bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-analysis of cortical thickness abnormalities in medication-free patients with major depressive disorder
Authors: Li Qian , Zhao Youjin , Chen Ziqi , Long Jingyi , Dai Jing , Huang Xiaoqi , Lui Su , Radua Joaquim , Vieta Eduard , Kemp Graham J. , Sweeney John A. , Li Fei , Gong Qiyong 
Published: November 2019

Abstract
Alterations in cortical thickness have been identified in major depressive disorder (MDD), but findings have been variable and inconsistent. To date, no reliable tools have been available for the meta-analysis of surface-based morphometric (SBM) studies to effectively characterize what has been learned in previous studies, and drug treatments may have differentially impacted findings. We conducted a comprehensive meta-analysis of magnetic resonance imaging (MRI) studies that explored cortical thickness in medication-free patients with MDD, using a newly developed meta-analytic mask compatible with seed-based d mapping (SDM) meta-analytic software. We performed the meta-regression to explore the effects of demographics and clinical characteristics on variation in cortical thickness in MDD. Fifteen studies describing 529 patients and 586 healthy controls (HCs) were included. Medication-free patients with MDD, relative to HCs, showed a complex pattern of increased cortical thickness in some areas (posterior cingulate cortex, ventromedial prefrontal cortex, and anterior cingulate cortex) and decreased cortical thickness in others (gyrus rectus, orbital segment of the superior frontal gyrus, and middle temporal gyrus). Most findings in the whole sample analysis were confirmed in a meta-analysis of studies recruiting medication-naive patients. Using the new mask specifically developed for SBM studies, this SDM meta-analysis provides evidence for regional cortical thickness alterations in MDD, mainly involving increased cortical thickness in the default mode network and decreased cortical thickness in the orbitofrontal and temporal cortex.
Virtual-photon-mediated spin-qubit–transmon coupling
Authors: Landig A. J. , Koski J. V. , Scarlino P. , Müller C. , Abadillo-Uriel J. C. , Kratochwil B. , Reichl C. , Wegscheider W. , Coppersmith S. N. , Friesen Mark , Wallraff A. , Ihn T. , Ensslin K. 
Published: November 2019

AbstractSpin qubits and superconducting qubits are among the promising candidates for realizing a solid state quantum computer. For the implementation of a hybrid architecture which can profit from the advantages of either approach, a coherent link is necessary that integrates and controllably couples both qubit types on the same chip over a distance that is several orders of magnitude longer than the physical size of the spin qubit. We realize such a link with a frequency-tunable high impedance SQUID array resonator. The spin qubit is a resonant exchange qubit hosted in a GaAs triple quantum dot. It can be operated at zero magnetic field, allowing it to coexist with superconducting qubits on the same chip. We spectroscopically observe coherent interaction between the resonant exchange qubit and a transmon qubit in both resonant and dispersive regimes, where the interaction is mediated either by real or virtual resonator photons.
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Authors: Johnson Jethro S. , Spakowicz Daniel J. , Hong Bo-Young , Petersen Lauren M. , Demkowicz Patrick , Chen Lei , Leopold Shana R. , Hanson Blake M. , Agresta Hanako O. , Gerstein Mark , Sodergren Erica , Weinstock George M. 
Published: November 2019

AbstractThe 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect. Here, we use in silico and sequence-based experiments to critically re-evaluate the potential of the 16S gene to provide taxonomic resolution at species and strain level. We demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene. We further demonstrate that full-length sequencing platforms are sufficiently accurate to resolve subtle nucleotide substitutions (but not insertions/deletions) that exist between intragenomic copies of the 16S gene. In consequence, we argue that modern analysis approaches must necessarily account for intragenomic variation between 16S gene copies. In particular, we demonstrate that appropriate treatment of full-length 16S intragenomic copy variants has the potential to provide taxonomic resolution of bacterial communities at species and strain level.
Geocoding of worldwide patent data
Authors: de Rassenfosse Gaétan , Kozak Jan , Seliger Florian 
Published: November 2019

AbstractThe dataset provides geographic coordinates for inventor and applicant locations in 18.8 million patent documents spanning over more than 30 years. The geocoded data are further allocated to the corresponding countries, regions and cities. When the address information was missing in the original patent document, we imputed it by using information from subsequent filings in the patent family. The resulting database can be used to study patenting activity at a fine-grained geographic level without creating bias towards the traditional, established patent offices.
New opportunities for designing effective small interfering RNAs
Authors: Valdés James J. , Miller Andrew D. 
Published: November 2019

AbstractSmall interfering RNAs (siRNAs) that silence genes of infectious diseases are potentially potent drugs. A continuing obstacle for siRNA-based drugs is how to improve their efficacy for adequate dosage. To overcome this obstacle, the interactions of antiviral siRNAs, tested in vivo, were computationally examined within the RNA-induced silencing complex (RISC). Thermodynamics data show that a persistent RISC cofactor is significantly more exothermic for effective antiviral siRNAs than their ineffective counterparts. Detailed inspection of viral RNA secondary structures reveals that effective antiviral siRNAs target hairpin or pseudoknot loops. These structures are critical for initial RISC interactions since they partially lack intramolecular complementary base pairing. Importing two temporary RISC cofactors from magnesium-rich hairpins and/or pseudoknots then kickstarts full RNA hybridization and hydrolysis. Current siRNA design guidelines are based on RNA primary sequence data. Herein, the thermodynamics of RISC cofactors and targeting magnesium-rich RNA secondary structures provide additional guidelines for improving siRNA design.
Combining super-resolution microscopy with neuronal network recording using magnesium fluoride thin films as cover layer for multi-electrode array technology
Authors: Schmidl L. , Schmidl G. , Gawlik A. , Dellith J. , Hübner U. , Tympel V. , Schmidl F. , Plentz J. , Geis C. , Haselmann H. 
Published: November 2019

AbstractWe present an approach for fabrication of reproducible, chemically and mechanically robust functionalized layers based on MgF2 thin films on thin glass substrates. These show great advantages for use in super-resolution microscopy as well as for multi-electrode-array fabrication and are especially suited for combination of these techniques. The transparency of the coated substrates with the low refractive index material is adjustable by the layer thickness and can be increased above 92%. Due to the hydrophobic and lipophilic properties of the thin crystalline MgF2 layers, the temporal stable adhesion needed for fixation of thin tissue, e.g. cryogenic brain slices is given. This has been tested using localization-based super-resolution microscopy with currently highest spatial resolution in light microscopy. We demonstrated that direct stochastic optical reconstruction microscopy revealed in reliable imaging of structures of central synapses by use of double immunostaining of post- (homer1 and GluA2) and presynaptic (bassoon) marker structure in a 10 µm brain slice without additional fixing of the slices. Due to the proven additional electrical insulating effect of MgF2 layers, surfaces of multi-electrode-arrays were coated with this material and tested by voltage-current-measurements. MgF2 coated multi-electrode-arrays can be used as a functionalized microscope cover slip for combination with live-cell super-resolution microscopy.
Performance of wild-Serbian Ganoderma lucidum mycelium in treating synthetic sewage loading using batch bioreactor
Authors: Mohd Hanafiah Zarimah , Wan Mohtar Wan Hanna Melini , Abu Hasan Hassimi , Jensen Henriette Stokbro , Klaus Anita , Wan-Mohtar Wan Abd Al Qadr Imad 
Published: November 2019

AbstractThe fluctuation of domestic wastewater characteristic inhibits the current conventional microbial-based treatment. The bioremediation fungi has received attention and reported to be an effective alternative to treat industrial wastewater. Similar efficient performance is envisaged for domestic wastewater whereby assessed performance of fungi for varying carbon-to-nitrogen ratios in domestic wastewater is crucial. Thus, the performance of pre-grown wild-Serbian Ganoderma lucidum mycelial pellets (GLMPs) was evaluated on four different synthetic domestic wastewaters under different conditions of initial pH (pH 4, 5, and 7) and chemical oxygen demand (COD) to nitrogen (COD/N) ratio of 3.6:1, 7.1:1, 14.2:1, and 17.8:1 (C3.6N1, C7.1N1, C14.2N1, and C17.8N1). The COD/N ratios with a constant concentration of ammonia–nitrogen (NH3–N) were chosen on the basis of the urban domestic wastewater characteristics sampled at the inlet basin of a sewage treatment plant (STP). The parameters of pH, COD, and NH3–N were measured periodically during the experiment. The wild-Serbian GLMPs efficiently removed the pollutants from the synthetic sewage. The COD/N ratio of C17.8N1 wastewater had the best COD and NH3–N removal, as compared to the lower COD/N ratio, and the shortest treatment time was obtained in an acidic environment at pH 4. The highest percentage for COD and NH3–N removal achieved was 96.0% and 93.2%, respectively. The results proved that the mycelium of GLMP has high potential in treating domestic wastewater, particularly at high organic content as a naturally sustainable bioremediation system.
Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma
Authors: Tang Xia , Feng Delong , Li Min , Zhou Jinxue , Li Xiaoyuan , Zhao Dachun , Hao Bingtao , Li Dewei , Ding Keyue 
Published: November 2019

AbstractFully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs. The DE RNAs were highly enriched in 21 functional pathways implicated in HCC (p < 0.05), including p53, MAPK, and NAFLD signaling. Potential pairwise interactions between DE ncRNAs and mRNAs were fully characterized using in silico prediction and experimentally-validated evidence. We for the first time constructed a MLMI network of reciprocal interactions for 16 miRNAs, three lncRNAs, and 253 mRNAs in HCC. The predominant role of MEG3 in the MLMI network was validated by its overexpression in vitro that the expression levels of a proportion of MEG3-targeted miRNAs and mRNAs was changed significantly. Our results suggested that the comprehensive MLMI network synergistically modulated carcinogenesis, and the crosstalk of the network provides a new avenue to accurately describe the molecular mechanisms of hepatocarcinogenesis.
Improved Cas9 activity by specific modifications of the tracrRNA
Authors: Scott Tristan , Urak Ryan , Soemardy Citradewi , Morris Kevin V. 
Published: November 2019

AbstractCRISPR/Cas is a transformative gene editing tool, that offers a simple and effective way to target a catalytic Cas9, the most widely used is derived fromStreptococcus pyogenes (SpCas9), with a complementary small guide RNA (sgRNA) to inactivate endogenous genes resulting from insertions and deletions (indels). CRISPR/Cas9 has been rapidly applied to basic research as well as expanded for potential clinical applications. Utilization ofspCas9 as an ribonuclearprotein complex (RNP) is considered the most safe and effective method to apply Cas9 technology, and the efficacy of this system is critically dependent on the ability of Cas9 to generate high levels of indels. We find here that novel sequence changes to the tracrRNA significantly improves Cas9 activity when delivered as an RNP. We demonstrate that a dual-guide RNA (dgRNA) with a modified tracrRNA can improve reporter knockdown and indel formation at several targets within the long terminal repeat (LTR) of HIV. Furthermore, the sequence-modified tracrRNAs improved Cas9-mediated reduction of CCR5 surface receptor expression in cell lines, which correlated with higher levels of indel formation. It was demonstrated that a Cas9 RNP with a sequence modified tracrRNA enhanced indel formation at the CCR5 target site in primary CD4+ T-cells. Finally, we show improved activity at two additional targets within the HBB locus and the BCL11A GATA site. Overall, the data presented here suggests that novel facile tracrRNA sequence changes could potentially be integrated with current dgRNA technology, and open up the possibility for the development of sequence modified tracrRNAs to improve Cas9 RNP activity.
Transcriptome analysis reveals autophagy as regulator of TGFβ/Smad-induced fibrogenesis in trabecular meshwork cells
Authors: Nettesheim April , Shim Myoung Sup , Hirt Josh , Liton Paloma B. 
Published: November 2019

AbstractThe trabecular meshwork (TM) is a specialized ocular tissue, which is responsible, together with the Schlemm’s canal (SC), for maintaining appropriate levels of intraocular pressure. Dysfunction of these tissues leads to ocular hypertension and increases the risk for developing glaucoma. Previous work by our laboratory revealed dysregulated autophagy in aging and in glaucomatous TM cells. In order to gain more insight in the role of autophagy in the TM pathophysiology, we have conducted transcriptome and functional network analyses of TM primary cells with silenced expression of the autophagy genes Atg5 and Atg7. Atg5/7-deficient TM cells showed changes in transcript levels of several fibrotic genes, including TGFβ2, BAMBI, and SMA. Furthermore, genetic and pharmacological inhibition of autophagy was associated with a parallel reduction in TGFβ-induced fibrosis, caused by a BAMBI-mediated reduced activation of Smad2/3 signaling in autophagy-deficient cells. At the same time, TGFβ treatment led to Smad2/3-dependent dysregulation of autophagy in TM cells, characterized by increased LC3-II levels and autophagic vacuoles content. Together, our results indicate a cross-talk between autophagy and TGFβ signaling in TM cells.
Electrochemical and DFT studies of brass corrosion inhibition in 3% NaCl in the presence of environmentally friendly compounds
Authors: Radovanović Milan B. , Tasić Žaklina Z. , Mihajlović Marija B. Petrović , Simonović Ana T. , Antonijević Milan M. 
Published: November 2019

AbstractThe effects of adenine, salicylaldoxime and 4(5)-methylimidazole on brass corrosion in NaCl were investigated. The investigation comprised electrochemical techniques, scanning electron microscopy and quantum chemical calculation. The results obtained by polarization measurements show that the examined compounds successfully inhibited the corrosion of brass. Additionally, the quantum mechanical calculations indicate that there is a correlation between energy gap and inhibition efficiency. Moreover, the inhibition mechanism includes the adsorption of the inhibitor on active sites on the electrode surface, which was confirmed by SEM-EDS analysis of the brass.
The intrinsic circadian clock in podocytes controls glomerular filtration rate
Authors: Ansermet Camille , Centeno Gabriel , Nikolaeva Svetlana , Maillard Marc P. , Pradervand Sylvain , Firsov Dmitri 
Published: November 2019

AbstractGlomerular filtration rate (GFR), or the rate of primary urine formation, is the key indicator of renal function. Studies have demonstrated that GFR exhibits significant circadian rhythmicity and, that these rhythms are disrupted in a number of pathologies. Here, we tested a hypothesis that the circadian rhythm of GFR is driven by intrinsic glomerular circadian clocks. We used mice lacking the circadian clock protein BMAL1 specifically in podocytes, highly specialized glomerular cells critically involved in the process of glomerular filtration (Bmal1lox/lox/Nphs2-rtTA/LC1 or, cKO mice). Circadian transcriptome profiling performed on isolated glomeruli from control and cKO mice revealed that the circadian clock controls expression of multiple genes encoding proteins essential for normal podocyte function. Direct assessment of glomerular filtration by inulin clearance demonstrated that circadian rhythmicity in GFR was lost in cKO mice that displayed an ultradian rhythm of GFR with 12-h periodicity. The disruption of circadian rhythmicity in GFR was paralleled by significant changes in circadian patterns of urinary creatinine, sodium, potassium and water excretion and by alteration in the diurnal pattern of plasma aldosterone levels. Collectively, these results indicate that the intrinsic circadian clock in podocytes participate in circadian rhythmicity of GFR.
A HARPS RV search for planets around young nearby stars
Authors: Grandjean A. , Lagrange A.-M. , Keppler M. , Meunier N. , Mignon L. , Borgniet S. , Chauvin G. , Desidera S. , Galland F. , Messina S. , Sterzik M. , Pantoja B. , Rodet L. , Zicher N. 
Published: November 2019

Context. Young nearby stars are good candidates in the search for planets with both radial velocity (RV) and direct imaging techniques. This, in turn, allows for the computation of the giant planet occurrence rates at all separations. The RV search around young stars is a challenge as they are generally faster rotators than older stars of similar spectral types and they exhibit signatures of magnetic activity (spots) or pulsation in their RV time series. Specific analyses are necessary to characterize, and possibly correct for, this activity.
Aims. Our aim is to search for planets around young nearby stars and to estimate the giant planet (GP) occurrence rates for periods up to 1000 days.
Methods. We used the HARPS spectrograph on the 3.6 m telescope at La Silla Observatory to observe 89 A−M young (<600 Myr) stars. We used our SAFIR (Spectroscopic data via Analysis of the Fourier Interspectrum Radial velocities) software to compute the RV and other spectroscopic observables. Then, we computed the companion occurrence rates on this sample.
Results. We confirm the binary nature of HD 177171, HD 181321 and HD 186704. We report the detection of a close low mass stellar companion for HIP 36985. No planetary companion was detected. We obtain upper limits on the GP (<13 MJup) and BD (∈ [13;80] MJup) occurrence rates based on 83 young stars for periods less than 1000 days, which are set, 2−2+3 and 1−1+3%.
Comparison of Radiation Exposure of the Surgeon in Minimally Invasive Treatment of Osteoporotic Vertebral Fractures – Radiofrequency Kyphoplasty versus Balloon Kyphoplasty with Cement Delivery Systems (CDS)
Authors: Reißberg Steffen , Lüdeke Lina , Fritsch Michael 
Published: November 2019

The aim of the present study was to compare the radiation exposure of the surgeon when using two different kyphoplasty systems for the minimally invasive treatment of osteoporotic vertebral body fractures. There was a preliminary investigation study by a Belgian working group from the ORAMED project (2010), which served as the basis and showed a dose reduction for the surgeon when using a balloon kyphoplasty system with cement delivery systems (CDS).
Materials and Methods A bipedicular balloon kyphoplasty system (Medtronic GmbH) with CDS and a unipedicular radiofrequency kyphoplasty system (StabiliT, DFine Europe GmbH) were used in solitary fractures in the thoracolumbar junction in 20 patients each. The patient groups were relatively homogeneous with a mean age of 76.9 years for balloon kyphoplasty and 75 years for radiofrequency kyphoplasty. As expected, the proportion of woman was higher in both groups. The mean BMI value was higher in the radiofrequency kyphoplasty group, and the patient with the highest BMI was also in this group. The workflows were defined in three steps. The working time and the fluoroscopic time were measured in the individual work steps and the dose was measured over all work steps by TLD chips (thermoluminescence detector) on the forehead, on the X-ray apron, on both wrists and on the left ankle. The dose area product was registered for the entire procedure.
Results In step 2, the main differences were found in working time and fluoroscopy time in transit. The difference was due to the bipedicular puncture for balloon kyphoplasty and the change of the working cannula, while only a unipedicular puncture was needed in radiofrequency kyphoplasty. The total fluoroscopy time over all procedures was three times longer than in balloon kyphoplasty and this was also reflected in the dose area product, which was more than twice that. The measured surface doses for the lenses were four times higher in balloon kyphoplasty. For the left wrist, the values for balloon kyphoplasty were about 8 times higher.
Conclusion Overall, from a radiophysical perspective, the use of a unipedicular kyphoplasty system must be recommended. Should balloon kyphoplasty be used for medical reasons, all radiation protection products (lead gloves, lead glass, radiation protection goggles and CDS) should be used, the surface doses for both hands must be detected by a ring dosimeter and the lens dose must be recorded and documented by a TLD on the radiation protection goggles.
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Citation Format
Gestationsdiabetes – Ist ein Screening kosteneffektiv?
Authors: Thiem Helena 
Published: November 2019

Fitria N et al. Cost-effectiveness of controlling gestational diabetes mellitus: a systematic review. Eur J Health Econ 2019: 20: 407–417
Als Gestationsdiabetes, auch Schwangerschaftsdiabetes genannt, bezeichnet man eine Glukosetoleranzstörung, die während der Schwangerschaft auftritt und diagnostiziert wird. Festgestellt wird diese Erkrankung durch einen Blutzuckerbelastungstest. Das rechtzeitige Screening auf Hyperglykämie in der Schwangerschaft verbessert die Früherkennung und Kontrolle des Gestationsdiabetes. Fitria et al. untersuchten, inwieweit diese Maßnahme auch kosteneffektiv ist.