Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 3 Advances in Agrobacterium-mediated Maize Transformation

One of the major limitations of maize transformation is the isolation of a large number of immature embryos using the time-consuming manual extraction method. In this article, we describe a novel bulk embryo extraction method for fast isolation of a large number of embryos suitable for both biolisticand Agrobacterium-mediated transformation. Optimal gene delivery and tissue culture conditions are also described for achieving high efficiency in Agrobacterium-mediated maize transformation using phosphomannose isomerase (PMI) as a selectable marker.
Judgment and classification of emotion terms by older and younger adults

ABSTRACT Objectives: Theoretical models of adult development suggest changes in emotion systems with age. This study determined how younger and older adults judged and classified 70 emotion terms that varied in valence and arousal, and that have been used in previous studies of adult aging and emotion. The terms were from the Positive and Negative Affect Schedule – Expanded (PANAS-X) and the (KS) affect scales. Method: Older (n = 32) and younger adults (n = 111) engaged in a card sort task which determined how the 70 emotion terms were classified (i.e. grouped) in relation to one another. Activation and valence ratings of emotion terms were collected. Results: There were 17 age group differences in item ratings for activation and 19 for valence. Older adults tended to rate emotion terms and scales as more positive and activating than younger persons. Card sort data indicated similarity in conceptualizations of emotion terms across groups with exceptions for serene, sad, and lonely. Conclusions: Research that utilizes self-report emotion data from older and younger persons should consider how perceptions of emotion terms may vary systematically with age. The constructs of sadness, loneliness, and serene may be age-variant and necessitate age-based adjustments in assessment and intervention. Further, older adults may perceive some emotion terms to be more activating and positive than younger persons.
The MJO‐SSW Teleconnection: Interaction Between MJO‐Forced Waves and the Midlatitude Jet

The Madden‐Julian Oscillation (MJO) was shown to affect both present‐day sudden stratospheric warming (SSW) events in the Arctic and their future frequency under global warming scenarios, with implications to the Arctic Oscillation and midlatitude extreme weather. This work uses a dry dynamic core model to understand the dependence of SSW frequency on the amplitude and longitudinal range of the MJO, motivated by the prediction that the MJO will strengthen and broaden its longitudinal range in a warmer climate. We focus on the response of the midlatitude jets and the corresponding generated stationary waves, which are shown to dominate the response of SSW events to MJO forcing. Momentum budget analysis of a large ensemble of spinup simulations suggests that the climatological jet response is driven by the MJO‐forced meridional eddy momentum transport. The results suggest that the trends in both MJO amplitude and longitudinal range are important for the prediction of the midlatitude jet response and for the prediction of SSWs in a future climate.
Cross-phenotype analysis of Immunochip data identifies KDM4C as a relevant locus for the development of systemic vasculitis

Objetive Systemic vasculitides represent a heterogeneous group of rare complex diseases of the blood vessels with a poorly understood aetiology. To investigate the shared genetic component underlying their predisposition, we performed the first cross-phenotype meta-analysis of genetic data from different clinically distinct patterns of vasculitis. Methods Immunochip genotyping data from 2465 patients diagnosed with giant cell arteritis, Takayasu’s arteritis, antineutrophil cytoplasmic antibody-associated vasculitis or IgA vasculitis as well as 4632 unaffected controls were analysed to identify common susceptibility loci for vasculitis development. The possible functional consequences of the associated variants were interrogated using publicly available annotation data. Results The strongest association signal corresponded with an intergenic polymorphism located between HLA-DQB1 and HLA-DQA2 (rs6932517, P=4.16E-14, OR=0.74). This single nucleotide polymorphism is in moderate linkage disequilibrium with the disease-specific human leucocyte antigen (HLA) class II associations of each type of vasculitis and could mark them. Outside the HLA region, we identified the KDM4C gene as a common risk locus for vasculitides (highest peak rs16925200, P=6.23E-07, OR=1.75). This gene encodes a histone demethylase involved in the epigenetic control of gene expression. Conclusions Through a combined analysis of Immunochip data, we have identified KDM4C as a new risk gene shared between systemic vasculitides, consistent with the increasing evidences of the crucial role that the epigenetic mechanisms have in the development of complex immune-mediated conditions.
Interleukin 1‐alpha deficiency increases the expression of Follicle‐stimulating hormone receptors in granulosa cells

Follicle‐stimulating hormone receptor (FSHR) is a pivotal regulator of ovarian response to hormonal stimulation. Inflammatory conditions have been linked to lower FSHR expression in granulosa cells (GCs) as well as an attenuated response to hormonal stimulation. The current study aimed to reveal if deficiency and/or blockage of the pro‐inflammatory cytokine interleukin 1‐alpha (IL1A) increased Fshr expression in rodent GCs. We found elevated Fshr transcript abundance, as assessed by quantitative PCR, in primary GCs isolated from Il1a‐knockout compared to wild‐type mice, and that the expression of FSHR is significantly higher in Il1a‐knockout compared to wild‐type ovaries. Supplementing GC cultures with recombinant IL1A significantly lowered Fshr expression in these cells. In accordance with the Fshr expression pattern, proliferation of GCs was higher in follicles from Il1a‐knockout mice compared to wild‐type mice, as indicated by the MKI67 immunohistochemical staining. Furthermore, treating wild‐type mice with anakinra, an IL1 receptor 1 antagonist, significantly increased the expression of Fshr in primary GCs from treated compared to control mice. These data highlight an important interdependency between the potent pro‐inflammatory cytokine IL1A and Fshr expression.
Chapter 1 Selective Data Acquisition for Machine Learning

In many applications, one must invest effort or money to acquire the data and other information required for machine learning and data mining. Careful selection of the information to acquire can substantially improve generalization performance per unit cost. The costly information scenario that has received the most research attention (see Chapter X) has come to be called ”active learning,” and focuses on choosing the instances for which target values (labels) will be acquired for training. However machine learning applications offer a variety of different sorts of information that may need to be acquired. This chapter focuses on settings and techniques for selectively acquiring information beyond just single training labels (the values of the target variable) for selected instances in order to improve a model’s predictive accuracy. The different kinds of acquired information include feature values, feature labels, entire examples, values at prediction time, repeated acquisition for the same data item, and more. For example, Figures 1.1 contrast the acquisition of training labels, feature values, and both. We will discuss all these sorts of information in detail. Broadening our view beyond simple active learning not only expands the set of applications to which we can apply selective acquisition strategies; it also
Facial Manifestations of Pachydermoperiostosis Treated with Botulinum Toxin Type-A: Report of 3 Cases

Pachydermoperiostosis (PDP) or primary hypertrophic osteoathropathy (PHO) (also known as Touraine-Solente-Golé syndrome; OMIM 167100) is a rare genetic disease involving formation of periosteal new bone, clubbing of the digits, enlargement of joints, arthralgias and hypertrophic skin changes, especially on the face, forehead, and scalp. PDP may also display additional symptoms such as seborrhea, hyperhidrosis and hypertrophic gastritis (1– 3). PDP is a chronic condition that, while not life-threatening, decreases the patient’s quality of life. Among other clinical manifestations, the thickened skin of the upper third of the face gives a leonine appearance to the face (4). We report here 3 cases of PDP that were treated by injections of botulinum toxin type A (BTX-A). To the best of our knowledge, this is only the third report describing the use of BTX-A for treatment of PDP, and the first in which a patient (Case 1) received a course of several injections.
Oscillometry and pulmonary MRI measurements of ventilation heterogeneity in obstructive lung disease: relationship to quality of life and disease control.

Ventilation heterogeneity is a hallmark finding in obstructive lung disease and may be evaluated using a variety of methods, including multiple-breath gas washout and pulmonary imaging. Such methods provide an opportunity to better understand the relationships between structural and functional abnormalities in the lungs, and their relationships with important clinical outcomes. We measured ventilation heterogeneity and respiratory impedance in 100 subjects [50 patients with asthma, 22 ex-smokers, and 28 patients with chronic obstructive pulmonary disease (COPD)] using oscillometry and hyperpolarized 3He magnetic resonance imaging (MRI) and determined their relationships with quality of life scores and disease control/exacerbations. We also coregistered MRI ventilation maps to a computational airway tree model to generate patient-specific respiratory impedance predictions for comparison with experimental measurements. In COPD and asthma patients, respectively, forced oscillation technique (FOT)-derived peripheral resistance (5-19 Hz) and MRI ventilation defect percentage (VDP) were significantly related to quality of life (FOT: COPD ρ = 0.4, P = 0.004; asthma ρ = -0.3, P = 0.04; VDP: COPD ρ = 0.6, P = 0.003; asthma ρ = -0.3, P = 0.04). Patients with poorly controlled asthma (Asthmatic Control Questionnaire >2) had significantly increased resistance (5 Hz: P = 0.01; 5-19 Hz: P = 0.006) and reactance (5 Hz: P = 0.03). FOT-derived peripheral resistance (5-19 Hz) was significantly related to VDP in patients with asthma and COPD patients (asthma: ρ = 0.5, P < 0.001; COPD: ρ = 0.5, P = 0.01), whereas total respiratory impedance was related to VDP only in patients with asthma (resistance 5 Hz: ρ = 0.3, P = 0.02; reactance 5 Hz: ρ = -0.5, P < 0.001). Model-predicted and FOT-measured reactance (5 Hz) were correlated in patients with asthma (ρ = 0.5, P = 0.001), whereas in COPD patients, model-predicted and FOT-measured resistance (5-19 Hz) were correlated (ρ = 0.5, P = 0.004). In summary, in patients with asthma and COPD patients, we observed significant, independent relationships for FOT-measured impedance and MRI ventilation heterogeneity measurements with one another and with quality of life scores. NEW & NOTEWORTHY In 100 patients, including patients with asthma and ex-smokers, 3He MRI ventilation heterogeneity and respiratory system impedance were correlated and both were independently related to quality of life scores and asthma control. These findings demonstrated the critical relationships between respiratory system impedance and ventilation heterogeneity and their role in determining quality of life and disease control. These observations underscore the dominant role that abnormalities in the lung periphery play in ventilation heterogeneity that results in patients' symptoms.
IspE Inhibitors Identified by a Combination of In Silico and In Vitro High-Throughput Screening

CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens.
Two convolutional neural networks for bird detection in audio signals

We present and compare two approaches to detect the presence of bird calls in audio recordings using convolutional neural networks on mel spectrograms. In a signal processing challenge using environmental recordings from three very different sources, only two of them available for supervised training, we obtained an Area Under Curve (AUC) measure of 89% on the hidden test set, higher than any other contestant. By comparing multiple variations of our systems, we find that despite very different architectures, both approaches can be tuned to perform equally well. Further improvements will likely require a radically different approach to dealing with the discrepancy between data sources.
Annexin A8 promotes VEGF-A driven endothelial cell sprouting

ABSTRACT The physiological and pathological process of angiogenesis relies on orchestrated endothelial cell (EC) adhesion, migration and formation of new vessels. Here we report that human umbilical vein endothelial cells (HUVECs) deficient in Annexin A8 (AnxA8), a member of the annexin family of Ca2+- and membrane binding proteins, are strongly deficient in their ability to sprout in response to vascular endothelial growth factor (VEGF)-A, and are strongly impaired in their ability to migrate and adhere to β1 integrin-binding extracellular matrix (ECM) proteins. We find that these cells are defective in the formation of complexes containing the tetraspanin CD63, the main VEGF-A receptor VEGFR2, and the β1 integrin subunit, on the cell surface. We observe that upon VEGF-A activation of AnxA8-depleted HUVECs, VEGFR2 internalization is reduced, phosphorylation of VEGFR2 is increased, and the spatial distribution of Tyr577-phosphorylated focal adhesion kinase (pFAK577) is altered. We conclude that AnxA8 affects CD63/VEGFR2/β1 integrin complex formation, leading to hyperactivation of the VEGF-A signal transduction pathway, and severely disturbed VEGF-A-driven angiogenic sprouting.
Absence of the Vitamin D Receptor Inhibits Atherosclerotic Plaque Calcification in Female Hypercholesterolemic Mice

Epidemiological and clinical data suggest adverse cardiovascular outcomes with respect to vitamin D deficiency. Here, we explored the effects of vitamin D in atherosclerotic plaque calcification in vivo by utilizing vitamin D receptor (Vdr)‐deficient mice in an Apoe−/− background. Animals were fed a high‐fat diet (HFD) for either 12 or 18 weeks and then examined for atherosclerotic plaque development. In order to prevent calcium deficiency, Vdr−/− and Apoe−/−;Vdr−/− animals were fed a high‐calcium rescue diet prior to initiation of the HFD feeding and supplemented with high‐calcium water during HFD feeding. Although calcium supplementation improved bone mass in Vdr−/− and Apoe−/−;Vdr−/− mice, neither strain was fully rescued. Systemic inflammatory responses observed in the absence of VDR were exaggerated in Apoe−/− mice. Whereas, hyperlipidemic profiles seen in Apoe−/− mice were ameliorated in the absence of VDR. Micro‐computed tomography (µCT) analysis revealed that six out of eight Apoe−/− animals developed atherosclerotic plaque calcification following 12 weeks of HFD feeding and 100% of the mice developed plaque calcification after 18 weeks. In contrast, although atherosclerotic lesions were evident in Apoe−/−;Vdr−/− mice at 12 and 18 weeks of HFD challenge, none of these animals developed plaque calcification at either time point. The active vitamin D hormone, 1,25(OH)2D3 likely increased calcification in aortic smooth muscle cells perhaps by directly modulating expression of Alpl, Rankl, and Opg. Our data suggest that the absence of VDR inhibits atherosclerotic plaque calcification in hypercholesterolemic Apoe−/− mice, providing additional insight into the role of vitamin D in atherosclerotic plaque calcification. J. Cell. Biochem. 118: 1050–1064, 2017. © 2016 Wiley Periodicals, Inc.
Externally excited coordination of autonomous formations

Inspired by the recent "Robot Sheepdog Project" in the literature, in this paper a new method for coordination of multi-agent systems moving in a 2-dimensional region with the obstacles along a collision free trajectory is presented. A two level decentralized control scheme is proposed. At lower level, for the agents within the formation, "the sheep", the only concern is to keep that of their formation shape intact and avoid inter-agent collision. At the higher level, an intelligent agent, "the sheepdog", is responsible for determining a collision free trajectory for both the formation and itself, and then coordinating the formation motion along this computed path sequence. This sheepdog utilizes a repulsive vector (acting as a source of repulsive force) to drive the formation along the planned path. The effectiveness of the proposed scheme is demonstrated via simulation results in the presence of multiple obstacles.
Parallelization, Modeling, and Performance Prediction in the Multi-/Many Core Area: A Systematic Literature Review

Context: Software developers face complex, connected, and large software projects. The development of such systems involves design decisions that directly impact the quality of the software. For an early decision making, software developers can use model-based prediction approaches for (non-)functional quality properties. Unfortunately, the accuracy of these approaches is challenged by newly introduced hardware features like multiple cores within a single CPU (multicores) and their dependence on shared memory and other shared resources. Objectives: Our goal is to understand whether and how existing model-based performance prediction approaches face this challenge. We plan to use gained insights as foundation for enriching existing prediction approaches with capabilities to predict systems running on multicores. Methods: We perform a Systematic Literature Review (SLR) to identify current model-based prediction approaches in the context of multicores. Results: Our SLR covers the software engineering, embedded systems, High Performance Computing, and Software Performance Engineering domains for which we examined 34 sources in detail. We found various performance prediction approaches which tries to increase prediction accuracy for multicore systems by including shared memory designs to the prediction models. Conclusion: However, our results show that the memory designs models are only in an initial phase. Further research has to be done to improve cache, memory, and memory bandwidth model as well as to include auto tuner support.
Influence of Different Nanofillers and their Dispersion Methods on the Properties of Natural Rubber Nanocomposites

Abstract The effects of varying morphological and chemical constitution of nanofillers and various dispersion methods on natural rubber nanocomposites prepared by conventional processing techniques were determined by incorporating various nanofillers like montmorillonite, sepiolite (SP), hectorite, carbon nanofiber (F) and expanded graphite. When compared with the gum, SP filled (4 phr) nanocomposite exhibited an increment of 26% in the modulus and F (6phr) increased the tear strength by 18%, over the gum. Nanofiller dispersion was enhanced by various compatibilization and dispersion techniques which helped SP introduce 56 and F 113% increment in the modulus of the nanocomposites, over the gum rubber vulcanizate. It also rendered 28% improvement in the tear strength of F filled system. Deeper insights into the material properties were obtained through dynamic mechanical and swelling studies. Property-morphology correlation of the hybrids was performed through X-ray Diffraction, Atomic Force Microscopy and.
Turkish entity discovery with word embeddings

Entity-linking systems link noun phrase mentions in a text to their corresponding knowledge base entities in order to enrich a text with metadata. Wikipedia is a popular and comprehensive knowledge base that is widely used in entity-linking systems. However, long-tail entities are not popular enough to have their own Wikipedia articles. Therefore, a knowledge base created by using Wikipedia entities would be limited to only popular entities. In order to overcome the knowledge base coverage limitation of Wikipedia-based entity-linking systems, this paper presents an entity-discovery system that can detect semantic types of entities that are not defined in Wikipedia. The effectiveness of the proposed system was validated empirically through the use of generated data sets for the Turkish language. The experimental results show that, in terms of accuracy, our system performs competitively in comparison to the previous methods in the literature. Its high performance is achieved through a method that learns word embeddings for candidate entities.
Localization Bias Reduction in Wireless Sensor Networks

In this paper, a novel bias-reduction method is proposed to analytically express and reduce the bias arising in sensor network localization problems, thereby improving the localization accuracy. The proposed bias-reduction method mixes Taylor series and a maximum-likelihood estimate and leads to an easily calculated analytical bias expression in terms of a known maximum-likelihood cost function. In contrast to existing contributions, this paper considers a sensor network as a whole when the bias is investigated by introducing the geometric structure of the sensor network into the proposed bias-reduction method via the rigidity matrix, a concept drawn from graph theory. The maximum-likelihood cost function is related to the rigidity matrix resulting in the final analytical expression of localization bias in terms of the rigidity matrix. Another important contribution of this paper is that, in addition to the presented simulation results, experimental results obtained by using a wireless localization system, which is developed based on reconfigurable software-defined radios (SDRs), are also provided to verify the performance of the proposed bias-reduction method. Both the simulation and experimental results demonstrate that the proposed method can reduce the bias, thereby improving the localization accuracy in different scenarios.