bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection
Authors: Fröhlich Fabian , Reiser Anita , Fink Laura , Woschée Daniel , Ligon Thomas , Theis Fabian Joachim , Rädler Joachim Oskar , Hasenauer Jan 
Published: December 2018

AbstractSingle-cell time-lapse studies have advanced the quantitative understanding of cellular pathways and their inherent cell-to-cell variability. However, parameters retrieved from individual experiments are model dependent and their estimation is limited, if based on solely one kind of experiment. Hence, methods to integrate data collected under different conditions are expected to improve model validation and information content. Here we present a multi-experiment nonlinear mixed effect modeling approach for mechanistic pathway models, which allows the integration of multiple single-cell perturbation experiments. We apply this approach to the translation of green fluorescent protein after transfection using a massively parallel read-out of micropatterned single-cell arrays. We demonstrate that the integration of data from perturbation experiments allows the robust reconstruction of cell-to-cell variability, i.e., parameter densities, while each individual experiment provides insufficient information. Indeed, we show that the integration of the datasets on the population level also improves the estimates for individual cells by breaking symmetries, although each of them is only measured in one experiment. Moreover, we confirmed that the suggested approach is robust with respect to batch effects across experimental replicates and can provide mechanistic insights into the nature of batch effects. We anticipate that the proposed multi-experiment nonlinear mixed effect modeling approach will serve as a basis for the analysis of cellular heterogeneity in single-cell dynamics.
Separation of Biological Particles in a Modular Platform of Cascaded Deterministic Lateral Displacement Modules
Authors: Pariset Eloise , Parent Charlotte , Fouillet Yves , François Boizot , Verplanck Nicolas , Revol-Cavalier Frédéric , Thuaire Aurélie , Agache Vincent 
Published: December 2018

AbstractDeterministic lateral displacement (DLD) has been extensively implemented in the last decade for size-based sample preparation, owing to its high separation performances for a wide range of particle dimensions. However, separating particles from 1 μm to 10 μm in one single DLD device is challenging because of the required diversity of pillar dimensions and inherent fabrication issues. This paper presents an alternative approach to achieve the extraction of E. coli bacteria from blood samples spiked with prostate cancer cells. Our approach consists in cascading individual DLD devices in a single automated platform, using flexible chambers that successively collect and inject the sample between each DLD stage without any external sample manipulation. Operating DLD separations independently enables to maximize the sorting efficiency at each step, without any disturbance from downstream stages. The proposed two-step automated protocol is applied to the separation of three types of components (bacteria, blood particles and cancer cells), with a depletion yield of 100% for cancer cells and 93% for red blood cells. This cascaded approach is presented for the first time with two DLD modules and is upscalable to improve the dynamic range of currently available DLD devices.
Vertical WS2/SnS2 van der Waals Heterostructure for Tunneling Transistors
Authors: Wang Jiaxin , Jia Rundong , Huang Qianqian , Pan Chen , Zhu Jiadi , Wang Huimin , Chen Cheng , Zhang Yawen , Yang Yuchao , Song Haisheng , Miao Feng , Huang Ru 
Published: December 2018

AbstractVan der Waals heterostructures composed of two-dimensional (2D) transition metal dichalcogenides (TMD) materials have stimulated tremendous research interest in various device applications, especially in energy-efficient future-generation electronics. Such ultra-thin stacks as tunnel junction theoretically present unprecedented possibilities of tunable relative band alignment and pristine interfaces, which enable significant performance enhancement for steep-slope tunneling transistors. In this work, the optimal 2D-2D heterostructure for tunneling transistors is presented and elaborately engineered, taking into consideration both electric properties and material stability. The key challenges, including band alignment and metal-to-2D semiconductor contact resistances, are optimized separately for integration. By using a new dry transfer technique for the vertical stack, the selected WS2/SnS2 heterostructure-based tunneling transistor is fabricated for the first time, and exhibits superior performance with comparable on-state current and steeper subthreshold slope than conventional FET, as well as on-off current ratio over 106 which is among the highest value of 2D-2D tunneling transistors. A visible negative differential resistance feature is also observed. This work shows the great potential of 2D layered semiconductors for new heterostructure devices and can guide possible development of energy-efficient future-generation electronics.
High-efficiency freezing-induced loading of inorganic nanoparticles and proteins into micron- and submicron-sized porous particles
Authors: German Sergei V. , Novoselova Marina V. , Bratashov Daniil N. , Demina Polina A. , Atkin Vsevolod S. , Voronin Denis V. , Khlebtsov Boris N. , Parakhonskiy Bogdan V. , Sukhorukov Gleb B. , Gorin Dmitry A. 
Published: December 2018

AbstractWe demonstrate a novel approach to the controlled loading of inorganic nanoparticles and proteins into submicron- and micron-sized porous particles. The approach is based on freezing/thawing cycles, which lead to high loading densities. The process was tested for the inclusion of Au, magnetite nanoparticles, and bovine serum albumin in biocompatible vaterite carriers of micron and submicron sizes. The amounts of loaded nanoparticles or substances were adjusted by the number of freezing/thawing cycles. Our method afforded at least a three times higher loading of magnetite nanoparticles and a four times higher loading of protein for micron vaterite particles, in comparison with conventional methods such as adsorption and coprecipitation. The capsules loaded with magnetite nanoparticles by the freezing-induced loading method moved faster in a magnetic field gradient than did the capsules loaded by adsorption or coprecipitation. Our approach allows the preparation of multicomponent nanocomposite materials with designed properties such as remote control (e.g. via the application of an electromagnetic or acoustic field) and cargo unloading. Such materials could be used as multimodal contrast agents, drug delivery systems, and sensors.
Backscattering design for a focusing grating coupler with fully etched slots for transverse magnetic modes
Authors: Hoffmann Jahn , Schulz K. Marvin , Pitruzzello Giampaolo , Fohrmann Lena Simone , Petrov Alexander Yu. , Eich Manfred 
Published: December 2018

AbstractGrating couplers are a fundamental building block of integrated optics as they allow light to be coupled from free-space to on-chip components and vice versa. A challenging task in designing any grating coupler is represented by the need for reducing back reflections at the waveguide-grating interface, which introduce additional losses and undesirable interference fringes. Here, we present a design approach for focusing TM grating couplers that minimizes these unwanted reflections by introducing a modified slot that fulfills an anti-reflection condition. We show that this antireflection condition can be met only for the Bloch mode of the grating that concentrates in the dielectric. As a consequence the light is scattered from the grating coupler with a negative angle, referred to as “backscattering design”. Our analytic model shows that the anti-reflection condition is transferrable to grating couplers on different waveguide platforms and that it applies for both TE and TM polarizations. Our experimentally realized focusing grating coupler for TM-modes on the silicon photonics platform has a coupling loss of (3.95 ± 0.15) dB at a wavelength of 1.55 µm. It has feature sizes above 200 nm and fully etched slots. The reflectivity between the grating coupler and the connected waveguide is suppressed to below 0.16%.
Regulation of phosphorus bioavailability by iron nanoparticles in a monomictic lake
Authors: Saeed H. , Hartland A. , Lehto N. J. , Baalousha M. , Sikder M. , Sandwell D. , Mucalo M. , Hamilton D. P. 
Published: December 2018

AbstractDissolved reactive phosphorous (DRP) in lake systems is conventionally considered to predominate over other dissolved P species, however, this view neglects an important set of interactions that occurs between P and reactive iron hydroxide surfaces. This study addresses the coupling of P with dispersed iron nanoparticles in lakes, an interaction that may fundamentally alter the bioavailability of P to phytoplankton. We used diffusive gradients in thin films (DGT) and ultrafiltration to study Fe-P coupling in the water column of a monomictic lake over a hydrological year. Fe and P were predominantly colloidal (particle diameters > ~5 nm < ~20 nm) in both oxic epilimnetic and anaerobic hypolimnetic waters, but they were both DGT-labile under sub-oxic conditions, consistent with diffusion and dissolution of Fe-and-P-bearing colloids within the DGT diffusive gel. During peak stratification, increases in Fe and P bioavailability were spatially and temporally coincident with Fe nanoparticle dissolution and the formation of a deep chlorophyll maximum at 5–8 m depth. These results provide a window into the coupling and decoupling of P with mobile iron colloids, with implications for our understanding of the behaviour of nutrients and their influence on phytoplankton community dynamics.
Quantification of protein mobility and associated reshuffling of cytoplasm during chemical fixation
Authors: Huebinger Jan , Spindler Jessica , Holl Kristin J. , Koos Björn 
Published: December 2018

AbstractTo understand cellular functionalities, it is essential to unravel spatio-temporal patterns of molecular distributions and interactions within living cells. The technological progress in fluorescence microscopy now allows in principle to measure these patterns with sufficient spatial resolution. However, high resolution imaging comes with long acquisition times and high phototoxicity. Therefore, physiological live cell imaging is often unfeasible and chemical fixation is employed. Yet, fixation methods have not been rigorously investigated, in terms of pattern preservation, at the resolution at which cells can now be imaged. A key parameter for this is the time required until fixation is complete. During this time, cells are under unphysiological conditions and patterns decay. We demonstrate here that formaldehyde fixation takes more than one hour for cytosolic proteins in cultured cells. Other small aldehydes, glyoxal and acrolein, did not perform better. Associated with this, we found a distinct displacement of proteins and lipids, including their loss from cells. Fixations using glutaraldehyde were faster than four minutes and retained most cytoplasmic proteins. Surprisingly, autofluorescence produced by glutaraldehyde was almost completely absent with supplementary addition of formaldehyde without compromising fixation speed. These findings indicate, which cellular processes can actually be reliably imaged after a certain chemical fixation.
Power laws and critical fragmentation in global forests
Authors: Saravia Leonardo A. , Doyle Santiago R. , Bond-Lamberty Ben 
Published: December 2018

AbstractThe replacement of forest areas with human-dominated landscapes usually leads to fragmentation, altering the structure and function of the forest. Here we studied the dynamics of forest patch sizes at a global level, examining signals of a critical transition from an unfragmented to a fragmented state, using the MODIS vegetation continuous field. We defined wide regions of connected forest across continents and big islands, and combined five criteria, including the distribution of patch sizes and the fluctuations of the largest patch over the last sixteen years, to evaluate the closeness of each region to a fragmentation threshold. Regions with the highest deforestation rates–South America, Southeast Asia, Africa–all met these criteria and may thus be near a critical fragmentation threshold. This implies that if current forest loss rates are maintained, wide continental areas could suddenly fragment, triggering extensive species loss and degradation of ecosystems services.
Transcriptome-wide analysis of a baculovirus using nanopore sequencing
Authors: Boldogkői Zsolt , Moldován Norbert , Szűcs Attila , Tombácz Dóra 
Published: December 2018

AbstractAutographa californica multiple nucleopolyhedrovirus (AcMNPV) is a prototypic baculovirus infecting specific insects. AcMNPV contains a large double-stranded DNA genome encoding a complex transcriptome. This virus has a widespread application as a vector for the expression of heterologous proteins. Here, we present a dataset, derived from Oxford Nanopore Technologies (ONT) long-read sequencing platform. We used both cDNA and direct RNA sequencing techniques. The dataset contains 520,310 AcMNPV and 1,309,481 host cell reads using the regular cDNA-sequencing method of ONT technique, whereas altogether 6,456 reads were produced by using direct RNA-sequencing. We also used a Cap-selection protocol for certain ONT samples, and obtained 2,568,669 reads by using this method. The raw reads were aligned to the AcMNPV reference genome (KM667940.1). Here, we openly released the ‘static’ and the dynamic transcript catalogue of AcMNPV. This dataset can be used for deep analyses of the transcriptomic and epitranscriptomic patterns of the AcMNPV and the host cell. The data can be also useful for the validation of different bioinformatics software packages and analysis tools.
Genome analysis of Mycobacterium avium subspecies hominissuis strain 109
Authors: Matern William M. , Bader Joel S. , Karakousis Petros C. 
Published: December 2018

AbstractInfection with Mycobacterium avium is a significant cause of morbidity and its treatment requires the use of multiple antibiotics for more than 12 months. In the current work, we provide the genome sequence, gene annotations, gene ontology annotations, and protein homology data for M. avium strain 109 (MAC109), which has been used extensively in preclinical studies. The de novo assembled genome consists of a circular chromosome of length 5,188,883 bp and two circular plasmids of sizes 147,100 bp and 16,516 bp. We have named the plasmids pMAC109a and pMAC109b, respectively. Based on its genome, we confirm that MAC109 should be classified as Mycobacterium avium subsp. hominissuis. Using genome annotation software, we identified 4,841 coding sequences and annotated these with Gene Ontology (GO) terms. Additionally, we wrote software to generate a database of homologous proteins among MAC109 and eight other commonly used mycobacterial laboratory strains. The resulting database may be useful for translating genetic data between various strains of mycobacteria, and the software may be applied readily to other organisms.
A linked open data representation of patents registered in the US from 2005–2017
Authors: Hassan Mofeed M. , Zaveri Amrapali , Lehmann Jens 
Published: December 2018

AbstractPatents are widely used to protect intellectual property and a measure of innovation output. Each year, the USPTO grants over

150
,
000

patents to individuals and companies all over the world. In fact, there were more than

280
,
000

patent grants issued in the US in

2015

. However, accessing, searching and analyzing those patents is often still cumbersome and inefficient. To overcome those problems, Google indexes patents and converts them to Extensible Markup Language (XML) files using Optical Character Recognition (OCR) techniques. In this article, we take this idea one step further and provide semantically rich, machine-readable patents using the Linked Data principles. We have converted the data spanning

12

years

−

i.e.

2005

−

2017

from XML to Resource Description Framework (RDF) format, conforming to the Linked Data principles and made them publicly available for re-use. This data can be integrated with other data sources in order to further simplify use cases such as trend analysis, structured patent search & exploration and societal progress measurements. We describe the conversion, publishing, interlinking process along with several use cases for the USPTO Linked Patent data.
LncRNAs, MALAT1 and lnc-DC as potential biomarkers for multiple sclerosis diagnosis
Authors: Shaker Olfat G. , Mahmoud Rania H. , Abdelaleem Omayma O. , Ibrahem Enas G. , Mohamed Abdelrahmaan A. , Zaki Othman M. , Abdelghaffar Noha K. , Ahmed Tarek I. , Hemeda Nada F. , Ahmed Naglaa A. , Mansour Dina F. 
Published: December 2018

Abstract
Long non-coding RNAs (lncRNAs) play an important role in gene regulation and show greater tissue specificity and complexity of biological functions. There is on-going research in their contribution in autoimmune diseases like multiple sclerosis (MS). Our study aimed at the evaluation of serum levels of lncRNAs, MALAT1 and lnc-DC in MS patients and the investigation of the association between these lncRNAs and the disease activity. Serum from 45 MS patients and 45 healthy controls was separated. MALAT1 and lnc-DC expression levels were assayed by qRT-PCR. MALAT1 and lnc-DC were significantly increased in MS patients (P=0.004 and P=0.006, respectively) in comparison with controls. There was a significant increase in expression of MALAT1 in secondary progressive MS (SPMS) subgroup compared with controls (P&lt;0.0001); however, significant elevation of lnc-DC was demonstrated in relapsing remitting MS (RRMS) subtype (P=0.003) compared with normal controls. A positive association between the expression levels of MALAT1 and lnc-DC (r = 0.513, P &lt; 0.0001) in MS patients was detected. Moreover, positive correlation was observed between MALAT1and lnc-DC in RRMS (r = 0.569, P = 0.001). Serum levels of MALAT1 and lnc-DC may serve as potential novel molecular biomarkers for MS diagnosis and may provide a new direction for its treatment.
AMPK: a therapeutic target of heart failure—not only metabolism regulation
Authors: Li Xuan , Liu Jia , Lu Qingguo , Ren Di , Sun Xiaodong , Rousselle Thomas , Tan Yi , Li Ji 
Published: December 2018

Abstract
Heart failure (HF) is a serious disease with high mortality. The incidence of this disease has continued to increase over the past decade. All cardiovascular diseases causing dysfunction of various physiological processes can result in HF. AMP-activated protein kinase (AMPK), an energy sensor, has pleiotropic cardioprotective effects and plays a critical role in the progression of HF. In this review, we highlight that AMPK can not only improve the energy supply in the failing heart by promoting ATP production, but can also regulate several important physiological processes to restore heart function. In addition, we discuss some aspects of some potential clinical drugs which have effects on AMPK activation and may have value in treating HF. More studies, especially clinical trials, should be done to evaluate manipulation of AMPK activation as a potential means of treating HF.
Low‐power, high‐speed output buffer with shared‐TIA for ultra‐large IRFPAs
Authors: Huang Zhaofeng , Niu Yuze , Lu Wengao , Zhu Yajun , Zhang Shengdong 
Published: December 2018

In this Letter, a low‐power, high‐speed output buffer for ultra‐large infrared focal plane arrays (IRFPAs) is proposed. This buffer adopts a shared trans‐impedance amplifier structure, which reduces parasitic resistance and capacitance of column‐level bus. A 1280 × 1024 array readout integrated circuit with 20 MHz output frequency is designed for cooled infrared detector using this novel structure. The chip has been realised with 0.35 μm 1P4M CMOS process and power consumption of the proposed single output buffer is 3.83 mW. Though the presented circuit has been designed for this design, it shows great potential to be employed in most ultra‐large readout integrated circuits.
Ökonomische Betrachtung von Genexpressionstests beim Mammakarzinom am Beispiel des Oncotype DX®
Authors: Thiem Helena , Lux Michael , Rebscher Herbert , Potempa Christoph 
Published: December 2018

Zusammenfassung
Zielsetzung Das Ziel der Übersichtsarbeit ist, die ökonomischen Auswirkungen von Genexpressionstests in der Therapie des frühen, Hormonrezeptor-positiven, Her2-negativen Mammakarzinoms zur Unterstützung der adjuvanten Therapieentscheidung am Beispiel des Oncotype DX® (ODX) zu erläutern. Im Fokus steht dabei, inwiefern dieser Genexpressionstest zu Kosteneinsparungen führt und ob er als kosteneffektiv bewertet werden kann.
Methodik In gängigen Literaturdatenbanken wurde eine Literaturrecherche zu gesundheitsökonomischen Analysen des ODX durchgeführt. Die Ergebnisse der eingeschlossenen Publikationen wurden ausgewertet und in einem narrativen Review zusammengefasst. Zusätzlich erfolgte eine separate Betrachtung im Kontext des deutschen Gesundheitssystems.
Ergebnisse Es konnten insgesamt 28 Arbeiten identifiziert werden, die sich mit der Wirtschaftlichkeit des ODX auseinandersetzen. Darunter waren 18 Kosten-Effektivitäts-Analysen, 5 Budget-Impact-Analysen sowie 5 Reviews. Die eingeschlossenen Kosten-Effektivitätsanalysen bewerteten den Test insgesamt als kosteneffektiv gegenüber der Regelversorgung, begründet durch ein verbessertes Outcome, eine geringere Anzahl an durchgeführten Chemotherapien, eine geringere Rezidivrate sowie eine höhere Lebenserwartung der Patientinnen. In Abhängigkeit vom jeweiligen Gesundheitssystem wird dem ODX in den Budget-Impact-Analysen ein Einsparpotenzial zugesprochen, teilweise kann es jedoch zu (kurzfristigen) Kostensteigerungen aufgrund der Kosten für die Testung kommen. Die Publikationen zur Wirtschaftlichkeit des ODX im deutschen Versorgungskontext berichten ebenfalls ein Einsparpotenzial.
Schlussfolgerung Die Ergebnisse lassen sich aufgrund unterschiedlicher monetärer Bewertungen zwar nur eingeschränkt auf das deutsche Gesundheitssystem übertragen, es kann dennoch davon ausgegangen werden, dass der Einsatz des ODX auch hier im Längsschnitt zu Kosteneinsparungen führen wird. Eine Erstattung von Genexpressionstests beim frühen Mammakarzinom im Rahmen der Regelversorgung ist demnach unter ökonomischen Gesichtspunkten sinnvoll.
Deep Plane Facelift: An Evaluation of the High-SMAS versus Standard Incision Points
Authors: Amodeo Chiara , Nabili Vishad , Keller Gregory , Sand Jordan 
Published: December 2018

AbstractIn surgery of the aging face, operative adjustments of the superficial musculoaponeurotic system (SMAS) enhance facial contours. The senior author has observed that the standard deep plane face lift entry points on the SMAS do not provide as much tissue movement in a vertical direction as high-SMAS deep plane face lift entry points. In this study, tissue movement was measured comparing the conventional SMAS entry point with a high-SMAS entry point for deep plane face lifts. Institutional review board approval was obtained. Fourteen facelift patients were enrolled, 10 female and 4 male. Average age was 63.4 (50–81) years. Tissue movement at three points along the jaw line was measured intraoperatively. Standard SMAS entry point suspension resulted in average vertical movements of 6.4, 10.3, and 13.8 mm and average horizontal movements of 3.5, 5.7, and 6.5 mm. High-SMAS entry point resulted in average vertical movements of 11.8, 17.9, and 24.1 mm and average horizontal movements of 5.8, 9.8, and 9.9 mm. This resulted in a 77.3% increase (p = 0.03) in vertical movement and a 61.4% increase (p = 0.02) in horizontal movement with a high-SMAS entry compared with standard SMAS entry. The high-SMAS entry point for a deep plane facelift resulted in a significant increase in lift for both the horizontal and vertical vector on the facial skin flap when compared with the conventional entry.