Miracle-dz/UniFAR-FTUs huggingface dataset:
Hydroponic Treatment of Nicotiana benthamiana with Kifunensine Modifies the N-glycans of Recombinant Glycoprotein Antigens to Predominantly Man9 High-Mannose Type upon Transient Overexpression

Nicotiana benthamiana transient overexpression systems offer unique advantages for rapid and scalable biopharmaceuticals production, including high scalability and eukaryotic post-translational modifications such as N-glycosylation. High-mannose-type glycans (HMGs) of glycoprotein antigens have been implicated in the effectiveness of some subunit vaccines. In particular, Man9GlcNAc2 (Man9) has high binding affinity to mannose-specific C-type lectin receptors such as the mannose receptor and dendritic cell-specific intracellular adhesion molecule 3-grabbing non-integrin (DC-SIGN). Here, we investigated the effect of kifunensine, an α-mannosidase I inhibitor, supplemented in a hydroponic culture of N. benthamiana for the production of Man9-rich HMG glycoproteins, using N-glycosylated cholera toxin B subunit (gCTB) and human immunodeficiency virus gp120 that are tagged with a H/KDEL endoplasmic reticulum retention signal as model vaccine antigens. Biochemical analysis using anti-fucose and anti-xylose antibodies as well as Endo H and PNGase F digestion showed that kifunensine treatment effectively reduced plant-specific glycoforms while increasing HMGs in the N-glycan compositions of gCTB. Detailed glycan profiling revealed that plant-produced gp120 had a glycan profile bearing mostly HMGs regardless of kifunensine treatment. However, the gp120 produced under kifunensine-treatment conditions showed Man9 being the most prominent glycoform (64.5%), while the protein produced without kifunensine had a substantially lower Man9 composition (20.3%). Our results open up possibilities for efficient production of highly mannosylated recombinant vaccine antigens in plants.
End-To-End Ego Lane Estimation Based on Sequential Transfer Learning for Self-Driving Cars

Autonomous cars establish driving strategies using the positions of ego lanes. The previous methods detect lane points and select ego lanes with heuristic and complex postprocessing with strong geometric assumptions. We propose a sequential end-to-end transfer learning method to estimate left and right ego lanes directly and separately without any postprocessing. We redefined a point-detection problem as a region-segmentation problem; as a result, the proposed method is insensitive to occlusions and variations of environmental conditions, because it considers the entire content of an input image during training. Also, we constructed an extensive dataset that is suitable for a deep neural network training by collecting a variety of road conditions, annotating ego lanes, and augmenting them systematically. The proposed method demonstrated improved accuracy and stability on input variations compared with a recent method based on deep learning. Our approach does not involve postprocessing, and is therefore flexible to change of target domain.
Imitation learning for a continuum trunk robot

The paper applies learning from demonstration (LfD) for high-level trajectory planning and movement control of the Bionic Handling Assistant (BHA) robot. For such soft continuum robot with mechanical elasticity and complex dynamics it is diﬃcult to use kinesthetic teaching to collect demonstration data. We propose to use an active compliant controller to this aim and record both position and orientation of the BHA’s end-eﬀector. Subsequently, this data is then encoded with a state-of-the-art task-parameterized probabilistic Gaussian mixture model and its performance and generalization is experimentally evaluated.
Achene structure, development and lipid accumulation in sunflower cultivars differing in oil content at maturity.

BACKGROUND AND AIMS Sunflower cultivars exhibit a wide range of oil content in the mature achene, but the relationship between this and the dynamics of oil deposition in the achene during grain filling is not known. Information on the progress, during the whole achene growth period, of the formation of oil bodies in the components of the achene and its relationship with variations in final oil content is also lacking. METHODS The biomass dynamics of achene components (pericarp, embryo, oil) in three cultivars of very different final oil concentration (30-56 % oil) were studied. In parallel, anatomical sections were used to follow the formation of oil and protein bodies in the embryo, and to observe pericarp anatomy. KEY RESULTS In all cultivars, oil bodies were first observed in the embryo 6-7 daa after anthesis (daa). The per-cell number of oil bodies increased rapidly from 10-12 daa until 25-30 daa. Oil bodies were absent from the outer cell layers of young fruit and from mature pericarps. In mature embryos, the proportion of cell cross-sectional area occupied by protein bodies increased with decreasing embryo oil concentration. The sclerenchymatic layer of the mature pericarp decreased in thickness and number of cell layers from the low-oil cultivar to the high-oil cultivar. Different patterns of oil accumulation in the embryo across cultivars were also found, leading to variations in ripe embryo oil concentration. In the high-oil cultivar, the end of oil deposition coincided with cessation of embryo growth, while in the other two cultivars oil ceased to accumulate before the embryo achieved maximum weight. CONCLUSIONS Cultivar differences in mature achene oil concentration reflect variations in pericarp proportion and thickness and mature embryo oil concentration. Cultivar differences in protein body proportion and embryo and oil mass dynamics during achene growth underlie variations in embryo oil concentration.
Determining features for discriminating PTB and normal lungs using phase congruency model

The appearance of the infected zone on the digital chest X-ray image for pulmonary tuberculosis (PTB) does not conform to standard shape, size or configuration. This study uses phase congruency (PC(x)) values to gather information from transition of adjacent pixel values that may be used as features to represent known disease type. The feature vector consisting of the average, variance, coefficient of variation and maximum PC(x)-values was found to be able to detect PTB with high accuracy.
The coupling between auditory and motor cortices is rate-restricted: Evidence for an intrinsic speech-motor rhythm

Auditory-motor neural synchronization during perception is restricted to a narrow frequency range and enhanced at ~4.5 Hz. The relation between perception and action remains a fundamental question for neuroscience. In the context of speech, existing data suggest an interaction between auditory and speech-motor cortices, but the underlying mechanisms remain incompletely characterized. We fill a basic gap in our understanding of the sensorimotor processing of speech by examining the synchronization between auditory and speech-motor regions over different speech rates, a fundamental parameter delimiting successful perception. First, using magnetoencephalography, we measure synchronization between auditory and speech-motor regions while participants listen to syllables at various rates. We show, surprisingly, that auditory-motor synchrony is significant only over a restricted range and is enhanced at ~4.5 Hz, a value compatible with the mean syllable rate across languages. Second, neural modeling reveals that this modulated coupling plausibly emerges as a consequence of the underlying neural architecture. The findings suggest that the temporal patterns of speech emerge as a consequence of the intrinsic rhythms of cortical areas.
Tensor methods and recommender systems

A substantial progress in development of new and efficient tensor factorization techniques has led to an extensive research of their applicability in recommender systems field. Tensor‐based recommender models push the boundaries of traditional collaborative filtering techniques by taking into account a multifaceted nature of real environments, which allows to produce more accurate, situational (e.g., context‐aware and criteria‐driven) recommendations. Despite the promising results, tensor‐based methods are poorly covered in existing recommender systems surveys. This survey aims to complement previous works and provide a comprehensive overview on the subject. To the best of our knowledge, this is the first attempt to consolidate studies from various application domains, which helps to get a notion of the current state of the field. We also provide a high level discussion of the future perspectives and directions for further improvement of tensor‐based recommendation systems. WIREs Data Mining Knowl Discov 2017, 7:e1201. doi: 10.1002/widm.1201
Local memory-aware kernel perforation

Many applications provide inherent resilience to some amount of error and can potentially trade accuracy for performance by using approximate computing. Applications running on GPUs often use local memory to minimize the number of global memory accesses and to speed up execution. Local memory can also be very useful to improve the way approximate computation is performed, e.g., by improving the quality of approximation with data reconstruction techniques. This paper introduces local memory-aware perforation techniques specifically designed for the acceleration and approximation of GPU kernels. We propose a local memory-aware kernel perforation technique that first skips the loading of parts of the input data from global memory, and later uses reconstruction techniques on local memory to reach higher accuracy while having performance similar to state-of-the-art techniques. Experiments show that our approach is able to accelerate the execution of a variety of applications from 1.6× to 3× while introducing an average error of 6%, which is much smaller than that of other approaches. Results further show how much the error depends on the input data and application scenario, the impact of local memory tuning and different parameter configurations.
Recrystallization of Amorphized α-TCP

Phase-pure α-TCP powder was milled using a high-energy planetary mill to obtain a partially X-ray amorphous material. Calcination at temperatures between 350 and 600 °C was employed to recrystallize the powder. The phase composition as a function of calcination time and temperature was determined in-situ using high-temperature XRD equipment. It was found that the amorphous fraction recrystallized mainly to α-TCP, with only small amounts of β-TCP formed. At low temperatures (≤ 450 °C), a stable composition with approximately 85 wt-% α-TCP was found once 100% crystallinity was reached. The time required to reach full crystallinity depended on the calcination temperature. For temperatures > 450 °C a slow transformation to β-TCP was observed. The transformation rate depended on the calcination temperature and on the milling intensity. A moderately milled powder recrystallized to α-TCP, followed by a slow transformation to β-TCP at 600 °C, whereas an intensely milled powder also recrystallized to α-TCP, followed by a fast transformation to β-TCP at the same temperature.
The Silkworm Coming of Age—Early

In order to grow, immature insects must periodically synthesize a new cuticle and shed the old one (a process of molting and ecdysis) until they have reached a stage permitting metamorphosis to the reproductive adult. Each molt is induced by a pulse of ecdysteroids, but the nature of the molt is determined by the juvenile hormones (JHs) [1]. These are sesquiterpenoids, synthesized from three isoprene units via the mevalonate pathway and decorated by an epoxide group on one end and a methyl ester on the other [1]. The JHs maintain larval characters, a status quo effect that is lifted when the level of JH drops. A threshold size must be attained for each molt and for metamorphosis to occur, and this size may relate to the limit of oxygen supply by the tracheal system [2], [3]. The number of molts varies among and sometimes within species; it is influenced by nutrition and by environmental and genetic signals. Yet, the mechanisms that “measure size” or “count the larval instars” are overridden by the experimental depletion of JHs. It has long been a tenet of insect endocrinology that removal of the corpora allata (CA), the endocrine glands that produce the JHs, causes precocious metamorphosis [1]. However, bringing the JH titer down experimentally is not as trivial as it may seem.
Dynamics of biofilm processes

Biofilms can develop on almost any surface exposed to an aqueous environment. The biofilm systems that result can be used beneficially, as exemplified by fixed-film wastewater treatment processes (for example, trickling filters and rotating biological contactors). In addition, biofilms play a major positive role in stream purification processes. However, biofilms can be quite troublesome in certain engineering systems. In water distribution systems and heat transfer equipment, for example, biofilms can cause substantial energy losses resulting from increased fluid frictional resistance and increased heat transfer resistance. The significance of biofilm development on various processes is summarized. (JMT)
The role of intrinsic muscle mechanics in the neuromuscular control of stable running in the guinea fowl

Here we investigate the interplay between intrinsic mechanical and neural factors in muscle contractile performance during running, which has been less studied than during walking. We report in vivo recordings of the gastrocnemius muscle of the guinea fowl (Numida meleagris), during the response and recovery from an unexpected drop in terrain. Previous studies on leg and joint mechanics following this perturbation suggested that distal leg extensor muscles play a key role in stabilisation. Here, we test this through direct recordings of gastrocnemius fascicle length (using sonomicrometry), muscle–tendon force (using buckle transducers), and activity (using indwelling EMG). Muscle recordings were analysed from the stride just before to the second stride following the perturbation. The gastrocnemius exhibits altered force and work output in the perturbed and first recovery strides. Muscle work correlates strongly with leg posture at the time of ground contact. When the leg is more extended in the drop step, net gastrocnemius work decreases (−5.2 J kg−1versus control), and when the leg is more flexed in the step back up, it increases (+9.8 J kg−1versus control). The muscle's work output is inherently stabilising because it pushes the body back toward its pre‐perturbation (level running) speed and leg posture. Gastrocnemius length and force return to level running means by the second stride following the perturbation. EMG intensity differs significantly from level running only in the first recovery stride following the perturbation, not within the perturbed stride. The findings suggest that intrinsic mechanical factors contribute substantially to the initial changes in muscle force and work. The statistical results suggest that a history‐dependent effect, shortening deactivation, may be an important factor in the intrinsic mechanical changes, in addition to instantaneous force–velocity and force–length effects. This finding suggests the potential need to incorporate history‐dependent muscle properties into neuromechanical simulations of running, particularly if high muscle strains are involved and stability characteristics are important. Future work should test whether a Hill or modified Hill type model provides adequate prediction in such conditions. Interpreted in light of previous studies on walking, the findings support the concept of speed‐dependent roles of reflex feedback.
Spiral Magnets as Magnetoelectrics

AbstractMagnetoelectric multiferroics is an old but emerging class of materials that combine coupled electric and magnetic dipole order. In these materials, ferroelectric and magnetic (ferromagnetic or antiferromagnetic) states coexist or compete with each other. The interaction leads to a so-called magnetoelectric effect, which is the induction of magnetization by an electric field or electric polarization by a magnetic field. In the past few years, a new set of magnetoelectric multiferroics such as TbMnO3 and Ni3V2O8 has been discovered. In these magnetoelectric multiferroics, ferroelectric order develops upon a magnetic phase transition into a spiral magnetic ordered phase. In addition, these systems show large magnetoelectric effects accompanied by metamagnetic transitions. Noncollinear spiral magnetism is the key to understanding the magnetoelectric properties in these systems. Here I discuss the magnetoelectric coupling in spiral magnets and review recent advances in the understanding of ferroelectr.
No Interactions of Stacked Bt Maize with the Non-target Aphid Rhopalosiphum padi and the Spider Mite Tetranychus urticae

In the agroecosystem, genetically engineered plants producing insecticidal Cry proteins from Bacillus thuringiensis (Bt) interact with non-target herbivores and other elements of the food web. Stacked Bt crops expose herbivores to multiple Cry proteins simultaneously. In this study, the direct interactions between SmartStax® Bt maize producing six different Cry proteins and two herbivores with different feeding modes were investigated. Feeding on leaves of Bt maize had no effects on development time, fecundity, or longevity of the aphid Rhopalosiphum padi (Hemiptera: Aphididae), and no effects on the egg hatching time, development time, sex ratio, fecundity, and survival of the spider mite Tetranychus urticae (Acari: Tetranychidae). The results thus confirm the lack of effects on those species reported previously for some of the individual Cry proteins. In the Bt maize leaves, herbivore infestation did not result in a consistent change of Cry protein concentrations. However, occasional statistical differences between infested and non-infested leaves were observed for some Cry proteins and experimental repetitions. Overall, the study provides evidence that the Cry proteins in stacked Bt maize do not interact with two common non-target herbivores.
A CNN-Based Fusion Method for Feature Extraction from Sentinel Data

Sensitivity to weather conditions, and specially to clouds, is a severe limiting factor to the use of optical remote sensing for Earth monitoring applications. A possible alternative is to benefit from weather-insensitive synthetic aperture radar (SAR) images. In many real-world applications, critical decisions are made based on some informative optical or radar features related to items such as water, vegetation or soil. Under cloudy conditions, however, optical-based features are not available, and they are commonly reconstructed through linear interpolation between data available at temporally-close time instants. In this work, we propose to estimate missing optical features through data fusion and deep-learning. Several sources of information are taken into account—optical sequences, SAR sequences, digital elevation model—so as to exploit both temporal and cross-sensor dependencies. Based on these data and a tiny cloud-free fraction of the target image, a compact convolutional neural network (CNN) is trained to perform the desired estimation. To validate the proposed approach, we focus on the estimation of the normalized difference vegetation index (NDVI), using coupled Sentinel-1 and Sentinel-2 time-series acquired over an agricultural region of Burkina Faso from May–November 2016. Several fusion schemes are considered, causal and non-causal, single-sensor or joint-sensor, corresponding to different operating conditions. Experimental results are very promising, showing a significant gain over baseline methods according to all performance indicators.
Treatment of striae distensae: An evidence-based approach

ABSTRACT Striae distensae (SD), otherwise known as “stretchmarks,” are a common presenting complaint, particularly in young healthy women. SD are hypothesized to form in a patient when the cross-linked collagen is “overstretched” and rupture of this collagen matrix causes the striae. Thus, many treatments work by increasing collagen synthesis. This review critically appraises the evidence to date for the treatment of SD, including both energy-based devices and topical treatments.
Comorbidities in Anti-Cyclic Citrullinated Peptide Positive At-Risk Individuals Do Not Differ from Those Patients with Early Inflammatory Arthritis

Objectives To compare comorbidities in a cohort of cyclic citrullinated peptide (CCP) antibody positive patients without or prior to onset of inflammatory arthritis (IA) to those in patients with early IA. Methods Baseline data from two established cohorts were used. The first recruited people at risk of IA: CCP antibody positive cases without IA (CCP Cohort, n = 296). The second cohort [the Inflammatory Arthritis CONtinuum study (IACON)] recruited patients with early IA (n = 725). Proportions of patients with given comorbidities were compared between cohorts and then logistic regression was used to determine odds ratios (OR) for the CCP cohort having specific comorbidities, compared to IACON patients. Analyses adjusted for gender, age, smoking status, and body mass index. Results Patients from the CCP cohort were younger (mean age 50, compared to 53 years). The proportion of patients with at least one comorbidity was higher in the IACON than the CCP cohort: (40% compared to 24%, respectively). Results of logistic regression analyses suggested the odds of hypertension, taking a lipid-lowering agent, ischemic heart disease, cerebrovascular disease, lung disease, and diabetes were not increased in either cohort. However, patients in the CCP cohort were more likely to be taking an antidepressant (OR = 1.62, 95% CI 1.03, 2.56, p = 0.037). Conclusion There was no significant difference in comorbidities among people with CCP antibodies but without IA, compared to those of patients with established IA.
Polygenic scores via penalized regression on summary statistics

Polygenic scores (PGS) summarize the genetic contribution of a person’s genotype to a disease or phenotype. They can be used to group participants into different risk categories for diseases, and are also used as covariates in epidemiological analyses. A number of possible ways of calculating polygenic scores have been proposed, and recently there is much interest in methods that incorporate information available in published summary statistics. As there is no inherent information on linkage disequilibrium (LD) in summary statistics, a pertinent question is how we can make use of LD information available elsewhere to supplement such analyses. To answer this question we propose a method for constructing PGS using summary statistics and a reference panel in a penalized regression framework, which we call lassosum. We also propose a general method for choosing the value of the tuning parameter in the absence of validation data. In our simulations, we showed that pseudovalidation often resulted in prediction accuracy that is comparable to using a dataset with validation phenotype and was clearly superior to the conservative option of setting the tuning parameter of lassosum to its lowest value. We also showed that lassosum achieved better prediction accuracy than simple clumping and p-value thresholding in almost all scenarios. It was also substantially faster and more accurate than the recently proposed LDpred.