bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon-based SERS biosensor: from substrate design to sensing and bioapplication
Authors: Liang Xiu , Li Ning , Zhang Runhao , Yin Penggang , Zhang Chenmeng , Yang Nan , Liang Kang , Kong Biao 
Published: January 2021

AbstractThe sensing of bioactive molecules based on photochemical techniques has become one of the fastest-growing scientific fields. Surface-enhanced Raman scattering (SERS) is a highly sensitive technique for the detection of low-concentration molecules, including DNA, microRNA, proteins, blood, and bacteria; single-cell detection and identification; bioimaging; and disease diagnosis, providing abundant structural information for biological analytes. One rapidly developing field of SERS biosensor design is the use of carbon-based nanomaterials as substrate materials, such as zero-dimensional carbon quantum dots, one-dimensional carbon nanotubes, two-dimensional graphene, and graphene oxide (GO) and three-dimensional spatial carbon nanomaterials or carbon-based core-shell nanostructures. In this review, we describe the recent developments in SERS biosensors, in particular carbon-based SERS, for the detection of bioactive molecules. We systematically survey recent developments in carbon nanomaterial-based SERS biosensors, focusing on fundamental principles for carbon-based materials for SERS biosensor design, fabrication, and operation, and provide insights into their rapidly growing future potential in the fields of biomedical and biological engineering, in situ analysis, quantitative analysis, and flexible photoelectric functional materials. As such, this review can play the role of a roadmap to guide researchers toward concepts that can be used in the design of next-generation SERS biosensors while also highlighting current advancements in this field.
Detection of aberrant splicing events in RNA-seq data using FRASER
Authors: Mertes Christian , Scheller Ines F. , Yépez Vicente A. , Çelik Muhammed H. , Liang Yingjiqiong , Kremer Laura S. , Gusic Mirjana , Prokisch Holger , Gagneur Julien 
Published: January 2021

AbstractAberrant splicing is a major cause of rare diseases. However, its prediction from genome sequence alone remains in most cases inconclusive. Recently, RNA sequencing has proven to be an effective complementary avenue to detect aberrant splicing. Here, we develop FRASER, an algorithm to detect aberrant splicing from RNA sequencing data. Unlike existing methods, FRASER captures not only alternative splicing but also intron retention events. This typically doubles the number of detected aberrant events and identified a pathogenic intron retention in MCOLN1 causing mucolipidosis. FRASER automatically controls for latent confounders, which are widespread and affect sensitivity substantially. Moreover, FRASER is based on a count distribution and multiple testing correction, thus reducing the number of calls by two orders of magnitude over commonly applied z score cutoffs, with a minor loss of sensitivity. Applying FRASER to rare disease diagnostics is demonstrated by reprioritizing a pathogenic aberrant exon truncation in TAZ from a published dataset. FRASER is easy to use and freely available.
Global patterns and climatic controls of forest structural complexity
Authors: Ehbrecht Martin , Seidel Dominik , Annighöfer Peter , Kreft Holger , Köhler Michael , Zemp Delphine Clara , Puettmann Klaus , Nilus Reuben , Babweteera Fred , Willim Katharina , Stiers Melissa , Soto Daniel , Boehmer Hans Juergen , Fisichelli Nicholas , Burnett Michael , Juday Glenn , Stephens Scott L. , Ammer Christian 
Published: January 2021

AbstractThe complexity of forest structures plays a crucial role in regulating forest ecosystem functions and strongly influences biodiversity. Yet, knowledge of the global patterns and determinants of forest structural complexity remains scarce. Using a stand structural complexity index based on terrestrial laser scanning, we quantify the structural complexity of boreal, temperate, subtropical and tropical primary forests. We find that the global variation of forest structural complexity is largely explained by annual precipitation and precipitation seasonality (R² = 0.89). Using the structural complexity of primary forests as benchmark, we model the potential structural complexity across biomes and present a global map of the potential structural complexity of the earth´s forest ecoregions. Our analyses reveal distinct latitudinal patterns of forest structure and show that hotspots of high structural complexity coincide with hotspots of plant diversity. Considering the mechanistic underpinnings of forest structural complexity, our results suggest spatially contrasting changes of forest structure with climate change within and across biomes.
Soft subdermal implant capable of wireless battery charging and programmable controls for applications in optogenetics
Authors: Kim Choong Yeon , Ku Min Jeong , Qazi Raza , Nam Hong Jae , Park Jong Woo , Nam Kum Seok , Oh Shane , Kang Inho , Jang Jae-Hyung , Kim Wha Young , Kim Jeong-Hoon , Jeong Jae-Woong 
Published: January 2021

AbstractOptogenetics is a powerful technique that allows target-specific spatiotemporal manipulation of neuronal activity for dissection of neural circuits and therapeutic interventions. Recent advances in wireless optogenetics technologies have enabled investigation of brain circuits in more natural conditions by releasing animals from tethered optical fibers. However, current wireless implants, which are largely based on battery-powered or battery-free designs, still limit the full potential of in vivo optogenetics in freely moving animals by requiring intermittent battery replacement or a special, bulky wireless power transfer system for continuous device operation, respectively. To address these limitations, here we present a wirelessly rechargeable, fully implantable, soft optoelectronic system that can be remotely and selectively controlled using a smartphone. Combining advantageous features of both battery-powered and battery-free designs, this device system enables seamless full implantation into animals, reliable ubiquitous operation, and intervention-free wireless charging, all of which are desired for chronic in vivo optogenetics. Successful demonstration of the unique capabilities of this device in freely behaving rats forecasts its broad and practical utilities in various neuroscience research and clinical applications.
Fetuin-A is a HIF target that safeguards tissue integrity during hypoxic stress
Authors: Rudloff Stefan , Janot Mathilde , Rodriguez Stephane , Dessalle Kevin , Jahnen-Dechent Willi , Huynh-Do Uyen 
Published: January 2021

AbstractIntrauterine growth restriction (IUGR) is associated with reduced kidney size at birth, accelerated renal function decline, and increased risk for chronic kidney and cardiovascular diseases in adults. Precise mechanisms underlying fetal programming of adult diseases remain largely elusive and warrant extensive investigation. Setting up a mouse model of hypoxia-induced IUGR, fetal adaptations at mRNA, protein and cellular levels, and their long-term functional consequences are characterized, using the kidney as a readout. Here, we identify fetuin-A as an evolutionary conserved HIF target gene, and further investigate its role using fetuin-A KO animals and an adult model of ischemia-reperfusion injury. Beyond its role as systemic calcification inhibitor, fetuin-A emerges as a multifaceted protective factor that locally counteracts calcification, modulates macrophage polarization, and attenuates inflammation and fibrosis, thus preserving kidney function. Our study paves the way to therapeutic approaches mitigating mineral stress-induced inflammation and damage, principally applicable to all soft tissues.
Nonreciprocal charge transport up to room temperature in bulk Rashba semiconductor α-GeTe
Authors: Li Yan , Li Yang , Li Peng , Fang Bin , Yang Xu , Wen Yan , Zheng Dong-xing , Zhang Chen-hui , He Xin , Manchon Aurélien , Cheng Zhao-Hua , Zhang Xi-xiang 
Published: January 2021

AbstractNonmagnetic Rashba systems with broken inversion symmetry are expected to exhibit nonreciprocal charge transport, a new paradigm of unidirectional magnetoresistance in the absence of ferromagnetic layer. So far, most work on nonreciprocal transport has been solely limited to cryogenic temperatures, which is a major obstacle for exploiting the room-temperature two-terminal devices based on such a nonreciprocal response. Here, we report a nonreciprocal charge transport behavior up to room temperature in semiconductor α-GeTe with coexisting the surface and bulk Rashba states. The combination of the band structure measurements and theoretical calculations strongly suggest that the nonreciprocal response is ascribed to the giant bulk Rashba spin splitting rather than the surface Rashba states. Remarkably, we find that the magnitude of the nonreciprocal response shows an unexpected non-monotonical dependence on temperature. The extended theoretical model based on the second-order spin–orbit coupled magnetotransport enables us to establish the correlation between the nonlinear magnetoresistance and the spin textures in the Rashba system. Our findings offer significant fundamental insight into the physics underlying the nonreciprocity and may pave a route for future rectification devices.
CTLA-4 expression by B-1a B cells is essential for immune tolerance
Authors: Yang Yang , Li Xiao , Ma Zhihai , Wang Chunlin , Yang Qunying , Byrne-Steele Miranda , Hong Rongjian , Min Qing , Zhou Gao , Cheng Yong , Qin Guang , Youngyunpipatkul Justin V. , Wing James B. , Sakaguchi Shimon , Toonstra Christian , Wang Lai-Xi , Vilches-Moure Jose G. , Wang Denong , Snyder Michael P. , Wang Ji-Yang , Han Jian , Herzenberg Leonore A. 
Published: January 2021

AbstractCTLA-4 is an important regulator of T-cell function. Here, we report that expression of this immune-regulator in mouse B-1a cells has a critical function in maintaining self-tolerance by regulating these early-developing B cells that express a repertoire enriched for auto-reactivity. Selective deletion of CTLA-4 from B cells results in mice that spontaneously develop autoantibodies, T follicular helper (Tfh) cells and germinal centers (GCs) in the spleen, and autoimmune pathology later in life. This impaired immune homeostasis results from B-1a cell dysfunction upon loss of CTLA-4. Therefore, CTLA-4-deficient B-1a cells up-regulate epigenetic and transcriptional activation programs and show increased self-replenishment. These activated cells further internalize surface IgM, differentiate into antigen-presenting cells and, when reconstituted in normal IgH-allotype congenic recipient mice, induce GCs and Tfh cells expressing a highly selected repertoire. These findings show that CTLA-4 regulation of B-1a cells is a crucial immune-regulatory mechanism.
Biomechanical characterization of human temporal muscle fascia in uniaxial tensile tests for graft purposes in duraplasty
Authors: Zwirner Johann , Ondruschka Benjamin , Scholze Mario , Schulze-Tanzil Gundula , Hammer Niels 
Published: January 2021

AbstractThe human temporal muscle fascia (TMF) is used frequently as a graft material for duraplasty. Encompassing biomechanical analyses of TMF are lacking, impeding a well-grounded biomechanical comparison of the TMF to other graft materials used for duraplasty, including the dura mater itself. In this study, we investigated the biomechanical properties of 74 human TMF samples in comparison to an age-matched group of dura mater samples. The TMF showed an elastic modulus of 36 ± 19 MPa, an ultimate tensile strength of 3.6 ± 1.7 MPa, a maximum force of 16 ± 8 N, a maximum strain of 13 ± 4% and a strain at failure of 17 ± 6%. Post-mortem interval correlated weakly with elastic modulus (r = 0.255, p = 0.048) and the strain at failure (r =  − 0.306, p = 0.022) for TMF. The age of the donors did not reveal significant correlations to the TMF mechanical parameters. Compared to the dura mater, the here investigated TMF showed a significantly lower elastic modulus and ultimate tensile strength, but a larger strain at failure. The human TMF with a post-mortem interval of up to 146 h may be considered a mechanically suitable graft material for duraplasty when stored at a temperature of 4 °C.
In-SEM micro-machining reveals the origins of the size effect in the cutting energy
Authors: Medina-Clavijo Bentejui , Ortiz-de-Zarate Gorka , Sela Andres , Arrieta Iñaki M. , Fedorets Aleksandr , Arrazola Pedro J. , Chuvilin Andrey 
Published: January 2021

AbstractHigh-precision metal cutting is increasingly relevant in advanced applications. Such precision normally requires a cutting feed in the micron or even sub-micron dimension scale, which raises questions about applicability of concepts developed in industrial scale machining. To address this challenge, we have developed a device to perform linear cutting with force measurement in the vacuum chamber of an electron microscope, which has been utilised to study the cutting process down to 200 nm of the feed and the tool tip radius. The machining experiments carried out in-operando in SEM have shown that the main classical deformation zones of metal cutting: primary, secondary and tertiary shear zones—were preserved even at sub-micron feeds. In-operando observations and subsequent structural analysis in FIB/SEM revealed a number of microstructural peculiarities, such as: a substantial increase of the cutting force related to the development of the primary shear zone; dependence of the ternary shear zone thickness on the underlaying grain crystal orientation. Measurement of the cutting forces at deep submicron feeds and cutting tool apex radii has been exploited to discriminate different sources for the size effect on the cutting energy (dependence of the energy on the feed and tool radius). It was observed that typical industrial values of feed and tool radius imposes a size effect determined primarily by geometrical factors, while in a sub-micrometre feed range the contribution of the strain hardening in the primary share zone becomes relevant.
INSPECTOR: free software for magnetic resonance spectroscopy data inspection, processing, simulation and analysis
Authors: Gajdošík Martin , Landheer Karl , Swanberg Kelley M. , Juchem Christoph 
Published: January 2021

AbstractIn vivo magnetic resonance spectroscopy (MRS) is a powerful tool for biomedical research and clinical diagnostics, allowing for non-invasive measurement and analysis of small molecules from living tissues. However, currently available MRS processing and analytical software tools are limited in their potential for in-depth quality management, access to details of the processing stream, and user friendliness. Moreover, available MRS software focuses on selected aspects of MRS such as simulation, signal processing or analysis, necessitating the use of multiple packages and interfacing among them for biomedical applications. The freeware INSPECTOR comprises enhanced MRS data processing, simulation and analytical capabilities in a one-stop-shop solution for a wide range of biomedical research and diagnostic applications. Extensive data handling, quality management and visualization options are built in, enabling the assessment of every step of the processing chain with maximum transparency. The parameters of the processing can be flexibly chosen and tailored for the specific research problem, and extended confidence information is provided with the analysis. The INSPECTOR software stands out in its user-friendly workflow and potential for automation. In addition to convenience, the functionalities of INSPECTOR ensure rigorous and consistent data processing throughout multi-experiment and multi-center studies.
Early bilingual experience is associated with change detection ability in adults
Authors: D’Souza Dean , Brady Daniel , Haensel Jennifer X. , D’Souza Hana 
Published: January 2021

AbstractTo adapt to their more varied and unpredictable (language) environments, infants from bilingual homes may gather more information (sample more of their environment) by shifting their visual attention more frequently. However, it is not known whether this early adaptation is age-specific or lasts into adulthood. If the latter, we would expect to observe it in adults who acquired their second language early, not late, in life. Here we show that early bilingual adults are faster at disengaging attention to shift attention, and at noticing changes between visual stimuli, than late bilingual adults. In one experiment, participants were presented with the same two visual stimuli; one changed (almost imperceptibly), the other remained the same. Initially, participants looked at both stimuli equally; eventually, they fixated more on the changing stimulus. This shift in looking occurred in the early but not late bilinguals. It suggests that cognitive processes adapt to early bilingual experiences.
Respiratory tract infections in children with allergic asthma on allergen immunotherapy during influenza season
Authors: Li Yuyun , Wang Dongming , Zhi Lili , Zhu Yunmei , Qiao Lan , Zhu Yan , Hu Xin , Wang Qian , Cao Yuan , Gao Yan , Chen Yousheng , Zhang Zeng , Bi Fangjie , Yan Guangxing 
Published: January 2021

AbstractTo describle how respiratory tract infections (RTIs) that occurred in children with allergic asthma (AA) on allergen immunotherapy (AIT) during an influenza season. Data including clinical symptoms and treatment history of children (those with AA on AIT and their siblings under 14 years old), who suffered from RTIs during an influenza season (Dec 1st, 2019–Dec 31st, 2019), were collected (by face to face interview and medical records) and analyzed. Children on AIT were divided into 2 groups: stage 1 (dose increasing stage) and stage 2 (dose maintenance stage). Their siblings were enrolled as control. During the study period, 49 children with AA on AIT (33 patients in stage 1 and 16 patients in stage 2) as well as 49 children without AA ( their siblings ) were included. There were no significant differences in occurrences of RTIs among the three groups (p > 0.05). Compared with children in the other two groups, patients with RTIs in stage 2 had less duration of coughing and needed less medicine. Children on AIT with maintenance doses had fewer symptoms and recovered quickly when they were attacked by RTIs, which suggested that AIT with dose maintenance may enhance disease resistance of the body.
Ultrahigh sensitive refractive index nanosensors based on nanoshells, nanocages and nanoframes: effects of plasmon hybridization and restoring force
Authors: Omrani MirKazem , Mohammadi Hamidreza , Fallah Hamidreza 
Published: January 2021

AbstractIn this study, the effect of the plasmon hybridization mechanism on the performance and refractive index (RI) sensitivity of nanoshell, nanocage and nanoframe structures is investigated using the finite-difference time-domain simulation. To create nanocage structure, we textured the cubic nanoshell surfaces and examined the impact of its key parameters (such as array of cavities, size of cavities and wall thickness) on the nanocage's RI-sensitivity. Synthesis of the designed nanocages is a challenging process in practice, but here the goal is to understand the physics lied behind it and try to answer the question “Why nanoframes are more sensitive than nanocages?”. Our obtained results show that the RI-sensitivity of nanocage structures increases continuously by decreasing the array of cavities. Transforming the nanocage to the nanoframe structure by reducing the array of cavities to a single cavity significantly increases the RI-sensitivity of the nanostructure. This phenomenon can be related to the simultaneous presence of symmetric and asymmetric plasmon oscillations in the nanocage structure and low restoring force of nanoframe compared to nanocage. As the optimized case shows, the proposed single nanoframe with aspect ratio (wall length/wall thickness) of 12.5 shows RI-sensitivity of 1460 nm/RIU, the sensitivity of which is ~ 5.5 times more than its solid counterpart.
Partridge and embryonated partridge egg as new preclinical models for candidiasis
Authors: Tavakkoli Hadi , Khosravi Ahmad , Sharifi Iraj , Salari Zohreh , Salarkia Ehsan , Kheirandish Reza , Dehghantalebi Kazem , Jajarmi Maziar , Mosallanejad Seyedeh Saedeh , Dabiri Shahriar , Keyhani Alireza 
Published: January 2021

AbstractCandida albicans (C. albicans) is the most common cause of candidiasis in humans and animals. This study was established to a new experimental infection model for systemic candidiasis using partridge and embryonated partridge egg. First, we tested the induction of systemic candidiasis in partridge and embryonated partridge egg. Finally, interaction between virulence factors of C. albicans and Bcl-2 family members was predicted. We observed that embryonic infection causes a decrease in survival time and at later embryonic days (11–12th), embryos showed lesions. Morphometric analysis of the extra-embryonic membrane (EEM) vasculature showed that vascular apoptotic effect of C. albicans was revealed by a significant reduction in capillary area. In immunohistochemistry assay, low expression of Bcl-2 and increased expression of Bax confirmed apoptosis. The gene expression of Bax and Bcl-2 was also altered in fungi-exposed EEM. Ourin silico simulation has shown an accurate interaction between aspartic proteinase, polyamine oxidase, Bcl-2 and BAX. We observed that the disease was associated with adverse consequences, which were similar to human candidiasis. Acquired results support the idea that partridge and embryonated partridge egg can be utilized as appropriate preclinical models to investigate the pathological effects of candidiasis.
Effects of carbon nanotubes on expanded glass and silica aerogel based lightweight concrete
Authors: Adhikary Suman Kumar , Rudžionis Žymantas , Tučkutė Simona , Ashish Deepankar Kumar 
Published: January 2021

AbstractThis study is aimed to investigate the effect of carbon nanotubes on the properties of lightweight aggregate concrete containing expanded glass and silica aerogel. Combinations of expanded glass (55%) and hydrophobic silica aerogel particles (45%) were used as lightweight aggregates. Carbon nanotubes were sonicated in the water with polycarboxylate superplasticizer by ultrasonication energy for 3 min. Study results show that incorporating multi-wall carbon nanotubes significantly influences the compressive strength and microstructural performance of aerogel based lightweight concrete. The addition of carbon nanotubes gained almost 41% improvement in compressive strength. SEM image of lightweight concrete shows a homogeneous dispersal of carbon nanotubes within the concrete structure. SEM image of the composite shows presence of C–S–H gel surrounding the carbon nanotubes, which confirms the cites of nanotubes for the higher growth of C–S–H gel. Besides, agglomeration of carbon nanotubes and the presence of ettringites was observed in the transition zone between the silica aerogel and cementitious materials. Additionally, flowability, water absorption, microscopy, X-ray powder diffraction, and semi-adiabatic calorimetry results were analyzed in this study.