bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks
Authors: Glöckner Gernot , Marwan Wolfgang 
Published: September 2017

AbstractActivation of a phytochrome photoreceptor triggers a program ofPhysarum polycephalumplasmodial cell differentiation through which a mitotic multinucleate protoplasmic mass synchronously develops into haploid spores formed by meiosis and rearrangement of cellular components. We have performed a transcriptome-wide RNAseq study of cellular reprogramming and developmental switching. RNAseq analysis revealed extensive remodeling of intracellular signaling and regulation in switching the expression of sets of genes encoding transcription factors, kinases, phosphatases, signal transduction proteins, RNA-binding proteins, ubiquitin ligases, regulators of the mitotic and meiotic cell cycleetc. in conjunction with the regulation of genes encoding metabolic enzymes and cytoskeletal proteins. About 15% of the differentially expressed genes shared similarity with members of the evolutionary conserved set of core developmental genes of social amoebae. Differential expression of genes encoding regulators that act at the transcriptional, translational, and post-translational level indicates the establishment of a new state of cellular function and reveals evolutionary deeply conserved molecular changes involved in cellular reprogramming and differentiation in a prototypical eukaryote.
Direct observation of nanowire growth and decomposition
Authors: Rackauskas Simas , Shandakov Sergey D. , Jiang Hua , Wagner Jakob B. , Nasibulin Albert G. 
Published: September 2017

AbstractFundamental concepts of the crystal formation suggest that the growth and decomposition are determined by simultaneous embedding and removal of the atoms. Apparently, by changing the crystal formation conditions one can switch the regimes from the growth to decomposition. To the best of our knowledge, so far this has been only postulated, but never observed at the atomic level. By means of in situ environmental transmission electron microscopy we monitored and examined the atomic layer transformation at the conditions of the crystal growth and its decomposition using CuO nanowires selected as a model object. The atomic layer growth/decomposition was studied by varying an O2 partial pressure. Three distinct regimes of the atomic layer evolution were experimentally observed: growth, transition and decomposition. The transition regime, at which atomic layer growth/decomposition switch takes place, is characterised by random nucleation of the atomic layers on the growing {111} surface. The decomposition starts on the side of the nanowire by removing the atomic layers without altering the overall crystal structure, which besides the fundamental importance offers new possibilities for the nanowire manipulation. Understanding of the crystal growth kinetics and nucleation at the atomic level is essential for the precise control of 1D crystal formation.
Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli
Authors: Oesterle Sabine , Gerngross Daniel , Schmitt Steven , Roberts Tania Michelle , Panke Sven 
Published: September 2017

AbstractMultiplexed gene expression optimization via modulation of gene translation efficiency through ribosome binding site (RBS) engineering is a valuable approach for optimizing artificial properties in bacteria, ranging from genetic circuits to production pathways. Established algorithms design smart RBS-libraries based on a single partially-degenerate sequence that efficiently samples the entire space of translation initiation rates. However, the sequence space that is accessible when integrating the library by CRISPR/Cas9-based genome editing is severely restricted by DNA mismatch repair (MMR) systems. MMR efficiency depends on the type and length of the mismatch and thus effectively removes potential library members from the pool. Rather than working in MMR-deficient strains, which accumulate off-target mutations, or depending on temporary MMR inactivation, which requires additional steps, we eliminate this limitation by developing a pre-selection rule of genome-library-optimized-sequences (GLOS) that enables introducing large functional diversity into MMR-proficient strains with sequences that are no longer subject to MMR-processing. We implement several GLOS-libraries in Escherichia coli and show that GLOS-libraries indeed retain diversity during genome editing and that such libraries can be used in complex genome editing operations such as concomitant deletions. We argue that this approach allows for stable and efficient fine tuning of chromosomal functions with minimal effort.
High-Affinity Functional Fluorescent Ligands for Human β-Adrenoceptors
Authors: Mitronova Gyuzel Y. , Lukinavičius Gražvydas , Butkevich Alexey N. , Kohl Tobias , Belov Vladimir N. , Lehnart Stephan E. , Hell Stefan W. 
Published: September 2017

AbstractVisualization of the G-protein coupled receptor (GPCR) is of great importance for studying its function in a native cell. We have synthesized a series of red-emitting fluorescent probes targeting β-adrenergic receptor (βAR) that are compatible with confocal and Stimulated Emission Depletion (STED) microscopy as well as with Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) binding assay in living cells. The probe based on the agonist BI-167107 and fluorescent dye KK114 demonstrates nanomolar binding affinity and up to nine-fold β2AR selectivity over β1AR. Carazolol-derived probes are fluorogenic and allow no-wash imaging experiments. STED microscopy of β2ARs stained at the native expression level on pancreatic CAPAN cells provides two-fold improvement in lateral optical resolution over confocal mode and reveals the formation of receptor microdomains. These probes retain their functional (agonist or antagonist) properties, allowing simultaneous modulation of cyclic adenosine monophosphate (cAMP) levels and receptor internalization as well as imaging receptor localization.
Subclass-specific IgG glycosylation is associated with markers of inflammation and metabolic health
Authors: Plomp Rosina , Ruhaak L. Renee , Uh Hae-Won , Reiding Karli R. , Selman Maurice , Houwing-Duistermaat Jeanine J. , Slagboom P. Eline , Beekman Marian , Wuhrer Manfred 
Published: September 2017

AbstractThis study indicates that glycosylation of immunoglobulin G, the most abundant antibody in human blood, may convey useful information with regard to inflammation and metabolic health. IgG occurs in the form of different subclasses, of which the effector functions show significant variation. Our method provides subclass-specific IgG glycosylation profiling, while previous large-scale studies neglected to measure IgG2-specific glycosylation. We analysed the plasma Fc glycosylation profiles of IgG1, IgG2 and IgG4 in a cohort of 1826 individuals by liquid chromatography-mass spectrometry. For all subclasses, a low level of galactosylation and sialylation and a high degree of core fucosylation associated with poor metabolic health, i.e. increased inflammation as assessed by C-reactive protein, low serum high-density lipoprotein cholesterol and high triglycerides, which are all known to indicate increased risk of cardiovascular disease. IgG2 consistently showed weaker associations of its galactosylation and sialylation with the metabolic markers, compared to IgG1 and IgG4, while the direction of the associations were overall similar for the different IgG subclasses. These findings demonstrate the potential of IgG glycosylation as a biomarker for inflammation and metabolic health, and further research is required to determine the additive value of IgG glycosylation on top of biomarkers which are currently used.
Spontaneous periodic ordering on the surface and in the bulk of dielectrics irradiated by ultrafast laser: a shared electromagnetic origin
Authors: Rudenko Anton , Colombier Jean-Philippe , Höhm Sandra , Rosenfeld Arkadi , Krüger Jörg , Bonse Jörn , Itina Tatiana E. 
Published: September 2017

AbstractPeriodic self-organization of matter beyond the diffraction limit is a puzzling phenomenon, typical both for surface and bulk ultrashort laser processing. Here we compare the mechanisms of periodic nanostructure formation on the surface and in the bulk of fused silica. We show that volume nanogratings and surface nanoripples having subwavelength periodicity and oriented perpendicular to the laser polarization share the same electromagnetic origin. The nanostructure orientation is defined by the near-field local enhancement in the vicinity of the inhomogeneous scattering centers. The periodicity is attributed to the coherent superposition of the waves scattered at inhomogeneities. Numerical calculations also support the multipulse accumulation nature of nanogratings formation on the surface and inside fused silica. Laser surface processing by multiple laser pulses promotes the transition from the high spatial frequency perpendicularly oriented nanoripples to the low spatial frequency ripples, parallel or perpendicular to the laser polarization. The latter structures also share the electromagnetic origin, but are related to the incident field interference with the scattered far-field of rough non-metallic or transiently metallic surfaces. The characteristic ripple appearances are predicted by combined electromagnetic and thermo-mechanical approaches and supported by SEM images of the final surface morphology and by time-resolved pump-probe diffraction measurements.
Enhanced ventral hippocampal synaptic transmission and impaired synaptic plasticity in a rodent model of alcohol addiction vulnerability
Authors: Almonte Antoine G. , Ewin Sarah E. , Mauterer Madelyn I. , Morgan James W. , Carter Eugenia S. , Weiner Jeffrey L. 
Published: September 2017

AbstractIt has long been appreciated that adolescence represents a uniquely vulnerable period when chronic exposure to stressors can precipitate the onset of a broad spectrum of psychiatric disorders and addiction in adulthood. However, the neurobiological substrates and the full repertoire of adaptations within these substrates making adolescence a particularly susceptible developmental stage are not well understood. Prior work has demonstrated that a rodent model of adolescent social isolation (aSI) produces robust and persistent increases in phenotypes relevant to anxiety/stressor disorders and alcohol addiction, including anxiogenesis, deficits in fear extinction, and increased ethanol consumption. Here, we used extracellular field recordings in hippocampal slices to investigate adaptations in synaptic function and synaptic plasticity arising from aSI. We demonstrate that this early life stressor leads to enhanced excitatory synaptic transmission and decreased levels of long-term potentiation at hippocampal Schaffer collateral-CA1 synapses. Further, these changes were largely confined to the ventral hippocampus. As the ventral hippocampus is integral to neurocircuitry that mediates emotional behaviors, our results add to mounting evidence that aSI has profound effects on brain areas that regulate affective states. These studies also lend additional support to our recent proposal of the aSI model as a valid model of alcohol addiction vulnerability.
Fibroblast Growth Factor 21 in Patients with Acromegaly
Authors: Halupczok-Żyła Jowita , Jawiarczyk-Przybyłowska Aleksandra , Skrzypski Marek , Strowski Mathias , Bolanowski Marek 
Published: September 2017

Abstract
Introduction The goal of the study was to investigate fibroblast growth factor-21 (FGF-21) levels in acromegalic patients in relation to the disease activity and to compare them with controls. Further, we aimed to evaluate the associations between FGF-21 and random growth hormone (GH), insulin-like growth factor-1 (IGF-1), metabolic and anthropometric parameters.
Materials and methods The study group consisted of 50 acromegalic patients divided into 3 subgroups on the basis of disease activity (AA – active acromegaly, CD – controlled disease, CA – cured acromegaly). 27 subjects were assigned to the control group (CG). Blood samples were obtained from all participants to assess FGF-21, GH, IGF-1, lipids, glucose and insulin levels. Body mass, body mass index and body composition were also evaluated.
Results There were no statistically significant differences in FGF-21 concentrations across all groups despite of subjects classification. FGF-21 correlated positively with random GH in the groups: CA, CD+CA, AA+CD+CA (r=0.48, p=0.049; r=0.39, p=0.023; r=0.33, p=0.02; respectively); with IGF-1 in the AA+CD+CA group (r=0.29, p=0.041); with triglycerides in the following groups: CD, CD+CA, AA+CD+CA (r=0.63, p=0.08; r=0.44, p=0.01; r=0.37, p=0.007; respectively) and with age in the CG and CD+CA groups (r=0.41, p=0.029; r=0.42, p=0.029; respectively). There were statistically significant negative correlations between FGF-21 and HDL-cholesterol levels in the groups: CD, CD+CA, AA+CD+CA (r=-0.53, p=0.03; r=-0.37, p=0.032; r=-0.29, p=0.036, respectively).
Conclusions FGF-21 levels were similar in patients with acromegaly compared to controls. However, our results indicate that FGF-21 may have a potential role in the development of acromegaly complications.
Organerhaltende Therapieoptionen des muskelinvasiven Harnblasenkarzinoms
Authors: Kempkensteffen Carsten 
Published: September 2017

ZusammenfassungDie radikale Zystektomie gilt gemäß nationaler und internationaler Leitlinien als Therapie der Wahl zur Behandlung des muskelinvasiven
Harnblasenkarzinoms. Insbesondere bei alten, komorbiden Patienten ist dieser Eingriff jedoch mit einem relativ hohen Komplikationsrisiko
assoziiert. Jüngere Patienten befürchten darüber hinaus vor allem postoperative Einschränkungen der Lebensqualität durch Störungen der
Sexualität, der Kontinenz und des Körperbildes infolge der möglicherweise notwendigen Anlage eines Urostomas. Daraus resultiert eine
zunehmende Nachfrage nach alternativen, organerhaltenden Therapieoptionen. Hier stehen derzeit die multimodale Therapie und die partielle
Zystektomie im Vordergrund. Unter der Voraussetzung einer stringenten Patientenselektion sowie einer engmaschigen Tumornachsorge, lassen
sich mit beiden Verfahren der radikalen Zystektomie vergleichbare onkologische Ergebnisse erreichen.
The Oral Dipeptidyl-Peptidase-4 Inhibitor Sitagliptin Increases Circulating Levels Of Stromal-Derived Factor-1 Alpha
Authors: Papazafiropoulou Athanasia , Papanas Nikolaos , Trikkalinou Aikaterini , Fousteris Evaggelos , Melidonis Andreas 
Published: September 2017

AbstractRecent studies have demonstrated that stromal derived factor-1α (SDF-1α) is a substrate of dipeptidyl-peptidase-4 (DPP-4) inhibitors. It has also been shown that SDF-1α shares anti-apoptotic as well as nephroprotective properties and exerts a beneficial effect in the cardiovascular system. Therefore, the aim of this study was to estimate the effect of treatment with the DDP-4 inhibitor sitagliptin on SDF-1α levels in subjects with type 2 diabetes mellitus (T2D). Overall, 32 patients (16 males) with T2D, mean age (±SD) 67.2±8.3 years, HbA1c 6.4±0.5%, body-mass index (BMI) 29.1±4.9 Kg/m2, T2D duration 8.5±4.0 years receiving metformin monotherapy (17 participants) or metformin plus sitagliptin (15 participants) without known cardiovascular disease were enrolled. Patients on metformin plus sitagliptin exhibited higher plasma levels of SDF-1α compared with those on metformin monotherapy (19.6±4.1 versus 6.9±1.3 pg/ml, respectively, p=0.01). Multivariate regression analysis after controlling for age, sex, body-mass index, smoking, arterial hypertension, dyslipidaemia and other confounders showed that SDF-1α levels were positively correlated with DPP-4 inhibitor treatment (beta=0.91, p=0.001), and negatively with T2D duration (beta=− 0.42, p=0.05), ΗDL-cholesterol levels (beta=− 0.46, p=0.02) and HbA1c (beta=− 0.41, p=0.05). In conclusion, these results suggest that sitagliptin treatment may exert a favourable effect on SDF-1α levels.
Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods
Authors: Oldfield Lauren M. , Grzesik Peter , Voorhies Alexander A. , Alperovich Nina , MacMath Derek , Najera Claudia D. , Chandra Diya Sabrina , Prasad Sanjana , Noskov Vladimir N. , Montague Michael G. , Friedman Robert M. , Desai Prashant J. , Vashee Sanjay 
Published: September 2017

Significance
Viruses with large DNA genomes, such as herpesviruses, are difficult to manipulate with existing genetic tools. We describe an application of synthetic genomics assembly tools that enables rapid and efficient generation of combinatorial mutations in herpesvirus genomes. The method provides the capacity to design, generate, and test numerous multiloci mutants in parallel, which can help us understand basic virus biology, facilitate vaccine development, and aid development of next-generation virus-based delivery systems. This class of viruses is being used as vectors for therapeutics and vaccines, with an oncolytic herpesvirus approved for the treatment of melanoma. Although such improvements in genome assembly and manipulation raise dual-use concerns, we believe the potential benefits substantially outweigh the risks.
The microstructure and mechanical properties of hot-extruded Mg-5Sn-4Al-2Ce rapidly solidified alloy
Authors: Cheng P. , Chen Y. , Ding W. , Wang C. 
Published: September 2017

The microstructure and mechanical properties of hot-extruded Mg-5Sn-4Al-2Ce alloy in the form of rapid solidification ribbons (RS-extruded TAE542) are investigated. The results show that rapid solidification causes ultra-fine a-Mg grains (250 nm) and massive dispersive Mg2Sn and Al11Ce3 particles (80–400 nm) in the rapidly solidified (RS)-extruded alloy. As a result, the yield strength and elongation of RS-extruded TAE542 alloy reached 366 MPa and 15.2%, increasing by 72 and 26%, respectively, when compared with that of hot-extruded TAE542 alloy made from a homogenised ingot (HI-extruded TAE542). This paper is part of a thematic issue on Light Alloys.
Temperature-dependent variation in dynamic deformation behaviour and dislocation substructure in AZ80 magnesium
Authors: Lee Woei-Shyan , Chou Cheng-Wen 
Published: September 2017

The dynamic deformation behaviour and dislocation substructure of AZ80 magnesium alloy are investigated at strain rates of 8 × 102, 1.5 × 103 and 2.2 × 103 s−1 and temperatures of −100, 25 and 300°C using a compressive split-Hopkinson pressure bar system. The flow stress, work hardening coefficient, strain rate sensitivity and temperature sensitivity all increase with increasing strain rate or decreasing temperature. Moreover, the dynamic deformation behaviour is well described by the Zerilli–Armstrong hexagonal close packed (hcp) constitutive equation. Catastrophic failure occurs at all three temperatures under strain rates of 1.5 × 103 and 2.2 × 103 s−1. Transmission electron microscopy observations show that the dislocation density increases with a higher strain rate or a lower temperature. Finally, the flow stress varies linearly with the square root of the dislocation density in accordance with the Bailey–Hirsch model. This paper is part of a thematic issue on Light Alloys.
The Conundrum of Opioid Tapering in Long-Term Opioid Therapy for Chronic Pain: A Commentary
Authors: Manhapra Ajay , Arias Albert J. , Ballantyne Jane C. 
Published: September 2017

Background In response to the opioid epidemic and new guidelines, many patients on high-dose long term opioid therapy (LTOT) for chronic pain are getting tapered off opioids. As a result, a unique clinical challenge is emerging: while many on LTOT have poor pain control, functional decline, psychiatric instability, aberrancies and misuse, these issues may often worsen with opioid tapering. Currently, a clear explanation and practical guidance on how to manage this perplexing clinical scenario is lacking. Methods We offer a commentary with our perspective on possible mechanisms involved in this clinical phenomena and offer practical management guidance, supported by available evidence. Results It is not well recognized that allostatic opponent process involved in development of opioid dependence can cause worsening pain, functional status, sleep and psychiatric symptoms over time, and significant fluctuation of pain and other affective symptoms due to their bidirectional dynamic interaction with opioid dependence (‘affective dynamism’). These elements of complex persistent dependence (CPD), the grey area between simple dependence and addiction, can lead to escalating and labile opioid need, often generating aberrant behaviors. Opioid tapering, a seemingly logical intervention in this situation, may lead to worsening of pain, function and psychiatric symptoms due to development of protracted abstinence syndrome. We offer practicing clinicians management principles and practical guidance focused on management of CPD in addition to chronic pain in these difficult clinical scenarios. Conclusion Awareness of the science of the neuroplasticity effects of repeated use of opioids is necessary to better manage these patients with complex challenges.
Euromet #608 comparison in neutron fields—EUROMET(III)-S1
Authors: Ryckeghem L Van , Vanhavere F , Kil-Oung C , Jozefowicz K , Valent J , Kralik M 
Published: September 2017

Six laboratories responsible for the calibration of neutron survey meters were able to participate in the EUROMET #608 comparison (EUROMET.RI(III)-S1). This report establishes the degree of equivalence and uncertainty for each laboratory, for various types of neutron fields 241Am/Be, 252Cf, (252Cf+D2O)/Cd and for the reference quantity, H*(10).

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
A review of parameter estimation used in solar photovoltaic system for a single diode model
Authors: Md Sabudin Siti Nurashiken , Jamil Norazaliza Mohd , Rosli Norhayati 
Published: September 2017

Abstract
With increased demand for theoretical solar energy, the mathematical modelling of the solar photovoltaic (PV) system has gained importance. Numerous mathematical models have been developed for different purposes. In this paper, we briefly review the progress made in the mathematical modelling of solar photovoltaic (PV) system over the last twenty years. First, a general classification of these models is made. Then, the basic characteristics of the models along with the objectives and different parameters considered in modelling are discussed. The assumptions and approximations made also parameter estimation method in solving the models are summarized. This may facilitate the mathematicians to adopt better understanding of the modelling strategies and further to develop suitable models in this direction relevant to the present scenario.
Segway 2.0: Gaussian mixture models and minibatch training
Authors: Chan Rachel C W , Libbrecht Maxwell W , Roberts Eric G , Bilmes Jeffrey A , Noble William Stafford , Hoffman Michael M 
Published: September 2017

Abstract

Summary
Segway performs semi-automated genome annotation, discovering joint patterns across multiple genomic signal datasets. We discuss a major new version of Segway and highlight its ability to model data with substantially greater accuracy. Major enhancements in Segway 2.0 include the ability to model data with a mixture of Gaussians, enabling capture of arbitrarily complex signal distributions, and minibatch training, leading to better learned parameters.

Availability and implementation
Segway and its source code are freely available for download at http://segway.hoffmanlab.org. We have made available scripts (https://doi.org/10.5281/zenodo.802939) and datasets (https://doi.org/10.5281/zenodo.802906) for this paper’s analysis.

Supplementary information
Supplementary data are available at Bioinformatics online.