Miracle-dz/UniFAR-FTUs huggingface dataset:
Discriminant Analysis as a Tool for Characterization of Oreochromis Niloticus (Chiclidae)

The growing demand on Oreochromis niloticus as a popular food increased interest in its aquaculture. This necessitated proper differentiation of O. niloticus from different localities to help in choosing the best specimens for brood stock production for Nile tilapia farming. Discriminant analysis was used to quantify morphometric measurements and meristic counts of O. niloticus from Kosti, Sinnar, Khashm El Girba and Al Sabloga area. Function 1 of Discriminant analysis separated O. niloticus sample from Kosti, Sinnar, and Khashm El Girba samples. Function 3 separated Kosti samples from other areas. Function 3 separated Kosti samples from other areas. Function 2 separated Kosti and Khashm El Girba samples from Sinnar and Al Sabloga samples. Discriminant analysis showed high degree of purity of O. niloticus with an overall average of 85.1%, this because the specimens from one location sharing characters with other from different location are very few. Wilks lambda analysis showed extremely highly significant difference (p<0.000) between the three functions. This analysis selected 12 morphometric characters (PP, HL, HW, IOW, AFB, CD, LAD, SNL, CPL, ED, CPD and PRP) to be used with high accuracy to discriminate between O. niloticus from the four sampling locations. Leave-one-out cross validation for O. niloticus from four locations by Discriminant analysis using 19 morphometric characters and 6 meristic counts confirmed the identity of the species.
PREDICTING INTERNAL RED OAK (QUERCUS RUBRA) LOG DEFECT FEATURES USING SURFACE DEFECT MEASUREMENTS

—Determining the defects located within a log is crucial to understanding the tree/log resource for effi cient processing. However, existing means of doing this non-destructively requires the use of expensive x-ray/CT (computerized tomography), MRI (magnetic resonance imaging), or microwave technology. Th ese methods do not lend themselves to fast, effi cient, and cost-eff ective analysis of logs and tree stems in the mill. Th is study quantifi ed the relationship between external defect indicators and internal defect characteristics for red oak logs. A series of models was developed to predict internal features using visible external features: surface indicator width, length, rise, and log diameter. Good correlations and small prediction errors were observed with sound (sawn), overgrown, and unsound knot defects. For less severe defects such as adventitious buds/clusters and distortion-type defects, weaker correlations were observed, but the magnitude of prediction errors was small and acceptable.
Modeling of filter-feeding behavior in the brown mussel, Perna perna (L.), exposed to natural variations of seston availability in Santa Catarina, Brazil

The aim of this study is to quantify and model the filter-feeding behavior of the mussel Perna perna feeding on natural seston. Models were generated that described each step of the feeding process and produced a predictive model of rates of food uptake by P. perna in culture areas from Southern Brazil. Feeding experiments using the biodeposition approach were conducted with mussels ranging in shell height from 3.94 to 9.22 cm of three sites, including turbid and clear water environments. Organic content of the seston (OCS, fraction) decreased as total particulate matter (TPM, mg L-1) increased. The maximum filtration rate (FR, mg L-1) measured for an individual mussel was 156.7 mg h-1 and was recorded when TPM was 33.9 mg L-1 and OCS was 0.18. Rejection rate of particles had a strong positive relationship with TPM, and an inverse relationship with OCS. Maximum rejection rate recorded was 124.1 mg h-1 and was measured under the same seston conditions as maximum filtration rate. Net organic selection efficiency by mussels (NOSE, fraction) was related to the amount of particulate organic matter (POM, mg L-1) and particulate inorganic matter (PIM, mg L-1) available in the water. NOSE was positive below PIM values of 2 mg L-1, but had negative values when POM was above 3 mg L-1 and PIM between 2 and 15 mg L-1, and positive values when POM was below 3 mg L-1 and PIM above 15 mg L-1. Maximum NOSE was 1.71, when PIM was 1.02 mg L-1 and POM was 0.67 mg L-1. Organic content of ingested matter (OCI, fraction) had a positive relationship with NOSE and TPM. Maximum OCI was 1.24 and was measured when TPM was 33.9 mg L-1, OCS was 0.18, FR was 151.30 mg h-1, and NOSE was 1.30. The net absorption efficiency of ingested organics (NAEIO) increased with increasing OCI in a hyperbolic relationship. The net organic absorption rate (NOAR, mg h-1) increased with both FR and OCI. The coupling of the equations that described filter-feeding processes for P. perna in the STELLA software environment produced a robust model with relatively low complexity and specificity. The model can predict the P. perna feeding behavior in turbid or clear water and can be used with different species if the correct coefficients are used. The coupling of this feeding model with future models of energy budget, population dynamics, seston hydrodynamics, and primary production will be valuable for the evaluation of shellfish carrying capacity.
Genome-Wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions

Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (~ 1/2,500), Asians have the highest prevalence (~1/500), Europeans and Latin Americans lie somewhere in the middle (~1/800 and 1/900, respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (~12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (<5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p = 6.27e-07), 10q22.2 (rs150952246, p = 3.14e-07), and 10q24.32 (rs118107597, p = 8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were (a) purely due to sample sizes, (b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.
Co-localization of EBV and Expression of P16- Cyclin-Dependent Kinase inhibitor Protein in Tissues from Patients with Non- Hodgkin's Lymphoma

ackground: EBV has been classified as a group 1 carcinogen associated with a variety of lymphoid and epithelial cancers. EBV was evidenced as a monogenic virus from its ability to transform normal human B cells, resulting in immortalization of the infected cells. A tumor suppressor protein, P16, is a cyclin-dependent kinase inhibitor plays a critical molecular role in cell senescence, regulation of the apoptosis pathway and G1 cell cycle arrest. Aim of the study: To analyze the concordant frequency and impact of P16 protein expression and EBV infection on tissues from a group of patients with NonHodgkin's Lymphoma (NHL). Patients and methods: Forty-five (45) formalin-fixed, paraffinembedded tissues from lymph nodes biopsies were enrolled in this study; (30) lymph nodes biopsies were related to patients with NHL and (15) lymph nodes autopsies have included as apparently normal control group. Detection of EBV was done by ultra-sensitive version of in situ hybridization (ISH) method whereas immunohistochemical (IHC) system was used to demonstrate the protein expression of P16 tumor suppressor gene. Results: Detection of EBV -ISH reactions in tissues with NHL was observed in 17 out of 30 (56.7%), while in the tissues from lymph nodes autopsies was detected in 6.7% (1 out of 15). Positive P16IHC reactions were observed in 14 out of 30 NHL cases (47.1%). No P16 positive – IHC reaction was detected in healthy lymph node tissues in the control group. The differences between the percentages of EBV and P16 detection in NHL tissues and control tissues group were statistically highly significant (P value = < 0.0001). Conclusions: The significant protein expression of P16 tumor suppressor gene as well as EBV infection in NHL in our results could indicate that cell cycle dysregulation and EBVrelated transformation are important events in the pathogenesis of subset of NHL. Keyword: EBV; P16; NonHodgkin's Lymphoma (NHL); In Situ hybridization; Immunohistochemistry.
Potential of Wood Vinegar for Enhancing Seed Germination of Three Upland Rice Varieties by Suppressing Malondialdehyde Production

Upland rice usually gives poor germination under rainfed upland environement. To improve the seed germination, seed priming technique was assessed in this study. Seed of three upland rice ( Oryza sativa L.) varieties (Leum Pua, ULR038 and Sakon Nakhon1, SKN) were primed with three different seed priming agents; distilled water, CaCl 2 and 300-fold diluted wood vinegar. Compared to untreated dry seeds, wood vinegar improved field emergence and improved drought tolerance of the rice seeds better than other priming agents, which 50 % for Leum Pua, 20 % for ULR038 and 16% for SKN, when watering was delayed for 7 days. All three priming agents increased the field emergence percentage by similar amounts when watering was delayed for 14 days. To understand how priming helped improvement of germination, antioxidation mechanism and sugar metabolism were examined. Level of malondialdehyde was markedly reduced in all three rice varieties in response to priming, which were associated with increased activity of antioxidant enzymes, guaiacol peroxidase and ascorbate peroxidase. Wood vinegar also accelerated amylase activity in ULR038 and SKN, but not the sugar content. The results suggest that wood vinegar is a potent priming agent for achieving rapid and uniform seed germination in upland rice.
Cobordism of Morse functions, and applications to map germs at boundary points

Cobordism relations for Morse functions are based on proper stable maps into the plane (see the works of Ikegami-Saeki [5], Kalmár [6], and Ikegami [3]). There are applications and connections to exotic spheres (see Saeki [11] and Wrazidlo [16]), to high-dimensional TQFT (see Banagl [2], MüllerWrazidlo [8], and Wrazidlo [15]), and to cut and paste invariants of manifolds and SKK-groups (see Wrazidlo [18]). In this talk, we use explicit methods of geometric topology to compute the cobordism groups of Morse functions on compact manifolds possibly with boundary. In doing so, we generalize previous work of Ikegami-Saeki [5], Saeki-Yamamoto [12], Yamamoto [19], and Wrazidlo [17]. The underlying stable map germs are fold points and cusps at interior points, and boundary fold points, boundary cusps, and B2 singularities at boundary points. Our approach also applies to the analogous problem for Morse maps into the circle. As an application, we study topological invariants for generic smooth map germs at boundary points into the plane.
Combination of Clove and Lemon Basil Essential Oils for Preservation of Chicken Meat

Background: Clove and lemon basil are widely used in Indonesian culinary and known for their antimicrobial properties. This study was designed to identify the chemical constituents of single clove and lemon basil Essential Oils (EOs) as well as determine the potential of the combinations of both EO for preserving chicken meats. Methods: The compositions of clove and lemon basil EOs were evaluated with Gas Chromatography-Mass Spectrometer. Three different concentration ratios of the combination of clove and lemon basil EOs (2:0.2, 1:1, and 0.1:2% v/v) were prepared along with single clove and lemon basil EOs in a concentration of 1% v/v. Their potential preservation effect was evaluated by observing the reduction of the microbial growth on the meats by evaluating Optical Density (OD) of cultured bacterial suspensions during 15 days of refrigerated storage. Statistical analyses were conducted by SPSS Statistics v. 20. Results: The major constituents of clove EO were eugenol, β-caryophyllene, and αhumulene, while those of lemon basil were estragol, linalool, E-citral, and Z-citral. Both treatment groups and storage time affected significantly on ODs of the samples. Combination of these two EOs, particularly at the optimum ratio of 1:1%, showed the best microbial inhibitory activity, and delayed the sensorial changes of the meats for 12 days. Conclusion: The combinations of cloves and lemon basil EOs showed a better microbial growth inhibitory activity and preservation potential than those of the single use. This meat preservation effects might be related to the presence of high fractions of oxygenated compounds, mainly eugenol, Z-citral, and E-citral in both clove and lemon basil EOs.
A Survey of Deep Networks Techniques All Classifiers

Deep neural networks (DNNs) have introduced novel and useful tools to the machine learning community. Other types of classifiers can potentially make use of these tools as well to improve their performance and generality. This paper reviews the current state of the art for deep learning classifier technologies that are being used outside of deep neural networks. Non-neural network classifiers can employ many components found in DNN architectures. In this paper, we review the feature learning, optimization, and regularization methods that form a core of deep network technologies. We then survey nonneural network learning algorithms that make innovative use of these methods to improve classifications. Because many opportunities and challenges still exist, we discuss directions that can be pursued to expand the area of deep learning for a variety of classification algorithms.
Hematopoietic Stem Cell Self-renewal, the Transcription Factor HoxB4, and the Polycomb and Trithorax Group Epigenetic Regulator Complexes

Lifelong hematopoiesis depends upon the sustained self-renewal activity of the long-term reconstituting hematopoietic stem cell (LTRC). A distinct multipotent downstream stage, the intermediate-term reconstituting cell (ITRC), also robustly self-renews during initial but not subsequent divisions. My work aimed at uncovering mechanisms that specify the longevity of self-renewal. Before I began my studies, the transcription factor HoxB4 had been extensively studied in the context of hematopoiesis and was believed to enhance LTRC self-renewal divisions, based on the dramatic expansion of reconstituting cell numbers following ectopic delivery to murine bone marrow. However, alternative mechanisms underlying this apparent expansion had not been explored, and details of where and when endogenous HoxB4 was expressed remained to be ascertained. I mapped expression of a panel of Hox cluster genes over the hematopoietic precursor hierarchy. Among this panel, expression of HoxB4 uniquely correlated with active cell cycling of permanently and transiently reconstituting cells, while expression was repressed in more advanced cycling progenitors. This expression pattern suggested that endogenous HoxB4 might specify self-renewal divisions, and that failure of more advanced precursors to sustain self-renewal might be explained by loss of HoxB4 expression. I
Efficacy of Enamel Matrix Proteins in Periodontal Regeneration of Intraosseous Defects: An Umbrella Review

Introduction Periodontitis is a chronic inflammatory disease, it affects tissues that support and surround the teeth [1], despite its multifactorial etiology, dental biofilm is considered a necessary although not sufficient cause for its development and progression [2]. When periodontal disease progresses, it is common to find intrabony defects, which can generate difficulties in the non-surgical treatment of the condition [3]. Intrabony defects can be classified according to the number of remaining bony walls, and it has been shown that their anatomy may affect periodontal therapy success [4,5]. Intrabony defects with 3 remaining walls do not show spontaneous resolution, but it is easier in these cases to stabilize the material compared to defects with 1 and 2 walls, in which factors that promote bone healing are decreased [6-8]. One goal of periodontal therapy is to regenerate support structures that may be affected because of the natural course of the disease. To achieve said objective, literature has proposed many procedures, among which are bone grafts, guided tissue regeneration, the use of enamel matrix derivatives (EMD) and even, associations between these procedures [10-12].
Cholesterol Uptake Capacity: A New Measure of HDL Functionality for Coronary Risk Assessment.

BACKGROUND Recent studies have shown that the cholesterol efflux capacity of HDL is a better predictor of cardiovascular disease (CVD) than HDL cholesterol. However, the standard procedures used for measuring cholesterol efflux capacity involve radioisotope-labeled cholesterol and cultured macrophages. Thus, a simpler method to measure HDL functionality is needed for clinical application. METHODS We established a cell-free assay system to evaluate the capacity of HDL to accept additional cholesterol, which we named cholesterol "uptake capacity," using fluorescently labeled cholesterol and an anti-apolipoprotein A1 antibody. We quantified cholesterol uptake capacity of apolipoprotein B (apoB)-depleted serum samples from patients with coronary artery disease who had previously undergone revascularization. RESULTS This assay system exhibited high reproducibility (CV <10%) and a short processing time (<6 h). The myeloperoxidase-mediated oxidation of apoB-depleted serum impaired cholesterol uptake capacity. Cholesterol uptake capacity correlated significantly with cholesterol efflux capacity (r2 = 0.47, n = 30). Furthermore, cholesterol uptake capacity correlated inversely with the requirement for revascularization because of recurrence of coronary lesions in patients with optimal control of LDL cholesterol (P < 0.01, n = 156). A multivariate analysis adjusted for traditional coronary risk factors showed that only cholesterol uptake capacity remained significant (odds ratio, 0.48; 95% CI, 0.29-0.80; P = 0.0048). CONCLUSIONS Cholesterol uptake capacity assay evaluates the functionality of HDL in a sensitive and high-throughput manner without using radioisotope label and cells. This assay system could be used for the assessment of CVD risk in the clinical settings.
Determining Combining Ability in Sunflower (Helianthus annus L.)

Sunflower is one of the important oilseed crop in India. Cultivation of sunflower in India started in 1972 with the introduction of Russian varieties, Peredovick (EC 68414) and Armavirskii (EC 68415). The introduction of the crop in India has helped a great deal in increasing oilseed production and the area under its cultivation is increasing due to its day neutrality, wide adaptability, short duration, high yield potential, remunerative market price and good quality oil. Although nearly every part of the sunflower has been used by human in one or other way, it is the oil that is most valuable. Sunflower oil, however, is nutritionally better and more stable than soybean oil and hence is better for human consumption. Sunflower oil is considered as premium oil because of its light colour, flavour, high smoke point and good nutritional quality. The oil concentration in whole seed varies from 30 to 45 per cent depending on the genotype and growing conditions. The high percentage of polyunsaturated fatty acids in the oil renders it International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 05 (2018) Journal homepage: http://www.ijcmas. com
Asymmetric Network Connectedness of Fears

Abstract This paper introduces forward-looking measures of the network connectedness of fears in the financial system arising due to the good and bad beliefs of market participants about uncertainty that spreads unequally across a network of banks. We argue that this asymmetric network structure extracted from call and put traded option prices of the main U.S. banks contains valuable information for predicting macroeconomic conditions and economic uncertainty, and it can serve as a tool for forward-looking systemic risk monitoring.
Theory and numerical modeling of photonic resonances: Quasinormal Modal Expansion -- Applications in Electromagnetics

The idea of the modal expansion in electromagnetics is derived from the research on electromagnetic resonators, which play an essential role in developments in nanophotonics. All of the electromagnetic resonators share a common property: they possess a discrete set of special frequencies that show up as peaks in scattering spectra and are called resonant modes. These resonant modes are soon recognized to dictate the interaction between electromagnetic resonators and light. This leads to a hypothesis that the optical response of resonators is the synthesis of the excitation of each physical-resonance-state in the system: Under the excitation of external pulses, these resonant modes are initially loaded, then release their energy which contributes to the total optical responses of the resonators. These resonant modes with complex frequencies are known in the literature as the Quasi-Normal Mode (QNM). Mathematically, these QNMs correspond to solutions of the eigenvalue problem of source-free Maxwell's equations. In the case where the optical structure of resonators is unbounded and the media are dispersive (and possibly anisotropic and non-reciprocal) this requires solving non-linear (in frequency) and non-Hermitian eigenvalue problems. Thus, the whole problem boils down to the study of the spectral theory for electromagnetic Maxwell operators. As a result, modal expansion formalisms have recently received a lot of attention in photonics because of their capabilities to model the physical properties in the natural resonance-state basis of the considered system, leading to a transparent interpretation of the numerical results. This manuscript is intended to extend the study of QNM expansion formalism, in particular, and nonlinear spectral theory, in general. At the same time, several numerical modelings are provided as examples for the application of modal expansion in computations.