Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical Evaluation of Variational Autoencoders for Data Augmentation

Since the beginning of Neural Networks, different mechanisms have been required to provide a sufficient number of examples to avoid overfitting. Data augmentation, the most common one, is focused on the generation of new instances performing different distortions in the real samples. Usually, these transformations are problem-dependent, and they result in a synthetic set of, likely, unseen examples. In this work, we have studied a generative model, based on the paradigm of encoder-decoder, that works directly in the data space, that is, with images. This model encodes the input in a latent space where different transformations will be applied. After completing this, we can reconstruct the latent vectors to get new samples. We have analysed various procedures according to the distortions that we could carry out, as well as the effectiveness of this process to improve the accuracy of different classification systems. To do this, we could use both the latent space and the original space after reconstructing the altered version of these vectors. Our results have shown that using this pipeline (encoding-altering-decoding) helps the generalisation of the classifiers that have been
Combinatorial Screening of Pancreatic Adenocarcinoma Reveals Sensitivity to Drug Combinations Including Bromodomain Inhibitor Plus Neddylation Inhibitor

Pancreatic adenocarcinoma (PDAC) is the fourth most common cause of cancer-related death in the United States. PDAC is difficult to manage effectively, with a five-year survival rate of only 5%. PDAC is largely driven by activating KRAS mutations, and as such, cannot be directly targeted with therapeutic agents that affect the activated protein. Instead, inhibition of downstream signaling and other targets will be necessary to effectively manage PDAC. Here, we describe a tiered single-agent and combination compound screen to identify targeted agents that impair growth of a panel of PDAC cell lines. Several of the combinations identified from the screen were further validated for efficacy and mechanism. Combination of the bromodomain inhibitor JQ1 and the neddylation inhibitor MLN4294 altered the production of reactive oxygen species in PDAC cells, ultimately leading to defects in the DNA damage response. Dual bromodomain/neddylation blockade inhibited in vivo growth of PDAC cell line xenografts. Overall, this work revealed novel combinatorial regimens, including JQ1 plus MLN4294, which show promise for the treatment of RAS-driven PDAC. Mol Cancer Ther; 16(6); 1041–53. ©2017 AACR.
Diagnostic Value of Glypican-3 for Hepatocellular Carcinomas

Background: Hepatocellular carcinoma (HCC) is a common and dangerous malignancy in many parts of the world, and especially in Egypt. Early diagnosis is the most important step in successful HCC management. However most cases are detected at late stage making effective intervention impossible. Aim: The aim of this study was to evaluate the potential of Glypican-3 (GPC-3) to aid in diagnosis of HCC, especially in patients with low serum alpha-fetoprotein (AFP). Subjects and methods: Serum GPC-3 was assessed by flow-cytometry and serum AFP by enzyme-linked immunosorbent assay (ELISA) in 40 HCC patients with AFP< 400ug\l. (GI), 40 HCC patients with AFP> 400ug\l. (GII) and 20 healthy controls (GIII). Results: GPC-3 was found to be significantly elevated in HCC as compared to healthy subjects (GI 38.2±22. 5, GII 50.2±22.6, and GIII 2.24±1.19), with sensitivities of 85% for GI and 84% for GII and specificities of 95% for GI and 92% for GII. AFP showed respective sensitivities of 50% and 79%, and specificities of 80% and 90%, for HCC diagnosis. The combination of GPC-3 with AFP achieved the highest sensitivity (98.5%) and specificity (97.8%). Conclusion: Serum GPC-3 has a better sensitivity than AFP for the diagnosis of HCC. Combination of two markers appears warranted for greatest accuracy
FORMULATION AND EVALUATION OF FELODIPINE SUBLINGUAL TABLET

Objective: Felodipine is the drug of choice in hypertension and congestive heart failure.Its bioavailability is very low about 15%. Present investigation was undertaken to formulate sublingual tablet of Felodipine to overcome the first pass metabolism and provide fast onset of action. Experimental Work: The solid dispersion of Felodipine were prepared with β-cyclodextrin, poloxamer 407, PEG 6000 and PVP K-30 in various ratios (1:2, 1:4, 1:6 1:8) and phase solubility study was performed to select the carrier. The selected solid dispersion was then utilized for the preparation of sublingual tablet by direct compression utilizing different superdisintegrant like Cross carmelose sodium, Crosspovidone, Kyron T-314 and Sodium starch glycolate. Prepared tablets were evaluated for weight variation, thickness, friability, content uniformity, hardness, disintegration time, wetting time and in-vitro drug release. Stability study of optimized formulation was performed as per ICH guideline. Result: The optimized formulation (batch F3) containing Drug-Poloxamer-407 (1:6) complex and Kyron-T314(5%) showed greater drug dissolution (87% in 15 min) and satisfactory in vitro disintegration time (22 sec). Stability study of optimized formulation showed that optimized formulation was stable at accelerated environment condition. Conclusion: Felodipine sublingual tablet were prepared successfully by the use of solid dispersion of Felodipine-poloxamer 407 (1:6) complex using Kyron-T314 as a superdisintegrant.Thus, sublingual tablet of Felodipine could be an alternative route to avoid gastrointestinal side effect as well as bypass hepatic first pass metabolism. The formulated sublingual tablets may act as a potential alternate for the Felodipine oral tablet.
Assessment of the toxic effect of pesticides on honey bee drone fertility using laboratory and semifield approaches: A case study of fipronil

Concern about the reproductive toxicity of plant protection products in honey bee reproducers is increasing. Because the reproductive capacity of honey bees is not currently considered during the risk assessment procedure performed during plant protection product registration, it is important to provide methods to assess such potential impairments. To achieve this aim, we used 2 different approaches that involved semifield and laboratory conditions to study the impact of fipronil on drone fertility. For each approach, the drones were reared for 20 d, from emergence to sexual maturity, and exposed to fipronil via a contaminated sugar solution. In both groups, the effects of fipronil were determined by studying life traits and fertility indicators. The results showed that the survival and maturity rates of the drones were better under laboratory conditions than under semifield conditions. Moreover, the drones reared under laboratory conditions produced more seminal fluid. Although these differences could be explained by environmental factors that may vary under semifield conditions, it was found that regardless of the approach used, fipronil did not affect survival rates, maturity rates, or semen volumes, whereas it did affect fertility by inducing a decrease in spermatozoa quantity that was associated with an increase in spermatozoa mortality. These results confirm that fipronil affects drone fertility and support the relevance of each approach for assessing the potential reproductive toxicity of plant protection products in honey bees. Environ Toxicol Chem 2017;36:2345–2351. © 2017 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Systematic comparison of biologically active foreign ions-codoped calcium phosphate microparticles on osteogenic differentiation in rat osteoporotic and normal mesenchymal stem cells

Osteoporosis is a disease characterized by structural deterioration of bone tissue, leading to skeletal fragility with increased fracture risk. Calcium phosphates (CaPs) are widely used in bone tissue engineering strategies as they have similarities to bone apatite except for the absence of trace elements (TEs) in the CaPs. Bioactive glasses (BGs) have also been used successfully in clinic for craniomaxillofacial and dental applications during the last two decades due to their excellent potential for bonding with bone and inducing osteoblastic differentiation. In this study, we evaluated the osteogenic effects of the ionic dissolution products of the quaternary Si-Sr-Zn-Mg-codoped CaP (TEs-CaP) or 45S5 Bioglass® (45S5 BG), both as mixtures and separately, on rat bone marrow-derived mesenchymal stem cells (rOMSCs & rMSCs) from osteoporotic and normal animals, using an MTT test and Alizarin Red S staining. The materials enhanced cell proliferation and osteogenic differentiation, especially the combination of the BG and TEs-CaP. Analysis by quantitative PCR and ELISA indicated that the expression of osteogenic-specific genes and proteins were elevated. These investigations suggest that the TEs-CaP and 45S5 BG operate synergistically to create an extracellular environment that promotes proliferation and terminal osteogenic differentiation of both osteoporotic and normal rMSCs.
Multilingual bottleneck features for subword modeling in zero-resource languages

How can we effectively develop speech technology for languages where no transcribed data is available? Many existing approaches use no annotated resources at all, yet it makes sense to leverage information from large annotated corpora in other languages, for example in the form of multilingual bottleneck features (BNFs) obtained from a supervised speech recognition system. In this work, we evaluate the benefits of BNFs for subword modeling (feature extraction) in six unseen languages on a word discrimination task. First we establish a strong unsupervised baseline by combining two existing methods: vocal tract length normalisation (VTLN) and the correspondence autoencoder (cAE). We then show that BNFs trained on a single language already beat this baseline; including up to 10 languages results in additional improvements which cannot be matched by just adding more data from a single language. Finally, we show that the cAE can improve further on the BNFs if high-quality same-word pairs are available.
Optimization of core-shell nanoparticle layers for optical biosensing

In this work we constructed and optimized a label-free biosensor which is based on a combination of surface plasmon resonance and reflectometric interference. Both techniques have been utilized for label-free biosensing for more than two decades as the corresponding extinction spectra undergo a wavelength shift upon molecule binding. In the present study it has been demonstrated that a combination of both effects can significantly improve sensitivity. The developed biosensor consists of dielectric spheres of 400-500 nm diameters, deposited on a flat solid substrate and coated with gold nanoparticles. The spectrum of such structure exhibits multiple extinction peaks resulting from the interference of beams reflected between the flat substrate and the surface of the dielectric spheres. These peaks are enhanced by the presence of gold on top of the spheres due to coherent oscillation of the free electrons of the metal, i.e. plasmon excitation. In a systematic study, the optical properties of the sensing element have been optimized, and its sensitivity towards molecule binding has been tested by fibrinogen adsorption for the different sensor geometries developed. In the wavelength regime from 400-900 nm two dominant peaks are observed. It was shown, that the sensitivity of the peak between 600 and 900 nm exhibits the higher sensitivity compared to the peak between 400 and 600 nm. Different deposition techniques for the dielectric spheres have been tested to find the most reproducible one with closed packed coverage. Here, a technique, in which the dielectric spheres are first floated on a liquid subphase and then transferred to the solid support in a Langmuir-Blodgett like approach, yielded improved lateral homogeneity of the optical response and higher sensitivity than film of randomly deposited spheres. Two kinds of metallization have been studied (i) deposition of metal nanoparticles from solution (seeding) followed by an enlargement of the nanoparticles (plating), and (ii) evaporation of a metal thin film on the top of the spheres by physical vapor deposition (PVD). The resulting optical response and morphology were characterized by UV-Vis spectroscopy and scanning electron microscopy (SEM). For gold metal deposition from gold solution we found out that the sensitivity decreases with increasing plating time and is highest for purely seeded surfaces. For gold films deposited by PVD we identified an optimum gold thin film thickness of 50 nm to provide enhanced sensitivity. Effects of metal composition (gold and silver) on the optical properties and sensitivity have been investigated, showing significantly higher sensitivity for silver than for gold nanoparticle coatings of the same coverage in range from 400-600 nm. We also observed that the sensitivity is improved by the presence of a dielectric layer of silicon oxide/dioxide in between the substrate and the gold-coated spheres. Independent of the type of substrate used (i.e. metalized or not), an optimum layer thickness of 40 nm was found.
EvoCells - A Treemap Layout Algorithm for Evolving Tree Data

We propose the rectangular treemap layout algorithm EvoCells that maps changes in tree-structured data onto an initial treemap layout. Changes in topology and node weights are mapped to insertion, removal, growth, and shrinkage of the layout rectangles. Thereby, rectangles displace their neighbors and stretche their enclosing rectangles with a run-time complexity of O(n logn). An evaluation using layout stability metrics on the open source ElasticSearch software system suggests EvoCells as a valid alternative for stable treemap layouting.
Syk Activity Is Dispensable for Platelet GP1b-IX-V Signaling

The binding of von Willebrand factor (VWF) to the platelet membrane glycoprotein 1b-IX (GP1b-IX) leads to activation of platelets. GP1b was shown to signal via the FcRγ-ITAM (Fc Receptor γ-Immunoreceptor tyrosine-based activation motif) pathway, activating spleen tyrosine kinase (Syk) and other tyrosine kinases. However, there have been conflicting reports regarding the role of Syk in GP1b signaling. In this study, we sought to resolve these conflicting reports and clarify the role of Syk in VWF-induced platelet activation. The inhibition of Syk with the selective Syk inhibitors, OXSI-2 and PRT-060318, did not inhibit VWF-induced platelet adhesion, agglutination, aggregation, or secretion. In contrast, platelets stimulated with the Glycoprotein VI (GPVI) agonist, collagen-related peptide (CRP), failed to cause any aggregation or secretion in presence of the Syk inhibitors. Furthermore, GP1b-induced platelet signaling was unaffected in the presence of Syk inhibitors, but GPVI-induced signaling was abolished under similar conditions. Thus, we conclude that Syk kinase activity does not play any functional role downstream of GP1b-mediated platelet activation.
In Vitro Wear Resistance of Nano‐Hybrid Composite Denture Teeth

PURPOSE To evaluate the wear resistance of nano-hybrid composite denture teeth as compared to two commonly used denture teeth: interpenetrating polymer network (IPN) and double crosslinking polymethylmethacrylate (PMMA) denture teeth. MATERIAL AND METHODS 18 styli and 18 disk specimens were prepared from the three denture tooth materials: nano-hybrid composite, IPN, and double crosslinking PMMA. The specimens were mounted in a two-body wear testing machine to simulate chewing in the complete denture. The amount of wear from the styli specimens were measured before and after using a digital micrometer, and the depth of the wear track from the disk specimens was measured using a noncontact 3D optical profilometer. The total wear from each denture tooth group was compared using one-way ANOVA with a 0.05 significance level. A Tukey post hoc test was used to determine differences between the three groups. RESULTS The mean total wear in the nano-hybrid composite teeth group was 1.16 mm, SD = 0.5 mm, statistically significantly higher (p ≤ 0.0001) than the IPN (mean = 0.13 mm, SD = 0.05) and double crosslinking PMMA tooth groups (mean = 0.31 mm, SD = 0.19). There was no statistically significant difference between IPN denture teeth and double crosslinking PMMA denture teeth in the amount of wear. CONCLUSIONS Nano-hybrid composite denture teeth exhibited statistically significantly more wear than the IPN and double crosslinking PMMA denture teeth.
Supplementary Methods

High resolution temporal analysis. Classifying near simultaneous (<1.2 ms) spiking events from multiple neurons recorded at the same tetrode is difficult because multiple action potential (AP) waveforms overlap. Here, we show that findings are not a result of detection failures due to this overlap, and that its quantitative effects are minor. We do this both by analyzing the size of the correction due to detection failures, and the fine temporal structure of the recorded spike trains. In the analyses below, we consider only the responses to pseudorandom stimuli. First, we consider the analysis used in the main text. We corrected for underestimates in near-synchronous firing events by a simple lockout correction, based on the assumption that firing probabilities are constant on a timescale of 10 to 15 ms (see main Methods). Supp. Fig. 2 shows that this correction has only a minimal effect on the fit of M pair , and, indeed, typically worsens it. Next, because synchronous firing on a millisecond timescale may differ from that on a timescale of 10-15 ms, we apply a more sophisticated correction (Supp. Fig. 3). Specifically, we add in an excess of near simultaneous spikes on a timescale of 1.5 ms. To do this, we bin each spike train into intervals of 0.5 ms and construct pairwise cross-correlograms for all pairs of neurons (Supp. Fig. 3a). For each pair of neurons (i and j), we find the peak number of coincident spikes (C ij) in a window +/-1.5 ms around 0 lag. Then, for each bin (t) on the interval [-1.5 ms 1.5 ms], we add-in λ C ij /2 spikes to each train, with each train's added spikes placed t ms after a randomly-chosen spike in the other train, and avoiding overlaps. For λ =1, this generates spike trains for which the zero-lag cross-correlation matches the peak cross-correlation (Supp. Fig. 3b), and for λ =2, it generates spike trains in which zero-lag cross-correlation is twice the peak (Supp. Fig. 3c). We then evaluate the performance of M pair and M obs on these datasets as described in Methods. As shown in Supp. Fig. 3d, adding fine-scale correlations worsens the fit of the pairwise model.
Comprehending Real Numbers: Development of Bengali Real Number Speech Corpus

Speech recognition has received a less attention in Bengali literature due to the lack of a comprehensive dataset. In this paper, we describe the development process of the first comprehensive Bengali speech dataset on real numbers. It comprehends all the possible words that may arise in uttering any Bengali real number. The corpus has ten speakers from the different regions of Bengali native people. It comprises of more than two thousands of speech samples in a total duration of closed to four hours. We also provide a deep analysis of our corpus, highlight some of the notable features of it, and finally evaluate the performances of two of the notable Bengali speech recognizers on it.
Snack chips fried in corn oil alleviate cardiovascular disease risk factors when substituted for low-fat or high-fat snacks.

BACKGROUND The perception that all high-fat snacks are unhealthy may be wrong. OBJECTIVE We aimed to assess whether replacing low-fat and high-fat snacks with snacks rich in polyunsaturated fatty acids (PUFAs) and low in saturated and trans fatty acids would improve cardiovascular health. DESIGN Thirty-three adults participated in a randomized crossover trial of 3 controlled feeding phases of 25 d each in which a different type of snack was provided: low-fat (30.8% of energy from fat, 5.2% of energy from PUFAs), high-PUFA (36.3% of energy from fat, 9.7% of energy from PUFAs), or high-fat (37.9% of energy from fat, 5.8% of energy from PUFAs) snack. RESULTS Each diet reduced LDL- and total cholesterol concentrations, but reductions were greater with the low-fat and the high-PUFA diets than with the high-fat diet: LDL cholesterol (11.8% and 12.5% compared with 8.8%, respectively; P = 0.03 and 0.01), total cholesterol (10.5% and 10.7% compared with 7.9%, respectively; P = 0.03 and 0.02). The high-PUFA diet tended to reduce triacylglycerol concentrations (9.4%; P = 0.06), and this change was greater than that with the low-fat (P = 0.028) and high-fat (P = 0.0008) diets. CONCLUSIONS These data show that snack type affects cardiovascular health. Consuming snack chips rich in PUFA and low in saturated or trans fatty acids instead of high-saturated fatty acid and trans fatty acid or low-fat snacks leads to improvements in lipid profiles concordant with reductions in cardiovascular disease risk.
Ultrasound measurements of intraabdominal fat estimate the metabolic syndrome better than do measurements of waist circumference.

BACKGROUND We recently developed an ultrasound technique to estimate intraabdominal fat (IAF). This method is more accurate than measurement of waist and hip circumferences and is simpler and less expensive than computed tomography or magnetic resonance imaging. OBJECTIVE We compared the associations of ultrasound and waist-circumference (WC) measurements of IAF with other components of the metabolic syndrome. DESIGN IAF was determined in 600 consecutive participants in the Secondary Manifestations of Arterial Disease (SMART) study. The mean (+/- SD) age was 56.1 +/- 12.6 y, 30.0% of participants were women, and the mean body mass index (BMI; in kg/m2) was 26.6+/- 4.1. RESULTS IAF increased with age (ultrasound: r = 0.28; WC: r = 0.25; P < 0.001 for both). Higher IAF, as measured by ultrasound but not by WC, was independently associated with higher metabolic risk factors. The correlation coefficients between IAF measured by ultrasound and plasma glucose, total cholesterol, HDL cholesterol, and triacylglycerol were 0.13, 0.16, -0.13, and 0.25, respectively (all P < 0.001; adjusted for age, sex, and BMI). The corresponding coefficients for IAF measured by WC were 0.17 (P < 0.001) and 0.01, -0.06, and 0.05 (all NS). CONCLUSIONS These results confirm the findings of computed tomography and magnetic resonance imaging investigations. When IAF is measured by ultrasound, the associations are more pronounced than when WC measurements are used and are independent of BMI. This suggests that IAF can be more reliably assessed by ultrasound measurements than by WC measurements.
Validity and reliability of the 3-min all-out running test to measure critical velocity in hot environments

ABSTRACT This study’s aim was to investigate the test–retest reliability of the 3-min all-out running test (3MRT) in hot environments. Twelve male sprinters (age 21.2 ± 1.8 years; height 1.78 ± 0.01 m; weight 71.0 ± 1.6 kg; 55.0 ± 1.0 mL kg−1 min−1) performed an incremental exercise test in a laboratory, during which the first and second ventilatory thresholds (VT1 and VT2) and were determined. In addition, they performed two 3MRTs on an outdoor track in a hot environment, during which the critical velocity (CV) and anaerobic capacity (D′) were estimated. Significant reproducibility was found in CV and D′ (ICC = 0.74 and 0.61, P < 0.05). The average CV in 3MRTs (3.09 ± 0.13 m s−1) correlated significantly with VT1 (3.13 ± 0.07 m s−1, P < 0.05). The 3MRT is a reliable tool for measuring CV and D′, while CV from 3MRT in a hot environment was identical to VT1.