bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the central 10 degrees visual field in glaucoma by applying a deep learning algorithm to optical coherence tomography images
Authors: Asano Shotaro , Asaoka Ryo , Murata Hiroshi , Hashimoto Yohei , Miki Atsuya , Mori Kazuhiko , Ikeda Yoko , Kanamoto Takashi , Yamagami Junkichi , Inoue Kenji 
Published: January 2021

AbstractWe aimed to develop a model to predict visual field (VF) in the central 10 degrees in patients with glaucoma, by training a convolutional neural network (CNN) with optical coherence tomography (OCT) images and adjusting the values with Humphrey Field Analyzer (HFA) 24–2 test. The training dataset included 558 eyes from 312 glaucoma patients and 90 eyes from 46 normal subjects. The testing dataset included 105 eyes from 72 glaucoma patients. All eyes were analyzed by the HFA 10-2 test and OCT; eyes in the testing dataset were additionally analyzed by the HFA 24-2 test. During CNN model training, the total deviation (TD) values of the HFA 10-2 test point were predicted from the combined OCT-measured macular retinal layers’ thicknesses. Then, the predicted TD values were corrected using the TD values of the innermost four points from the HFA 24-2 test. Mean absolute error derived from the CNN models ranged between 9.4 and 9.5 B. These values reduced to 5.5 dB on average, when the data were corrected using the HFA 24-2 test. In conclusion, HFA 10-2 test results can be predicted with a OCT images using a trained CNN model with adjustment using HFA 24-2 test.
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis–Lycium barbarum coupled-herbs against oligoasthenozoospermia
Authors: Bai Xue , Tang Yibo , Li Qiang , Chen Yafei , Liu Dan , Liu Guimin , Fan Xiaolei , Ma Ru , Wang Shuyan , Li Lingru , Zhou Kailin , Zheng Yanfei , Liu Zhenquan 
Published: January 2021

AbstractOligoasthenozoospermia (OA) is one of the most common types of male infertility affecting sperm count and sperm motility. Unfortunately, it is difficult for existing drugs to fundamentally improve the sperm quality of OA patients, because the pathological mechanism of OA has not been fully elucidated yet.Morinda officinalis–Lycium barbarumcoupled-herbs (MOLBCH), as traditional Chinese Medicines, has been widely used for treating OA over thousands of years, but its molecular mechanism is still unclear. For this purpose, we adopted a comprehensive approach integrated network pharmacology and molecular docking to reveal the bioactive components and potential targets of MOLBCH against OA. The results showed that MOLBCH alleviated apoptosis, promoted male reproductive function, and reduced oxidant stress in the treatment of OA. Ohioensin-A, quercetin, beta-sitosterol and sitosterol were the key bioactive components. Androgen receptor (AR), Estrogen receptor (ESR1), Mitogen-activated protein kinase 3 (MAPK3), RAC-alpha serine/threonine-protein kinase (AKT1), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were the core potential targets. PI3K/Akt signaling pathway, prostate cancer, AGE-RAGE signaling pathway in diabetic complications were the most representative pathways. Moreover, molecular docking was performed to validate the strong binding interactions between the obtained core components and targets. These observations provide deeper insight into the pathogenesis of OA and can be used to design new drugs and develop new therapeutic instructions to treat OA.
Changes in melon plant phytochemistry impair Aphis gossypii growth and weight under elevated CO2
Authors: Moreno-Delafuente Ana , Morales Ignacio , Garzo Elisa , Fereres Alberto , Viñuela Elisa , Medina Pilar 
Published: January 2021

AbstractElevated CO2(eCO2) modifies plant primary and secondary metabolism that subsequently impacts herbivore insect performance due to changes in its nutritional requirements. This laboratory study evaluated interactions betweenAphis gossypiiGlover (Hemiptera: Aphididae) and melon (Cucumis meloL., Cucurbitaceae), previously acclimated two or six weeks to different CO2levels, eCO2(700 ppm) or ambient CO2(400 ppm). Under eCO2, melon plants decreased nitrogen foliar concentration and increased carbon to nitrogen ratio, independently of acclimation period, significantly reducing the content of some amino acids (alanine, asparagine, glycine, isoleucine, lysine, serine, threonine, and valine) and increasing the carbohydrate (sucrose) content in melon leaves. The dilution in some essential amino acids for aphid nutrition could have aggravated the reduction inA. gossypiipopulation growth reared on melon previously acclimated two weeks to eCO2, as well as the loss of aphid body mass from two successive generations ofA. gossypiireared under eCO2on plants previously acclimated two or six weeks to eCO2. The response to eCO2of phloem feeders, such as aphids, is actually variable, but this study highlights a negative response ofA. gossypiito this climate change driver. Potential implications on control of this pest in a global change scenario are discussed.
A new SYBR Green real-time PCR to detect SARS-CoV-2
Authors: Marinowic D. R. , Zanirati G. , Rodrigues F. V. F. , Grahl M. V. C. , Alcará A. M. , Machado D. C. , Da Costa J. C. 
Published: January 2021

AbstractPhylogenetic analysis has demonstrated that the etiologic agent of the 2020 pandemic outbreak is a betacoronavirus named SARS-CoV-2. For public health interventions, a diagnostic test with high sensitivity and specificity is required. The gold standard protocol for diagnosis by the Word Health Organization (WHO) is RT-PCR. To detect low viral loads and perform large-scale screening, a low-cost diagnostic test is necessary. Here, we developed a cost-effective test capable of detecting SARS-CoV-2. We validated an auxiliary protocol for molecular diagnosis with the SYBR Green RT-PCR methodology to successfully screen negative cases of SARS-CoV-2. Our results revealed a set of primers with high specificity and no homology with other viruses from the Coronovideae family or human respiratory tract pathogenic viruses, presenting with complementarity only for rhinoviruses/enteroviruses and Legionella spp. Optimization of the annealing temperature and polymerization time led to a high specificity in the PCR products. We have developed a more affordable and swift methodology for negative SARS-CoV-2 screening. This methodology can be applied on a large scale to soften panic and economic burden through guidance for isolation strategies.
The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content
Authors: Hereira-Pacheco Stephanie E. , Navarro-Noya Yendi E. , Dendooven Luc 
Published: January 2021

AbstractRhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.
In vitro optoacoustic flow cytometry with light scattering referencing
Authors: Seeger Markus , Stiel Andre C. , Ntziachristos Vasilis 
Published: January 2021

AbstractMorphological and functional optoacoustic imaging is enhanced by dedicated transgene reporters, in analogy to fluorescence methods. The development of optoacoustic reporters using protein engineering and directed evolution would be accelerated by high-throughput in-flow screening for intracellular, genetically encoded, optoacoustic contrast. However, accurate characterization of such contrast is impeded because the optoacoustic signals depend on the cell’s size and position in the flow chamber. We report herein an optoacoustic flow cytometer (OA-FCM) capable of precise measurement of intracellular optoacoustic signals of genetically-encoded chromoproteins in flow. The novel system records light-scattering as a reference for the detected optoacoustic signals in order to account for cell size and position, as well as excitation light flux in the focal volume, which we use to reference the detected optoacoustic signals to enhance the system’s precision. The OA-FCM was calibrated using micrometer-sized particles to showcase the ability to assess in-flow objects in the size range of single-cells. We demonstrate the capabilities of our OA-FCM to identify sub-populations in a mixture of two E. coli stocks expressing different reporter-proteins with a precision of over 90%. High-throughput screening of optoacoustic labels could pave the way for identifying genetically encoded optoacoustic reporters by transferring working concepts of the fluorescence field such as directed evolution and activated cell sorting.
The impact of tinnitus distress on cognition
Authors: Neff P. , Simões J. , Psatha S. , Nyamaa A. , Boecking B. , Rausch L. , Dettling-Papargyris J. , Funk C. , Brueggemann P. , Mazurek B. 
Published: January 2021

AbstractTinnitus is the chronic perception of a phantom sound with different levels of related distress. Past research has elucidated interactions of tinnitus distress with audiological, affective and further clinical variables. The influence of tinnitus distress on cognition is underinvestigated. Our study aims at investigating specific influences of tinnitus distress and further associated predictors on cognition in a cohort of n = 146 out-ward clinical tinnitus patients. Age, educational level, hearing loss, Tinnitus Questionnaire (TQ) score, tinnitus duration, speech in noise (SIN), stress, anxiety and depression, and psychological well-being were included as predictors of a machine learning regression approach (elastic net) in three models with scores of a multiple choice vocabulary test (MWT-B), or two trail-making tests (TMT-A and TMT-B), as dependent variables. TQ scores predicted lower MWT-B scores and higher TMT-B test completion time. Stress, emotional, and psychological variables were not found to be relevant predictors in all models with the exception of small positive influences of SIN and depression on TMT-B. Effect sizes were small to medium for all models and predictors. Results are indicative of specific influence of tinnitus distress on cognitive performance, especially on general or crystallized intelligence and executive functions. More research is needed at the delicate intersection of tinnitus distress and cognitive skills needed in daily functioning.
Overcoming limitations in the availability of swabs systems used for SARS-CoV-2 laboratory diagnostics
Authors: Nairz Manfred , Bellmann-Weiler Rosa , Ladstätter Miriam , Schüllner Falko , Zimmermann Martina , Koller Anna-Maria , Blunder Silvia , Naschberger Helene , Klotz Werner , Herold Manfred , Kerndler Sylvia , Jeske Martina , Haschka David , Petzer Verena , Schroll Andrea , Sonnweber Thomas , Tancevski Ivan , Fritsche Gernot , de Araujo Mariana E. G. , Stasyk Taras , Huber Lukas A. , Griesmacher Andrea , Theurl Igor , Weiss Günter 
Published: January 2021

AbstractThe diagnosis of COVID-19 relies on the direct detection of SARS-CoV-2 RNA in respiratory specimens by RT-PCR. The pandemic spread of the disease caused an imbalance between demand and supply of materials and reagents needed for diagnostic purposes including swab sets. In a comparative effectiveness study, we conducted serial follow-up swabs in hospitalized laboratory-confirmed COVID-19 patients. We assessed the diagnostic performance of an in-house system developed according to recommendations by the US CDC. In a total of 96 serial swabs, we found significant differences in the accuracy of the different swab systems to generate a positive result in SARS-CoV-2 RT-PCR, ranging from around 50 to 80%. Of note, an in-house swab system was superior to most commercially available sets as reflected by significantly lower Ct values of viral genes. Thus, a simple combination of broadly available materials may enable diagnostic laboratories to bypass global limitations in the supply of swab sets.
Electrosynthesis of polydopamine-ethanolamine films for the development of immunosensing interfaces
Authors: Almeida Luís C. , Frade Tânia , Correia Rui D. , Niu Yu , Jin Gang , Correia Jorge P. , Viana Ana S. 
Published: January 2021

AbstractWe report a straightforward and reproducible electrochemical approach to develop polydopamine-ethanolamine (ePDA-ETA) films to be used as immunosensing interfaces. ETA is strongly attached to polydopamine films during the potentiodynamic electropolymerization of dopamine. The great advantage of the electrochemical methods is to generate the oxidized species (quinones), which can readily react with ETA amine groups present in solution, with the subsequent incorporation of this molecule in the polymer. The presence of ETA and its effect on the electrosynthesis of polydopamine was accessed by cyclic voltammetry, ellipsometry, atomic force microscopy, FTIR and X-ray photoelectron spectroscopy. The adhesive and biocompatible films enable a facile protein linkage, are resilient to flow assays, and display intrinsic anti-fouling properties to block non-specific protein interactions, as monitored by real-time surface plasmon resonance, and confirmed by ellipsometry. Immunoglobulin G (IgG) and Anti-IgG were used in this work as model proteins for the affinity sensor. By using the one-step methodology (ePDA-ETA), the lower amount of immobilized biorecognition element, IgG, compared to that deposited on ePDA or on ETA post-modified film (ePDA/ETA), allied to the presence of ETA, improved the antibody-antigen affinity interaction. The great potential of the developed platform is its versatility to be used with any target biorecognition molecules, allowing both optical and electrochemical detection.
Cognitive underpinnings of multidimensional Japanese literacy and its impact on higher-level language skills
Authors: Otsuka Sadao , Murai Toshiya 
Published: January 2021

AbstractThis study aimed to identify the cognitive underpinnings of Japanese kanji abilities and clarify the contributions of kanji acquisition to the development of higher-level language skills based on a three-dimensional view of kanji abilities encompassing reading accuracy, writing accuracy, and semantic comprehension. First, a series of regression analyses was used to identify the multifactorial models of each dimension of Japanese kanji acquisition. These models suggest that, among basic cognitive skills, naming speed, visuospatial processing, and syntactic processing underpin kanji abilities in a dimension-specific manner, whereas phonological processing is a common factor. Second, although all the dimensions of kanji abilities predicted acquired verbal knowledge equally, writing skills on the text level, measured as idea density, were only predicted by the writing dimension (indirectly via acquired knowledge). Our findings represent the first evidence of the dimension-specific relationships of the three dimensions of Japanese kanji abilities with their cognitive predictors, as well as with higher-level language skills. They suggest the importance of handwriting acquisition during school years for the development of language skills through to adulthood. Finally, taking the seminal “Nun study,” which suggests that higher idea density is protective against dementia, into account, we propose a theoretical framework for the lifelong trajectory of literacy acquisition.
Accurate dating of stalagmites from low seasonal contrast tropical Pacific climate using Sr 2D maps, fabrics and annual hydrological cycles
Authors: Faraji Mohammadali , Borsato Andrea , Frisia Silvia , Hellstrom John C. , Lorrey Andrew , Hartland Adam , Greig Alan , Mattey David P. 
Published: January 2021

AbstractTropical Pacific stalagmites are commonly affected by dating uncertainties because of their low U concentration and/or elevated initial230Th content. This poses problems in establishing reliable trends and periodicities for droughts and pluvial episodes in a region vulnerable to climate change. Here we constrain the chronology of a Cook Islands stalagmite using synchrotron µXRF two-dimensional mapping of Sr concentrations coupled with growth laminae optical imaging constrained by in situ monitoring. Unidimensional LA-ICP-MS-generated Mg, Sr, Ba and Na variability series were anchored to the 2D Sr and optical maps. The annual hydrological significance of Mg, Sr, Ba and Na was tested by principal component analysis, which revealed that Mg and Na are related to dry-season, wind-transported marine aerosols, similar to the host-rock derived Sr and Ba signatures. Trace element annual banding was then used to generate a calendar-year master chronology with a dating uncertainty maximum of ± 15 years over 336 years. Our approach demonstrates that accurate chronologies and coupled hydroclimate proxies can be obtained from speleothems formed in tropical settings where low seasonality and problematic U–Th dating would discourage the use of high-resolution climate proxies datasets.
Episodic-like memory of rats as retrospective retrieval of incidentally encoded locations and involvement of the retrosplenial cortex
Authors: Sato Nobuya 
Published: January 2021

AbstractTo examine episodic memory in rats, we trained rats to perform two tasks and tested them for memory of past self-behavior without making them expect to be asked about the memory later when encoding. One of the trained tasks was a delayed matching-to-position task in which the rats were required to remember the location of a presented lever. The other was a tone discrimination task in which the rats were required to discriminate between two pure tones. After learning both tasks, the rats were unexpectedly asked the location of the pressed lever after responding to the cue tone in probe trials during test sessions. The rats demonstrated a response bias that suggests that they have the ability to retrospectively recollect their self-behavior, i.e., episodic memory. We next made excitotoxic lesions in the retrosplenial cortex (RSC) and investigated the effects of the lesions on the unexpected recollection. In the rats with lesions of the RSC, the response bias disappeared. This suggests that the RSC has a role in retrospectively answering unexpected questions about self-behavior.
A new method for measuring treadmill belt velocity fluctuations: effects of treadmill type, body mass and locomotion speed
Authors: Willwacher Steffen , Oberländer Kai Daniel , Mai Patrick , Mählich Daniela , Kurz Markus , Koopmann Till , Fohrmann Dominik , Kantarev Artur , Kersting Uwe Gustav 
Published: January 2021

AbstractTreadmills are essential to the study of human and animal locomotion as well as for applied diagnostics in both sports and medicine. The quantification of relevant biomechanical and physiological variables requires a precise regulation of treadmill belt velocity (TBV). Here, we present a novel method for time-efficient tracking of TBV using standard 3D motion capture technology. Further, we analyzed TBV fluctuations of four different treadmills as seven participants walked and ran at target speeds ranging from 1.0 to 4.5 m/s. Using the novel method, we show that TBV regulation differs between treadmill types, and that certain features of TBV regulation are affected by the subjects’ body mass and their locomotion speed. With higher body mass, the TBV reductions in the braking phase of stance became higher, even though this relationship differed between locomotion speeds and treadmill type (significant body mass × speed × treadmill type interaction). Average belt speeds varied between about 98 and 103% of the target speed. For three of the four treadmills, TBV reduction during the stance phase of running was more intense (> 5% target speed) and occurred earlier (before 50% of stance phase) unlike the typical overground center of mass velocity patterns reported in the literature. Overall, the results of this study emphasize the importance of monitoring TBV during locomotor research and applied diagnostics. We provide a novel method that is freely accessible on Matlab’s file exchange server (“getBeltVelocity.m”) allowing TBV tracking to become standard practice in locomotion research.
Algorithms for the selection of fluorescent reporters
Authors: Vaidyanathan Prashant , Appleton Evan , Tran David , Vahid Alexander , Church George , Densmore Douglas 
Published: January 2021

AbstractMolecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve with ad hoc methods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through.
Amplitude death and restoration in networks of oscillators with random-walk diffusion
Authors: Clusella Pau , Miguel M. Carmen , Pastor-Satorras Romualdo 
Published: January 2021

AbstractSystems composed of reactive particles diffusing in a network display emergent dynamics. While Fick’s diffusion can lead to Turing patterns, other diffusion schemes might display more complex phenomena. Here we study the death and restoration of collective oscillations in networks of oscillators coupled by random-walk diffusion, which modifies both the original unstable fixed point and the stable limit-cycle, making them topology-dependent. By means of numerical simulations we show that, in some cases, the diffusion-induced heterogeneity stabilizes the initially unstable fixed point via a Hopf bifurcation. Further increasing the coupling strength can moreover restore the oscillations. A numerical stability analysis indicates that this phenomenology corresponds to a case of amplitude death, where the inhomogeneous stabilized solution arises from the interplay of random walk diffusion and heterogeneous topology. Our results are relevant in the fields of epidemic spreading or ecological dispersion, where random walk diffusion is more prevalent.