bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman
Authors: Abed Raeid M. M. , Tamm Alexandra , Hassenrück Christiane , Al-Rawahi Ahmed N. , Rodríguez-Caballero Emilio , Fiedler Sabine , Maier Stefanie , Weber Bettina 
Published: April 2019

AbstractBiological soil crusts (biocrusts) occur within drylands throughout the world, covering ~12% of the global terrestrial soil surface. Their occurrence in the deserts of the Arabian Peninsula has rarely been reported and their spatial distribution, diversity, and microbial composition remained largely unexplored. We investigated biocrusts at six different locations in the coastal and central deserts of Oman. The biocrust types were characterized, and the bacterial and fungal community compositions of biocrusts and uncrusted soils were analysed by amplicon sequencing. The results were interpreted based on the environmental parameters of the different sites. Whereas at lowland sites, mainly cyanobacteria-dominated biocrusts were observed, both cyanobacteria- and lichen-dominated biocrusts occurred at mountain sites. The majority of bacterial sequences (32–83% of total sequences) belonged to Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes, whereas fungal sequences belonged to Ascomycota, Basidiomycota, and Chytridiomycota (>95%). With biocrust development, a notable increase in cyanobacterial and decrease in actinobacterial proportions was observed for cyanobacteria-dominated crusts. In coastal areas, where salinity is high, biocrusts were replaced by a unique marine mat-like microbial community, dominated by halotolerant taxa. Redundancy analysis revealed a significant contribution of soil texture, cover type, carbon content, and elevation to the variations in bacterial and fungal communities. Multivariate analysis placed microbial communities in significantly separated clusters based on their carbon content, elevation and electrical conductivity. We conclude that Oman hosts a variety of cyanobacteria- and lichen-dominated crusts with their bacterial and fungal communities being largely dictated by soil properties and environmental parameters.
Binding studies of a putative C. pseudotuberculosis target protein from Vitamin B12 Metabolism
Authors: Peinado Rafaela dos S. , Olivier Danilo S. , Eberle Raphael J. , de Moraes Fabio R. , Amaral Marcos S. , Arni Raghuvir K. , Coronado Monika A. 
Published: April 2019

AbstractVitamin B12 acts as a cofactor for various metabolic reactions important in living organisms. The Vitamin B12 biosynthesis is restricted to prokaryotes, which means, all eukaryotic organisms must acquire this molecule through diet. This study presents the investigation of Vitamin B12 metabolism and the characterization of precorrin-4 C(11)-methyltransferase (CobM), an enzyme involved in the biosynthesis of Vitamin B12 in Corynebacterium pseudotuberculosis. The analysis of the C. pseudotuberculosis genome identified two Vitamin B12-dependent pathways, which can be strongly affected by a disrupted vitamin metabolism. Molecular dynamics, circular dichroism, and NMR-STD experiments identified regions in CobM that undergo conformational changes after s-adenosyl-L-methionine binding to promote the interaction of precorrin-4, a Vitamin B12 precursor. The binding of s-adenosyl-L-methionine was examined along with the competitive binding of adenine, dATP, and suramin. Based on fluorescence spectroscopy experiments the dissociation constant for the four ligands and the target protein could be determined; SAM (1.4 ± 0.7 µM), adenine (17.8 ± 1.5 µM), dATP (15.8 ± 2.0 µM), and Suramin (6.3 ± 1.1 µM). The results provide rich information for future investigations of potential drug targets within the C. pseudotuberculosis’s Vitamin B12 metabolism and related pathways to reduce the pathogen’s virulence in its hosts.
The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival
Authors: Zhang Jing , Caruso Francesca P. , Sa Jason K. , Justesen Sune , Nam Do-Hyun , Sims Peter , Ceccarelli Michele , Lasorella Anna , Iavarone Antonio 
Published: April 2019

AbstractGlioblastoma (GBM) is resistant to multimodality therapeutic approaches. A high burden of tumor-specific mutant peptides (neoantigens) correlates with better survival and response to immunotherapies in selected solid tumors but how neoantigens impact clinical outcome in GBM remains unclear. Here, we exploit the similarity between tumor neoantigens and infectious disease-derived immune epitopes and apply a neoantigen fitness model for identifying high-quality neoantigens in a human pan-glioma dataset. We find that the neoantigen quality fitness model stratifies GBM patients with more favorable clinical outcome and, together with CD8+ T lymphocytes tumor infiltration, identifies a GBM subgroup with the longest survival, which displays distinct genomic and transcriptomic features. Conversely, neither tumor neoantigen burden from a quantitative model nor the isolated enrichment of CD8+ T lymphocytes were able to predict survival of GBM patients. This approach may guide optimal stratification of GBM patients for maximum response to immunotherapy.
Exploring and mapping the universe of evolutionary graphs identifies structural properties affecting fixation probability and time
Authors: Möller Marius , Hindersin Laura , Traulsen Arne 
Published: April 2019

AbstractPopulation structure can be modeled by evolutionary graphs, which can have a substantial influence on the fate of mutants. Individuals are located on the nodes of these graphs, competing to take over the graph via the links. Applications for this framework range from the ecology of river systems and cancer initiation in colonic crypts to biotechnological search for optimal mutations. In all these applications, both the probability of fixation and the associated time are of interest. We study this problem for all undirected and unweighted graphs up to a certain size. We devise a genetic algorithm to find graphs with high or low fixation probability and short or long fixation time and study their structure searching for common themes. Our work unravels structural properties that maximize or minimize fixation probability and time, which allows us to contribute to a first map of the universe of evolutionary graphs.
Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds
Authors: Yuan Shuguang , Dahoun Thamani , Brugarolas Marc , Pick Horst , Filipek Slawomir , Vogel Horst 
Published: April 2019

AbstractThe mammalian olfactory system uses hundreds of specialized G-protein-coupled olfactory receptors (ORs) to discriminate a nearly unlimited number of odorants. Cognate agonists of most ORs have not yet been identified and potential non-olfactory processes mediated by ORs are unknown. Here, we used molecular modeling, fingerprint interaction analysis and molecular dynamics simulations to show that the binding pocket of the prototypical olfactory receptor Olfr73 is smaller, but more flexible, than binding pockets of typical non-olfactory G-protein-coupled receptors. We extended our modeling to virtual screening of a library of 1.6 million compounds against Olfr73. Our screen predicted 25 Olfr73 agonists beyond traditional odorants, of which 17 compounds, some with therapeutic potential, were validated in cell-based assays. Our modeling suggests a molecular basis for reduced interaction contacts between an odorant and its OR and thus the typical low potency of OR-activating compounds. These results provide a proof-of-principle for identifying novel therapeutic OR agonists.
EPAS 1, congenital heart disease, and high altitude: disclosures by genetics, bioinformatics, and experimental embryology
Authors: Sergi Consolato 
Published: April 2019

AbstractThe high-altitude environment is a challenge for human settlement. Low oxygen concentrations, extreme cold, and a harsh arid climate are doubtlessly challenges for the colonization of the Tibetan plateau. I am delighted to comment on the article of Pan et al. (2018) on mutations in endothelial PAS domain-containing protein 1 (EPAS1) in congenital heart disease in Tibetans. In humans, the EPAS1 gene is responsible for coding EPAS1 protein, an alias of which is HIF2α, an acronym for hypoxia-inducible factor 2 alpha. EPAS1 is a type of hypoxia-inducible factors, which are collected as a group of transcription factors involved in body response to oxygen level. EPAS1 gene is active under hypoxic conditions and plays an essential role in the development of the heart and in the management of the catecholamine balance, mutations of which have been identified in neuroendocrine tumors. In this article, Pan et al. investigated Tibetan patients with and without non-syndromic congenital heart disease. They identified two novel EPAS1 gene mutations, of which N203H mutation significantly affected the transcription activity of the vascular endothelial growth factor (VEGF) promoter, particularly in situations of hypoxia. VEGF is a downstream target of HIF-2 (other than HIF-1), and the expression levels of either HIF-1α or HIF-2α correlate positively to VEGF expression. Pan et al.’s data may be of incitement to further evaluate protein–protein interaction and using experimental animal models. Moreover, it may also be a stimulus for setting up genetic epidemiologic studies for other populations living at high altitudes.
Punicalagin protects H9c2 cardiomyocytes from doxorubicin-induced toxicity through activation of Nrf2/HO-1 signaling
Authors: Ye Mingfang , Zhang Linlin , Yan Yuanming , Lin Huizhong 
Published: April 2019

Abstract
Doxorubicin (DOX) is a wide-spectrum antitumor agent, but its clinical application is largely limited by its cardiotoxicity. Therefore, identification of effective agents against DOX-induced cardiotoxicity is of critical importance. The present study aimed to determine the beneficial role of punicalagin (PUN), a polyphenol isolated from pomegranate, in DOX-induced cardiotoxicity in vitro and explored the underlying mechanisms. H9c2 cardiomyocytes were pretreated with different concentrations (50, 100 and 200 μM) of PUN prior to DOX exposure. The results showed that PUN pretreatment significantly increased cell viability, inhibited lactate dehydrogenase (LDH) release and suppressed cell apoptosis induced by DOX. Additionally, PUN pretreatment attenuated the loss of mitochondrial membrane potential and cytochrome c release. Besides, PUN further enhanced the expression of nuclear Nrf2 and HO-1 in DOX-treated H9c2 cells, and the aforementioned beneficial effects of PUN were partially abolished by small interfering RNA (siRNA)-mediated Nrf2 knockdown. Hence, our findings clearly revealed that PUN might be a promising agent for alleviating the cardiotoxicity of DOX, and Nrf2/HO-1 signaling might serve a critical role during this process.
The nucleosomes that mark centromere location on chromosomes old and new
Authors: Gambogi Craig W. , Black Ben E. 
Published: April 2019

Abstract
Proper segregation of chromosomes is an essential component of cell division. The centromere is the locus at which the kinetochore—the proteinaceous complex that ties chromosomes to microtubules—forms during mitosis and meiosis. Thus, the centromere is critical for equal segregation of chromosomes. The centromere is characterized by both protein and DNA elements: the histone H3 variant CENP-A epigenetically defines the location of the centromere while centromeric DNA sequences are neither necessary nor sufficient for centromere function. Paradoxically, the DNA sequences play a critical role in new centromere formation. In this essay, we discuss the contribution of both epigenetics and genetics at the centromere. Understanding these contributions is vital to efforts to control centromere formation on synthetic/artificial chromosomes and centromere strength on natural ones.
Chirurgische Entfernung eines untypischen follikulären
Schilddrüsenkarzinoms bei einem Schlangenkopffisch (Channa barca,
HAMILTON, 1822)
Authors: Lange Christine , Fischer Dominik , Eskens Hans Ulrich , Wüst Elisa , Nilz Joachim , Lierz Michael 
Published: April 2019

ZusammenfassungZubildungen im Bereich der Kiemen können auf verschiedene Ursachen wie
entzündliche Prozesse, Neoplasien und selten auf dysontogenetische Missbildungen
zurückzuführen sein. Im vorliegenden Fall wird von einem Schilddrüsenkarzinom
und dessen operativer Entfernung bei einem Schlangenkopffisch berichtet und auf
die Einordnung dieser Neoplasie bei Fischen eingegangen. Nach Durchführung von
klinischen, röntgenologischen, zytologischen und sonografischen Untersuchungen
wurde die im Bereich der Kiemen befindliche teils zystische Umfangsvermehrung
unvollständig entfernt. Histologisch wurde die Zubildung als follikuläres
Schilddrüsenkarzinom identifiziert. Da der größte Anteil der Gewebszubildung
nicht neoplastischer Natur war, wird das Auftreten eines seltenen Hamartoms als
Ausgangspunkt des Schilddrüsenkarzinoms für möglich erachtet. Bakteriologische
und mykologische Sekundärinfektionen wurden nicht festgestellt. Dies ist der
erste Bericht über das Auftreten und die chirurgische Entfernung eines malignen
Tumors bei Schlangenkopffischen.
Current Insights into the Potential Misuse of Platelet-based Applications for Doping in Sports
Authors: Scully David , Matsakas Antonios 
Published: April 2019

AbstractPlatelet-based applications are currently used for the delivery of growth factors and other biomolecules as autologous biomaterials in regenerative medicine and cosmetic therapies. Many studies have revealed that platelet-based applications such as platelet-rich plasma and platelet releasate exhibit beneficial biological effects after a sports injury or trauma when administered locally by intramuscular injections. At present, treatment of the public, patients and athletes with platelet-based applications is permitted and regulated by the Food and Drug Administration and the World Anti-Doping Agency. Since 2011 the use of autologous platelet-rich plasma is permitted in competitive sports by the World Anti-Doping Agency, due to the lack of evidence in performance enhancement and anabolic effects. However, accumulating research has recently shed light on the role of platelet-derived growth factors in wound healing, skeletal myogenesis, muscle stem cell function and tissue regeneration. Although any ergogenic potential of platelet-rich plasma and platelet releasate on intact skeletal muscle and human sports performance remain to be established, novel evidence suggests that platelet-derived growth factors can modulate muscle, tendon, ligament, protein synthesis/degradation, vascularization, energy utilization and regenerative capacity in various experimental settings. Since platelet-based applications are currently not prohibited, they constitute a tool for potential abuse and doping in sports. The aim of this review is to critically discuss and assimilate current insights and biological evidence that set the ground for exploitation and misuse in competitive sports, and develop strategies to combat these activities.
Epicondylopathie Therapie myofaszialer Triggerpunkte
Authors: Irnich Dominik 
Published: April 2019

SummaryDie Epicondylopathie, medial und lateral, gehört zu den häufigsten Erkrankungen des Ellbogens. Der Verlauf ist oft langwierig, dabei ist die zugrundeliegende Pathophysiologie noch weitgehend ungeklärt. Die in der Praxis angewendeten Verfahren sind nicht langfristig evidenzbasiert, Therapiestandards existieren nicht. In diesem Beitrag wird eine häufig unterschätzte Pathologie bei Ellbogenbeschwerden vorgestellt, nämlich die Beteiligung myofaszialer Triggerpunkte an Entstehung und Aufrechterhaltung der Epicondylopathie. Es zeigt sich, dass insbesondere der M. supinator, der M. brachioradialis und der M. extensor carpi radialis longus mit dem M. extensor carpi radialis brevis myofasziale Triggerpunkte ausbilden können, die an den Epicondylus ausstrahlen. Werden diese nicht mit behandelt kann es zu therapieresistenten Beschwerden und unnötigen invasiven Maßnahmen kommen.
Thirty Years of Minimally Invasive Surgery in Children: Analysis of Meta-Analyses
Authors: Kuebler Joachim F. , Dingemann Jens , Ure Benno M. , Schukfeh Nagoud 
Published: April 2019

Abstract
Introduction In the last three decades, minimally invasive surgery (MIS) has been widely used in pediatric surgery. Meta-analyses (MAs) showed that studies comparing minimally invasive with the corresponding open operations are available only for selected procedures. We evaluated all available MAs comparing MIS with the corresponding open procedure in pediatric surgery.
Materials and Methods A literature search was performed on all MAs listed on PubMed. All analyses published in English, comparing pediatric minimally invasive with the corresponding open procedures, were included. End points were advantages and disadvantages of MIS. Results of 43 manuscripts were included. MAs evaluating the minimally invasive with the corresponding open procedures were available for 11 visceral, 4 urologic, and 3 thoracoscopic types of procedures. Studies included 34 randomized controlled trials. In 77% of MAs, at least one advantage of MIS was identified. The most common advantages of MIS were a shorter hospital stay in 20, a shorter time to feeding in 11, and a lower complication rate in 7 MAs. In 53% of MAs, at least one disadvantage of MIS was found. The most common disadvantages were longer operation duration in 16, a higher recurrence rate of diaphragmatic hernia in 4, and gastroesophageal reflux in 2 MAs. A lower native liver survival rate after laparoscopic Kasai-portoenterostomy was reported in one MA.
Conclusion In the available MAs, the advantages of MIS seem to outnumber the disadvantages. However, for some types of procedures, MIS may have considerable disadvantages. More randomized controlled trials are required to confirm the advantage of MIS for most procedures.
DNA methylation analysis and editing in single mammalian oocytes
Authors: Wei Yanchang , Lang Jingwen , Zhang Qian , Yang Cai-Rong , Zhao Zhen-Ao , Zhang Yixin , Du Yanzhi , Sun Yun 
Published: April 2019

Significance
Many mammalian nongenetic diseases and developmental disorders originate from oocyte DNA methylation abnormalities. However, prevention and correction of this maternally transmitted nongenetic disorder remains challenging because of the lack of strategy that can evaluate and manipulate specific methylation at single oocyte level. In this study, using several models of epigenetic inheritance via oocytes, we have shown that specific methylation in a single oocyte can be evaluated from its sibling PB1 and can be edited in a targeted manner. Our study provides a strategy for prevention and correction of maternally transmitted nongenetic diseases or disorders, and will also facilitate the investigation of maternally transmitted nongenetic information at the very beginning of life.
Gravitational instabilities in binary granular materials
Authors: McLaren Christopher P. , Kovar Thomas M. , Penn Alexander , Müller Christoph R. , Boyce Christopher M. 
Published: April 2019

SignificanceFlow of granular materials, such as sand and catalytic particles, is critical to a wide range of natural phenomena and industrial processes. However, the physics underlying granular flows is poorly understood. We report the discovery of gravitational instabilities in binary granular materials driven by a gas channeling mechanism unseen in fluids. A Rayleigh–Taylor instability analog is observed despite a lack of surface tension between grains, while a droplet branching phenomenon demonstrates a deviation from fluid motion due to solidification of particles. These discoveries shed light on granular dynamics and can potentially explain geological formations and enable process technologies.
Testing the deconditioning hypothesis of low back pain: A study in 1182 older women
Authors: Tagliaferri Scott D , Armbrecht Gabriele , Miller Clint T , Owen Patrick J , Mundell Niamh L , Felsenberg Dieter , Thomasius Friederike , Belavy Daniel L 
Published: April 2019

AbstractThis study assessed the deconditioning hypothesis of low back pain (LBP) by examining physical function in relation to LBP and self‐reported physical activity in women. This cross‐sectional study recruited a representative population‐based sample of females aged greater than 60 years. In total, 1182 women were included in the study and completed questionnaires (physical activity and LBP intensity) and functional testing (countermovement jump, chair rise, gait speed and grip strength). Individuals were stratified into four groups based on physical activity and LBP status and analysed via a two‐way ANOVA. Most participants (87%) reported current LBP and 25% were physically active. Countermovement jump height, chair rise and grip strength were lower in physically inactive women (p ≤ 0.005), but not women with LBP (p ≥ 0.21). Gait speed was not associated with physical activity or LBP status. There was no association between LBP and physical activity status. Whilst LBP was associated with lower physical activity, contrary to the deconditioning hypothesis, LBP status itself was not associated with reduced physical function in community‐dwelling women 60 years and older. This implies that LBP may not be related to physical function in this population group, but rather to their physical activity levels.
A systematic social observation tool to measure the restorative potential of urban settings / Diseño de una herramienta de observación social sistemática del potencial restaurador de espacios urbanos
Authors: Subiza-Pérez Mikel , Vozmediano Laura , San Juan César 
Published: April 2019

The study of psychological restoration in urban settings has undergone significant growth in recent years. The aim of this paper is to develop an instrument for the objective evaluation of the restorative potential of urban public spaces. Perceived restoration scales and a large number of systematic social observation instruments were reviewed, selecting items that might be suitable for the aims of this study and adding other items designed ad hoc. The resulting tool is made up of 183 items, grouped into 12 domains. The final format of the instrument was used by a group of four evaluators in a total of six urban squares. This paper reports the statistics obtained for the internal consistency of the instrument (inter-judge agreement) and convergent validity through correlations of the objective scores from each public square with the perceived and experienced restoration of a sample of users of said public squares ( N = 296). The tool delivered an adequate level of reliability, and its scores were related to restoration measures, although the size of this association was small.
The Casimir-like effect in a one-dimensional Bose gas
Authors: Reichert Benjamin , Ristivojevic Zoran , Petković Aleksandra 
Published: April 2019

Abstract
The electromagnetic Casimir effect manifests as the interaction between uncharged conducting objects that are placed in a vacuum. More generally, the Casimir-like effect denotes an induced interaction between external bodies in a fluctuating medium. We study the Casimir-like interaction between two impurities embedded in a weakly interacting one-dimensional Bose gas. We develop a theory based on the Gross–Pitaevskii equation that accounts for the effect of quantum fluctuations. At small separations, the induced interaction between the impurities decays exponentially with the distance. This is a classical result that can be understood using the mean-field Gross–Pitaevskii equation. We find that at larger distances, the induced interaction crosses over into a power law dependence due to the quantum fluctuations. We obtain an analytic expression for the interaction that interpolates between the two limiting behaviors. The obtained result does not require any regularization.