Miracle-dz/UniFAR-FTUs huggingface dataset:
Adipocyte abundances of CES1, CRYAB, ENO1 and GANAB are modified in-vitro by glucose restriction and are associated with cellular remodelling during weight regain

ABSTRACT Long-term weight loss maintenance is a problem of overweight and obesity. Changes of gene expression during weight loss (WL) by calorie restriction (CR) are linked to the risk of weight regain (WR). However, detailed information on genes/proteins involved in the mechanism is still lacking. Therefore, we developed an in-vitro model system for glucose restriction (GR) and refeeding (RF) to uncover proteome differences between GR with RF vs normal feeding, of which we explored the relation with WR after WL. Human Simpson-Golabi-Behmel Syndrome cells were subjected to changing levels of glucose to mimic the condition of CR and RF. Proteome profiling was performed by liquid chromatography tandem mass spectrometry. This in-vitro model revealed 44 proteins differentially expressed after GR and RF versus feeding including proteins of the focal adhesions. Four proteins showed a persistent up- or down-regulation: liver carboxylesterase (CES1), mitochondrial superoxide dismutase [Mn] (SOD2), alpha-crystallin B-chain (CRYAB), alpha-enolase (ENO1). In-vivo weight loss-induced RNA expression changes linked CES1, CRYAB and ENO1 to WR. Moreover, of these 44 proteins, CES1 and glucosidase II alpha subunit (GANAB) during follow up correlated with WR. Correlation clustering of in-vivo protein expression data indicated an interaction of these proteins with structural components of the focal adhesions and cytoplasmic filaments in the adipocytes.
A study on gait analysis using moving silhouettes: Striking a balance with simplicity between feature generalization and specificity

Feature selection has been identified as one of the most effective ways to differentiate patterns. Feature generalization and specificity are two major challenging problems that are hard to satisfy at the same time. This study aims to propose a method that makes an attempt to retain both feature generalization and specificity. Simplicity is another factor that we take into account. The proposed model is applied to extract features so as to separate different walkers in motion. Feature selection is performed by extracting silhouettes. Two sets of features, i.e. temporal features and flexibilities, are tested and then eliminated to improve the generalization capability. Experimental result shows that the proposed method achieves a satisfactory result in separating different walkers and tolerating noises. More importantly, it demonstrates well in striking a balance between generalization and specificity with satisfactory simplicity.
Bayesian inference for genomic imprinting underlying developmental characteristics

The identification of imprinted genes is becoming a standard procedure in searching for quantitative trait loci (QTL) underlying complex traits. When a developmental characteristic such as growth or drug response is observed at multiple time points, understanding the dynamics of gene function governing the underlying feature should provide more biological information regarding the genetic control of an organism. Recognizing that differential imprinting can be development-specific, mapping imprinted genes considering the dynamic imprinting effect can provide additional biological insights into the epigenetic control of a complex trait. In this study, we proposed a Bayesian imprinted QTL (iQTL) mapping framework considering the dynamics of imprinting effects and model multiple iQTLs with an efficient Bayesian model selection procedure. The method overcomes the limitation of likelihood-based mapping procedure, and can simultaneously identify multiple iQTLs with different gene action modes across the whole genome with high computational efficiency. An inference procedure using Bayes factors to distinguish different imprinting patterns of iQTL was proposed. Monte Carlo simulations were conducted to evaluate the performance of the method. The utility of the approach was illustrated through an analysis of a body weight growth data set in an F(2) family derived from LG/J and SM/J mouse stains. The proposed Bayesian mapping method provides an efficient and computationally feasible framework for genome-wide multiple iQTL inference with complex developmental traits.
High Throughput In vivo Analysis of Plant Leaf Chemical Properties Using Hyperspectral Imaging

Image-based high-throughput plant phenotyping in greenhouse has the potential to relieve the bottleneck currently presented by phenotypic scoring which limits the throughput of gene discovery and crop improvement efforts. Numerous studies have employed automated RGB imaging to characterize biomass and growth of agronomically important crops. The objective of this study was to investigate the utility of hyperspectral imaging for quantifying chemical properties of maize and soybean plants in vivo. These properties included leaf water content, as well as concentrations of macronutrients nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), calcium (Ca), and sulfur (S), and micronutrients sodium (Na), iron (Fe), manganese (Mn), boron (B), copper (Cu), and zinc (Zn). Hyperspectral images were collected from 60 maize and 60 soybean plants, each subjected to varying levels of either water deficit or nutrient limitation stress with the goal of creating a wide range of variation in the chemical properties of plant leaves. Plants were imaged on an automated conveyor belt system using a hyperspectral imager with a spectral range from 550 to 1,700 nm. Images were processed to extract reflectance spectrum from each plant and partial least squares regression models were developed to correlate spectral data with chemical data. Among all the chemical properties investigated, water content was predicted with the highest accuracy [R2 = 0.93 and RPD (Ratio of Performance to Deviation) = 3.8]. All macronutrients were also quantified satisfactorily (R2 from 0.69 to 0.92, RPD from 1.62 to 3.62), with N predicted best followed by P, K, and S. The micronutrients group showed lower prediction accuracy (R2 from 0.19 to 0.86, RPD from 1.09 to 2.69) than the macronutrient groups. Cu and Zn were best predicted, followed by Fe and Mn. Na and B were the only two properties that hyperspectral imaging was not able to quantify satisfactorily (R2 < 0.3 and RPD < 1.2). This study suggested the potential usefulness of hyperspectral imaging as a high-throughput phenotyping technology for plant chemical traits. Future research is needed to test the method more thoroughly by designing experiments to vary plant nutrients individually and cover more plant species, genotypes, and growth stages.
Human behavior sensing for tag relevance assessment

Users react differently to non-relevant and relevant tags associated with content. These spontaneous reactions can be used for labeling large multimedia databases. We present a method to assess tag relevance to images using the non-verbal bodily responses, namely, electroencephalogram (EEG), facial expressions, and eye gaze. We conducted experiments in which 28 images were shown to 28 subjects once with correct and another time with incorrect tags. The goal of our system is to detect the responses to non-relevant tags and consequently filter them out. Therefore, we trained classifiers to detect the tag relevance from bodily responses. We evaluated the performance of our system using a subject independent approach. The precision at top 5% and top 10% detections were calculated and results of different modalities and different classifiers were compared. The results show that eye gaze outperforms the other modalities in tag relevance detection both overall and for top ranked results.
Characterization of the fusogenic properties of Sendai virus: kinetics of fusion with erythrocyte membranes.

A novel fluorescence assay [Hoekstra, D. , De Boer, T. , Klappe, K. , & Wilschut, J. (1984) Biochemistry 23, 5675-5681] has been used to characterize the fusogenic properties of Sendai virus, using erythrocyte ghosts and liposomes as target membranes. This assay involves the incorporation of the "fusion-reporting" probe in the viral membrane, allowing continuous monitoring of the fusion process in a very sensitive manner. Fusion was inhibited upon pretreatment of Sendai virus with trypsin. Low concentrations of the reducing agent dithiothreitol (1 mM) almost completely abolished viral fusion activity, whereas virus binding was reduced by ca. 50%, indicating that the fusogenic properties of Sendai virus are strongly dependent on the integrity of intramolecular disulfide bonds in the fusion (F) protein. Pretreatment of erythrocyte ghosts with nonlabeled Sendai virus inhibited subsequent fusion of fluorophore-labeled virus irrespective of the removal of nonbound virus, thus suggesting that the initial binding of the virus to the target membrane is largely irreversible. As a function of pH, Sendai virus displayed optimal fusion activity around pH 7.5-8.0. Preincubation of the virus at suboptimal pH values resulted in an irreversible diminishment of its fusion capacity. Since virus binding was not affected by the pH, the results are consistent with a pH-induced irreversible conformational change in the molecular structure of the F protein, occurring under mild acidic and alkaline conditions. In contrast to virus binding, fusion appeared to be strongly dependent on temperature, increasing ca. 25-fold when the temperature was raised from 23 to 37 degrees C. (ABSTRACT TRUNCATED AT 250 WORDS)
Early Behavioral Inhibition and Emotion Regulation: Pathways Toward Social Competence in Middle Childhood.

This study examined emotion regulation (ER) as a mediator in the relation between early behavioral inhibition (BI) and later social competence (N = 257), and whether this mediation varied depending on BI levels. Maternal report and observational measures were used to assess BI (ages 2 and 3). Children's ER strategies (age 5) and social competence with an unfamiliar peer (age 7) were measured using observational measures. Results showed that BI predicted less engaged ER strategies during a disappointment task, and engaged ER predicted higher social competence. Engaged ER mediated the effect of BI on social competence, but only for highly inhibited children. Findings elucidate developmental trajectories of risk and resilience, and suggest targeting regulatory strategies in early prevention efforts with highly inhibited children.
Testing the biological embedding hypothesis: Is early life adversity associated with a later proinflammatory phenotype?

Abstract Accumulating evidence suggests that the experience of early life adversity is a risk factor for a range of poor outcomes across development, including poor physical health in adulthood. The biological embedding model of early adversity (Miller, Chen, & Parker, 2011) suggests that early adversity might become embedded within immune cells known as monocytes/macrophages, programming them to be overly aggressive to environmental stimuli and insensitive to inhibitory signals, creating a “proinflammatory phenotype” that increases vulnerability to chronic diseases across the life span. We tested this hypothesis in the present study. Adolescent girls (n = 147) had blood drawn every 6 months across a 2.5-year period. To assess inflammatory responses to challenge, their monocytes were stimulated in vitro with a bacterial product, and production of the cytokine interleukin-6 was quantified. Hydrocortisone was added to cultures to assess the cells’ sensitivity to glucocorticoids’ anti-inflammatory signal. Using cluster analyses, we found that early life adversity was associated with greater odds of displaying a proinflammatory phenotype characterized by relatively larger interleukin-6 responses and relatively less sensitivity to glucocorticoids. In contrast, ongoing social stress was not associated with increasing odds of being categorized in the proinflammatory cluster. These findings suggest that early life adversity increases the probability of developing a proinflammatory phenotype, which, if sustained, could forecast risk for health problems later in life.
Linking the business view to requirements engineering: long-term product planning by roadmapping

Companies moving into the software product business and growing in size face new challenges that cannot be tackled completely with old practices. For example, the future development steps of the off-the-shelf products cannot be negotiated with just one or a few customers any more. This means that practitioners should be able to take aspects such as their company's own strategy and available market information more effectively into account in such decision-making. However, usually the company or business unit strategy is so high level that the gap to single requirements documents is far too long. Roadmapping is one technique that companies have used for long-term product planning in order to link the business view to requirements engineering (RE), and to make more business oriented product development decisions. In addition, roadmapping has been used to share a common understanding about the future development steps of products with different stakeholders. However, the application of the technique is not always easy. This paper gives an overview of roadmapping as a technique, and describes lessons learned from one Finnish software product company that has developed and evaluated its own roadmapping processes in their organization.
Complexity, Two-Level Morphology and Finnish

Although, Two-Level Morphology has been found in practice to be an extremely efficient method for processing Finnish words on very small machines, [Barton86] has recently shown the method to be NP-hard. This paper will discuss Barton's theoretical argument and explain why it has not been a problem for us in practice.
Bit rate comparison of adaptive OFDM and cyclic prefixed single-carrier with DFE

This letter considers two variants of a cyclic prefixed block transmission: (i) orthogonal frequency division multiplexing (OFDM), (ii) cyclic prefixed single-carrier (CPSC) transmission with decision feedback equalization (DFE). We aim at comparing these two schemes in terms of achievable bit rate with adaptive bit loading. It is analytically demonstrated that, for all signal to noise ratio values, OFDM achieves a bit rate greater than or equal to that of DFE-CPSC, independently of whether uniform or optimal power allocation is considered.
GPGPU-Aided Ensemble Empirical-Mode Decomposition for EEG Analysis During Anesthesia

Ensemble empirical-mode decomposition (EEMD) is a novel adaptive time-frequency analysis method, which is particularly suitable for extracting useful information from noisy nonlinear or nonstationary data. Unfortunately, since the EEMD is highly compute-intensive, the method does not apply in real-time applications on top of commercial-off-the-shelf computers. Aiming at this problem, a parallelized EEMD method has been developed using general-purpose computing on the graphics processing unit (GPGPU), namely, G-EEMD. A spectral entropy facilitated by G-EEMD was, therefore, proposed to analyze the EEG data for estimating the depth of anesthesia (DoA) in a real-time manner. In terms of EEG data analysis, G-EEMD has dramatically improved the run-time performance by more than 140 times compared to the original serial EEMD implementation. G-EEMD also performs far better than another parallelized implementation of EEMD bases on conventional CPU-based distributed computing technology despite the latter utilizes 16 high-end computing nodes for the same computing task. Furthermore, the results obtained from a pharmacokinetics/pharmacodynamic (PK/PD) model analysis indicate that the EEMD method is slightly more effective than its precedent alternative method (EMD) in estimating DoA, the coefficient of determination R2 by EEMD is significantly higher than that by EMD (p <; 0.05, paired Mest) and the prediction probability Pk by EEMD is also slighter higher than that by EMD (p <; 0.2, paired t-test).
Thyroid tissue: US-guided percutaneous interstitial laser ablation-a feasibility study.

PURPOSE To evaluate percutaneous interstitial laser photocoagulation (ILP) as a palliative treatment of recurrent thyroid carcinoma untreatable with surgery or radioiodine administration. MATERIALS AND METHODS By using 18 resected thyroid glands, the volume and histologic pattern of ILP-induced thyroid damage were assessed. In vivo treatment feasibility was evaluated by using a low-energy laser in two volunteers before thyroidectomy for huge autonomously functioning nodules. With ultrasonographic (US) monitoring, a 21-gauge spinal needle was inserted into the thyroid nodules. A 300-microm quartz fiberoptic guide was inserted through the needle lumen, and the fiber tip was placed in direct contact with the tissue. Laser irradiation was performed with a 1.064-nm Nd:YAG laser in surgically resected glands, which were treated with 2, 3, 5, or 7 W. RESULTS Tissue ablation was well-defined histologically, and its area was related to laser irradiation parameters (range, 0-26 mm). No correlation was found between US images and the actual extent of laser-induced lesions. Large colloid or fluid collections did not permit regular heat diffusion within the tissue. In vivo low-energy ILP was performed without technical difficulties or complications. CONCLUSION ILP induces well-defined tissue ablation correlated with energy parameters in thyroid glands devoid of cystic areas. ILP could be a therapeutic tool for highly selected problems in thyroid tumor treatment.
A : Specific Biological Rationales for the Utility of New Sequence Data

Hemichordates are the phylum of bilateral animals most closely related to chordates, the phylum that includes vertebrates such as human. The hemichordate is a three-part worm-like animal, but possesses many chordate-like traits long thought to hold insights into chordate evolution. These traits include gill slits (1), a post-anal tail-like extension (2), a notochord-like stomocord (3), a neurulated portion of the nervous system, a podocyte-containing kidney (3), possibly a pituitary-like proboscis pore (4), and possibly an endostylelike pharyngeal region with homology to the thyroid (5). In addition, recent in situ hybridization studies have revealed extensive hemichordate–chordate similarities in the expression domains of 22 neural patterning genes (6). We propose the generation of a 6X assembly of the hemichordate Saccoglossus kowalevskii (the acorn worm) genome to advance hemichordate–chordate comparisons and to illuminate chordate origins. The S. kowalevskii genome sequence will also accelerate work on the development and organization of members of the hemichordate phylum. In Section A of this White Paper, we discuss the specific biological advances anticipated from the availability of a hemichordate genome by highlighting its potential contribution to informing human biology, informing the human sequence, providing a better connection between the sequences of nonhuman organisms and the human sequence, expanding our understanding of basic biological processes such as development and neurobiology, and expanding our understanding of evolutionary processes (biological innovation) in general and human evolution in particular. We address the phylogenetic position of hemichordates and their numerous chordate-like characteristics. In Section B we consider the strategic issues associated with producing a Saccoglossus genome sequence. We comment on the value of such sequence information, its anticipated widespread use, and the rapid expansion of the research community once the genome sequence is available. In addition, we highlight the suitability of Saccoglossus for experimentation. We then discuss our proposed sequencing strategy and summarize current genomic resources that will significantly complement the sequencing effort.
Der Rostocker Kopfschmerzfragen-Komplex („Rokoko“) – Validierung einer schnellen diagnostischen Hilfe bei der Einordnung primärer Kopfschmerzen

Die Einordnung einer Kopfschmerzerkrankung erfolgt in der Regel durch eine ausfuhrliche Anamnese des Patienten. Dabei sind es nur wenige Fragen, deren Beantwortung durch den Patienten eine Zuordnung zu einer Migrane, einem Kopfschmerz vom Spannungstyp oder weiteren primaren Kopfschmerzarten ermoglicht. Der vorliegende Rostocker Kopfschmerzfragen-Komplex („Rokoko“) eignet sich zur Selbstbearbeitung durch den Untersucher oder den Patienten und kann innerhalb weniger Minuten ausgefullt werden. Anhand einer Eichstichprobe von n = 87 Patienten (Altersmedian: 44 Jahre) mit gesicherter Diagnose (Migrane oder Kopfschmerz vom Spannungstyp) konnte unter Verwendung der Schmerzfrequenz (attackenformig vs. permanent) und des Vorhandenseins von Aurasymptomen eine Sensitivitat/Spezifitat fur Migrane ohne Aura von 0,87/0,51, fur Migrane mit Aura von 0,71/0,95 und fur Kopfschmerz vom Spannungstyp von 0,57/0,93 erreicht werden. Eine Unterscheidung des Kopfschmerzes vom Spannungstyp in „episodisch“ oder „chronisch“ erfolgt durch individuelle Auswertung der entsprechenden Fragen. Aufgrund der Ausfuhrlichkeit der Fragen konnen mit dem Fragebogen weitere, wertvolle Hinweise uber das Kopfschmerzgeschehen des Patienten dokumentiert werden. Der Kopfschmerzfragebogen „Rokoko“ ist wegen seiner kurzen Bearbeitungsdauer und der zufriedenstellenden Sensitivitat und Spezifitat eine effiziente diagnostische Hilfe bei der Einordnung primarer Kopfschmerzen sowohl in der neurologischen und psychiatrischen Praxis als auch in der Praxis des Allgemeinmediziners. Er ersetzt jedoch nicht die zur Kopfschmerzdiagnose erforderliche allgemeine und neurologische Untersuchung.
Facile Precursor for Synthesis of Silver Nanoparticles Using Alkali Treated Maize Starch

Silver nanoparticles were prepared by using alkali treated maize starch which plays a dual role as reducer for AgNO3 and stabilizer for the produced AgNPs. The redox reaction which takes a place between AgNO3 and alkali treated starch was followed up and controlled in order to obtain spherical shaped silver nanoparticles with mean size 4–6 nm. The redox potentials confirmed the principle role of alkali treatment in increasing the reducibility of starch macromolecules. The measurements of reducing sugars at the end of reaction using dinitrosalicylic acid reagent (DNS) were carried out in order to control the chemical reduction reaction. The UV/Vis spectra show that an absorption peak, occurring due to surface plasmon resonance (SPR), exists at 410 nm, which is characteristic to yellow color of silver nanoparticles solution. The samples have been characterized by transmission electron microscopy (TEM), which reveal the nanonature of the particles.