s Disease Mouse Model
Authors: Ciccone Roselia , Franco Cristina , Piccialli Ilaria , Boscia Francesca , Casamassa Antonella , de Rosa Valeria , Cepparulo Pasquale , Cataldi Mauro , Annunziato Lucio , Pannaccione Anna 
Published: September 2019

AbstractHyperexcitability and alterations in neuronal networks contribute to cognitive impairment in Alzheimer’s Disease (AD). Voltage-gated sodium channels (NaV), which are crucial for regulating neuronal excitability, have been implicated in AD-related hippocampal hyperactivity and higher incidence of spontaneous non-convulsive seizures. Here, we show by using primary hippocampal neurons exposed to amyloid-β1–42 (Aβ1–42) oligomers and from Tg2576 mouse embryos, that the selective upregulation of NaV1.6 subtype contributes to membrane depolarization and to the increase of spike frequency, thereby resulting in neuronal hyperexcitability. Interestingly, we also found that NaV1.6 overexpression is responsible for the aberrant neuronal activity observed in hippocampal slices from 3-month-old Tg2576 mice. These findings identify the NaV1.6 channels as a determinant of the hippocampal neuronal hyperexcitability induced by Aβ1–42 oligomers. The selective blockade of NaV1.6 overexpression and/or hyperactivity might therefore offer a new potential therapeutic approach to counteract early hippocampal hyperexcitability and subsequent cognitive deficits in the early stages of AD.
An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder
Authors: Majewski Maciej , Ruiz-Carmona Sergio , Barril Xavier 
Published: September 2019

AbstractThe predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. However, structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, it entails an entropic penalty that counters complex formation. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Since hydrogen bonds have been described as essential for structural stability, here we investigate 469 such interactions across two diverse structure sets, comprising of 79 drug-like and 27 fragment ligands, respectively. Completely constricted protein-ligand complexes are rare and may fulfill a functional role. Most complexes balance order and disorder by combining a single anchoring point with looser regions. 25% do not contain any robust hydrogen bond and may form loose structures. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
Topologically stable helices in exchange coupled rare-earth/rare-earth multilayer with superspin-glass like ordering
Authors: Ye Jingfan , Baldauf Thomas , Mattauch Stefan , Paul Neelima , Paul Amitesh 
Published: September 2019

AbstractExistence of 2π-planar domain walls (DWs) are often reported for transition metal-rare-earth (TM/RE) layered systems. The magnetization process of such two-dimensional randomly anisotropical system in the form of 2π-DWs is directly correlated with topologically stable helices. Here, instead of TM/RE, we have investigated [Dy/Tb]10 multilayers involving two different anisotropic layers of rare-earth/rare-earth (RE/RE). Using magnetization and susceptibility as function of temperature along with thermo-remanent magnetization measurements we have confirmed superspin-glass type of behavior within this RE/RE system. Additionally, an exchange bias field up to –0.88 kOe (–88 mT) was also revealed for such rare-earth based multilayers. Interestingly, using detailed analysis of the polarized neutron reflectometry profiles, we find evidences of superimposed helical magnetic configurations within both materials of Dy and Tb associated with spin-frustrated interfaces. Furthermore, magnetization fluctuations around the mean magnetization from vertically uncorrelated domains were observed with polarized off-specular neutron scattering. We believe that coexistence of helical ground states with superspin-glass-like ordering are fundamentally instrumental for topologically stability in RE/RE systems, which in principle, can be exploited in all-spin-based technology.
A candidate activation pathway for coagulation factor VII
Authors: Misenheimer Tina M. , Kumfer Kraig T. , Bates Barbara E. , Nettesheim Emily R. , Schwartz Bradford S. 
Published: September 2019

Abstract
The mechanism of generation of factor VIIa, considered the initiating protease in the tissue factor-initiated extrinsic limb of blood coagulation, is obscure. Decreased levels of plasma VIIa in individuals with congenital factor IX deficiency suggest that generation of VIIa is dependent on an activation product of factor IX. Factor VIIa activates IX to IXa by a two-step removal of the activation peptide with cleavages occurring after R191 and R226. Factor IXaα, however, is IX cleaved only after R226, and not after R191. We tested the hypothesis that IXaα activates VII with mutant IX that could be cleaved only at R226 and thus generate only IXaα upon activation. Factor IXaα demonstrated 1.6% the coagulant activity of IXa in a contact activation-based assay of the intrinsic activation limb and was less efficient than IXa at activating factor X in the presence of factor VIIIa. However, IXaα and IXa had indistinguishable amidolytic activity, and, strikingly, both catalyzed the cleavage required to convert VII to VIIa with indistinguishable kinetic parameters that were augmented by phospholipids, but not by factor VIIIa or tissue factor. We propose that IXa and IXaα participate in a pathway of reciprocal activation of VII and IX that does not require a protein cofactor. Since both VIIa and activated IX are equally plausible as the initiating protease for the extrinsic limb of blood coagulation, it might be appropriate to illustrate this key step of hemostasis as currently being unknown.
Leonurus cardiaca L., das Echte Herzgespann
Authors: Zhang Xinting , Melzig Matthias F 
Published: September 2019

Zusammenfassung
Leonurus cardiaca L. ist eine seit Langem genutzte europäische traditionelle Heilpflanze, die v. a. Terpene, Flavonoide, Stachydrin und das Pseudoalkaloid Leonurin enthält. Zubereitungen aus der Arzneidroge besitzen sedative, blutdrucksenkende, antioxidative bzw. entzündungshemmende Wirkungen. Ein therapeutischer Einsatz im Rahmen einer traditionellen Anwendung erfolgt bei nervösen Herzbeschwerden, Schilddrüsenüberfunktion und klimakterischen Beschwerden. Zurzeit gibt es nur unzureichende klinische Studien, und die den Wirkungen zugrundeliegenden Mechanismen sind noch nicht vollständig geklärt.
Zu den molekularbiologischen Grundlagen der antientzündlichen Wirkungen von Thymiankrautextrakt, Thymus vulgaris L. und Thymus zygis L., herba
Authors: Appel Kurt , Rose Thorsten , Collado Rojas Juan Antonio , Washausen Ute 
Published: September 2019

ZUsammenfassungBereits früher publizierte Daten zeigten günstige Effekte von Thymian bei entzündlichen Prozessen. Um diese Erkenntnisse zu vertiefen, wurde in verschiedenen experimentellen Modellen ein Thymianextrakt auf die hier zugrundeliegenden molekularbiologischen Mechanismen in vitro untersucht. Nachgewiesen wurde eine Hemmung der LPS-induzierten Zytokin-Freisetzung von IL-1β, PGE2 sowie TNF-α in humanen Monozyten, eine Hemmung der LPS-induzierten Phosphorylierung und eine Aktivierung von IκBα sowie eine Inhibition der Transkriptionsaktivität von NF-κB und AP-1 in der Bronchialepithel-Zelllinie A549. Ein weiterer interessanter Befund war eine antagonistische Aktivität des untersuchten Thymianextraktes am TRPA1-Rezeptor, ein Rezeptor, der Hustenreize vermitteln kann. Die Anwendung des Thymianextraktes bei Erkältungs- bzw. Bronchitis-bedingtem Husten, bei dem entzündliche Prozesse auf bzw. in der Schleimhaut involviert sind, darf daher als plausibel gelten.
Kalzium, Magnesium und Phosphat
Authors: Ketteler Markus 
Published: September 2019

ZUSAMMENFASSUNGWährend die Hyperkalzämie in allen Stadien der Niereninsuffizienz inkl. des Dialysestadiums als bedenklich eingeschätzt wird, werden milde und asymptomatische Hypokalzämien als zumeist tolerabel betrachtet, insbesondere wenn sie im Kontext einer Calcimimetika-Therapie auftreten. Hypomagnesiämien sind bei Dialysepatienten mit erhöhtem Mortalitäts- und Frakturrisiko assoziiert – eindeutige Empfehlungen zu Magnesium-Zielbereichen bzw. zur Dosierung von Supplementationen lassen sich allerdings auf dem Boden der derzeitigen Datenlage noch nicht machen. Die Hyperphosphatämie als Mortalitätsrisikofaktor bei Dialysepatienten wird durch weitere aktuelle Studien bestätigt – interessanterweise existieren nun erste Hinweise, dass eine hohe Phosphat-Zufuhr auch eine Hypertonieentwicklung begünstigen kann.