Miracle-dz/UniFAR-FTUs huggingface dataset:
Invited review: Reproductive and genomic technologies to optimize breeding strategies for genetic progress in dairy cattle

Abstract. Dairy cattle breeders have exploited technological advances that have emerged in the past in regards to reproduction and genomics. The implementation of such technologies in routine breeding programs has permitted genetic gains in traditional milk production traits as well as, more recently, in low-heritability traits like health and fertility. As demand for dairy products increases, it is important for dairy breeders to optimize the use of available technologies and to consider the many emerging technologies that are currently being investigated in various fields. Here we review a number of technologies that have helped shape dairy breeding programs in the past and present, along with those potentially forthcoming. These tools have materialized in the areas of reproduction, genotyping and sequencing, genetic modification, and epigenetics. Although many of these technologies bring encouraging opportunities for genetic improvement of dairy cattle populations, their applications and benefits need to be weighed with their impacts on economics, genetic diversity, and society.
'Recombinant Nature': Transgenics and the Emergence of Hum-animals

The advent of transgenic technologies have be a controversial area in science. For example critics argue that transgenics blurs the barrier between humans and animals. Another reason is that transgenics may diminish human belief of its superiority in the animal kingdom which has been asserted by various religious and philosophical worldviews. On the contrary, genetic research has brought to our attention of human similarity with the animal kingdom. The aim of this paper is to provide some philosophical understanding of transgenics and proffer new ways for exploring transgenics. Introduction The growth of new biotechnologies and their ability to ‘tinker with evolution’ has been a showpiece for science. In particular, genetic engineering has captured the attention of popular culture, due mainly to a plethora of sci-fi movies and programs which regularly depict genetically engineered societies and futures. The present ‘genetic mythos’ is sustained by a pan-mythic imagination which has for many millennia generated a litany of hybrid creatures – fusions of humans and animals (i.e harpies, centaurs, satyrs, minotaur, sphinx, mermaids, gorgons, hum-animal incarnations of Vishnu, totemic animals in indigenous societies). The symbolic representations of these fantastical creatures signified an “unnatural
Time-frequency dynamics of resting-state functional connectivity measured using fMRI based on Hilbert-Huang Transform

fMRI based on Hilbert-Huang Transform Tong Wu1, Xia Wu1,* 1College of Information Science and Technology, Beijing Normal University, 100875, Beijing, China *wuxia@bnu.edu. cn Background: The functional connectivity (FC) has emerged as an effective measurement of the functional interactions between the different brain regions (Van et al. 2010), particularly in the resting state functional magnetic resonance imaging (fMRI) studies. The time-domain FC analysis can only examine the time-point-to-time-point relationship between fMRI signals. Recent studies have shown that the dependency between the fMRI signals on frequency domain may convey more information regarding the interaction between the brain regions (Wei et al. 2012; Wen et al. 2012). So far, common frequencydomain approaches always assume that the fMRI signals are temporally stationary and FC was fixed from time to time. However, previous studies suggest that FC may changes in seconds or minutes, reflecting the important dynamic nature of the real neural systems (Chang et al. 2010; Kiviniemi et al. 2011;), which is still elucidate in many aspects. For analyzing the time-frequency dynamic nature of FC, Hilbert-Huang Transform (HHT) which was a novel time-frequency method providing more accurate instantaneous frequency (Huang et al. 2005; Huang et al. 2008; Donnelly et al. 2006; Peng et al. 2005) was applied. The aim of this study was to reveal the time-frequency dynamics of the resting-state FC using HHT.
Intraoperative Corneal Incision Evaluation with Trypan Blue Technique

C l i n M e d International Library Citation: Kayikcioglu O, Bilgin S, Ulusoy MO (2016) Intraoperative Corneal Incision Evaluation with Trypan Blue Technique. Int J Ophthalmol Clin Res 3:050 Received: January 12, 2016: Accepted: May 10, 2016: Published: May 13, 2016 Copyright: © 2016 Kayikcioglu O, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Kayikcioglu et al. Int J Ophthalmol Clin Res 2016, 3:050
Biological and structure-activity evaluation of chalcone derivatives against bacteria and fungi

O presente trabalho descreve as atividades antibacterianas e antifungicas de diversas chalconas obtidas diretamente atraves da condensacao aldolica tipo Claisen-Schmidt das quais se determinou a concentracao inibitoria minima frente a diferentes microrganismos (bacterias Gram-positivas e Gram-negativas e fungos). Estruturas no estado solido cristalino de sete chalconas foram determinadas por analise de difracao de raios X (XRD). Estudos quimiometricos foram realizados com intuito de identificar uma potencial relacao entre estrutura e atividade.
Validating the RedMIT/GFP-LC3 Mouse Model by Studying Mitophagy in Autosomal Dominant Optic Atrophy Due to the OPA1Q285STOP Mutation

Background: Autosomal dominant optic atrophy (ADOA) is usually caused by mutations in the essential gene, OPA1. This encodes a ubiquitous protein involved in mitochondrial dynamics, hence tissue specificity is not understood. Dysregulated mitophagy (mitochondria recycling) is implicated in ADOA, being increased in OPA1 patient fibroblasts. Furthermore, autophagy may be increased in retinal ganglion cells (RGCs) of the OPA1Q285STOP mouse model. Aims: We developed a mouse model for studying mitochondrial dynamics in order to investigate mitophagy in ADOA. Methods: We crossed the OPA1Q285STOP mouse with our RedMIT/GFP-LC3 mouse, harboring red fluorescent mitochondria and green fluorescent autophagosomes. Colocalization between mitochondria and autophagosomes, the hallmark of mitophagy, was quantified in fluorescently labeled organelles in primary cell cultures, using two high throughput imaging methods Imagestream (Amnis) and IN Cell Analyzer 1000 (GE Healthcare Life Sciences). We studied colocalization between mitochondria and autophagosomes in fixed sections using confocal microscopy. Results: We validated our imaging methods for RedMIT/GFP-LC3 mouse cells, showing that colocalization of red fluorescent mitochondria and green fluorescent autophagosomes is a useful indicator of mitophagy. We showed that colocalization increases when lysosomal processing is impaired. Further, colocalization of mitochondrial fragments and autophagosomes is increased in cultures from the OPA1Q285STOP/RedMIT/GFP-LC3 mice compared to RedMIT/GFP-LC3 control mouse cells that were wild type for OPA1. This was apparent in both mouse embryonic fibroblasts (MEFs) using IN Cell 1000 and in splenocytes using ImageStream imaging flow cytometer (Amnis). We confirmed that this represents increased mitophagic flux using lysosomal inhibitors. We also used microscopy to investigate the level of mitophagy in the retina from the OPA1Q285STOP/RedMIT/GFP-LC3 mice and the RedMIT/GFP-LC3 control mice. However, the expression levels of fluorescent proteins and the image signal-to-background ratios precluded the detection of colocalization so we were unable to show any difference in colocalization between these mice. Conclusions: We show that colocalization of fluorescent mitochondria and autophagosomes in cell cultures, but not fixed tissues from the RedMIT/GFP-LC3, can be used to detect mitophagy. We used this model to confirm that mitophagy is increased in a mouse model of ADOA. It will be useful for cell based studies of diseases caused by impaired mitochondrial dynamics.
Measuring financial risk : comparison of alternative procedures to estimate VaR and ES

We review several procedures for estimating and backtesting two of the most important measures of risk, the Value at Risk (VaR) and the Expected Shortfall (ES). The alternative estimators differ in the way the specify and estimate the conditional mean and variance and the conditional distribution of returns. The results are illustrated by estimating the VaR and ES of daily S&P500 returns.
Phenotypic Characterization of Antimicrobial Resistance in Kerala Bacillus Spp Isolated from Paddy Field

Rice paddy environment is an exceptional reservoir for different microorganisms (Pathogenic and Non-Pathogenic). Fertilizers, Fungicides, Antibiotics and Insecticides were used for boosting rice paddy growth and preventing agronomy diseases. Enormous use of fertilizers, Fungicides, Antibiotics and Insecticides will develop drug resistance in the microorganisms present in the crop [figure-1]. Ninety dried rice paddy samples were collected from different places around regions of Kerala. Forty rod-shaped gram-stain-Positive endospore forming obligate aerobic bacteria were isolated from the samples. All the forty strains were subjected to for antibiotic susceptibility by using the standard antibiotic disc (Cefoxitin). Significant drug resistance and massive growth observed in the strain (SCOP-2) among other isolated bacteria. SCOP-2 was subjected for sensitivity to differ different Antimicrobial disc by using Kirby-Bauer disc diffusion method. The results show that SCOP-2 drug resistant against all the five Antibiotics. The Minimum Inhibitory Concentration (MIC) was determined by two fold serial dilution against Ciprofloxacin (CIP) and Linezolid (LNZ). From the results it is concluded that CIP and LNZ shows resistance against SCOP-2.
The National Study of Youth and Religion in a Nutshell Making

Editor's Note: On August 27, Kenda Creasy Dean and her book Almost Christian: What the Faith of Our Teenagers is Telling the American Church were featured in a news piece by CNN. Five years ago, the National Study of Youth and Religion was published in Soul Searching: The Religious and Spiritual Lives of American Teenagers, by Christian Smith and Melinda Lundquist Denton. This study diagnosed the anemic faith of teens. In Almost Christian, Dean offers a treatment plan. Below is a synopsis of the initial study written as part of a Lilly Foundation grant to the Center for Youth Ministry Training and YMtoday.com. The National Study of Youth and Religion Soul Searching: The Religious and Spiritual Lives of American Teenagers (2005) The Research in a Nutshell
Super-Resolution in RSS-Based Direction-of-Arrival Estimation

For the evolving Internet-of-Things ubiquitous positioning is a core feature. Hence, energy- and location-awareness are essential properties of wireless sensor networks (WSNs). In terms low power consumption received signal strength (RSS)-based localization techniques outperform timing-based localization approaches. Therefore, RSS-based direction finding is prospective approach to location-aware, low-power sensor nodes. However, RSS-based direction-of-arrival (DOA) estimation is prone to multipath propagation. In this paper, a subspace-based approach to frequency-domain multipath resolution is presented. Resolution of multipath components allows for a RSS-based DOA estimation considering the power of the line of sight (LOS) component only. The impact of the multipath channel is considerably reduced with our approach. In contrast to common broadband DOA estimation techniques, the presented approach does not need phase-coherent receive channels or a synchronized sensor network. Hence, the proposed super-resolution technique is applicable to low-power sensor networks and brings accurate positioning to small-sized and energy-efficient sensor nodes.
Fracture Modeling of Crack Propagation in Wood and Wood Composites Including Crack Tip Processes and Fiber Bridging Mechanics

Many materials develop process zones during fracture. For example, solid wood and wood composites develop process zones often consisting of fibers bridging the crack surfaces. After crack initiation, a process zone develops causing the toughness (or R curve) to increase with crack length. For materials with large process zones, the entire crack propagation data may be a rising R curve and thus there is a need to realistically model process zone development. This paper discusses the principles needed to model rising R curves, applies them in a new numerical model based on the material point method, and applies the concepts to crack growth in wood composites. Where previous models have used either fracture mechanics or cohesive zone methods, it will be argued that realistic modeling requires both fracture mechanics and a process zone.
Chemical controls on ferrierite crystallization during diagenesis of silicic pyroclastic rocks near Lovelock, Nevada

The zeolites ferrierite, mordenite, and clinoptilolite have formed with smectite through hydration reactions in a sequence of rhyolitic pyroclastic rocks near Lovelock, Nevada. Fiigh activities of silica and magnesia were required simultaneously for the large-scale crystallization of ferrierite in these diagenetically altered rocks. Post-depositional addition of Mg coincided with ferrierite and smectite formation. The source of the Mg is not known, but it could have originated either from a brackish, saline lake or from nearby leached basalts. Thus, origins of the Lovelock ferrierite deposit may have involved both lacustrine deposition and an open ground water system for the transformation of vitric tuffs into zeolites. Ferrierite crystallized early, mainly in the pore space of the tuffs. Clinoptilolite and cristobalite grew later by replacement of glass shards. Orthoclase and mordenite crystallized somewhat later, orthoclase usually in intimate association with ferrierite in K-rich
Composition and Genetic Diversity of the Nicotiana tabacum Microbiome in Different Topographic Areas and Growth Periods

Fungal endophytes are the most ubiquitous plant symbionts on earth and are phylogenetically diverse. Studies on the fungal endophytes in tobacco have shown that they are widely distributed in the leaves, stems, and roots, and play important roles in the composition of the microbial ecosystem of tobacco. Herein, we analyzed and quantified the endophytic fungi of healthy tobacco leaves at the seedling stage (SS), resettling growth stage (RGS), fast-growing stage (FGS), and maturing stage (MS) at three altitudes (600, 1000, and 1300 m). We sequenced the internal transcribed spacer (ITS) region of fungal samples to delimit operational taxonomic units (OTUs) and phylogenetically characterize the communities. The results showed that the numbers of clustering OTUs at SS, RGS, FGS, and MS were 516, 709, 469, and 428, respectively. At the phylum level, species in Ascomycota and Basidiomycota had absolute predominance, representing 97.8% and 2.0% of the total number of species, respectively. We also found the number of fungi at the RGS and FGS stages was higher than those at the other two stages. Additionally, OTU richness was determined by calculating the Observed Species, Shannon, Simpson, Chao1, abundance-based coverage estimator (ACE), Good’s coverage and phylogenetic distance (PD)_whole_tree indices based on the total number of species. Our results showed RGS samples had the highest diversity indices. Furthermore, we found that the diversity of fungal communities tended to decrease with increasing altitude. The results from this study indicated that tobacco harbors an abundant and diverse endophytic fungal community, which provides new opportunities for exploring their potential utilization.
A Lattice Boltzmann Model to Study Sedimentation Phenomena in Irrigation Canals MARCOU

Fresh water is one of the most significant resources for human activities and survival, and irrigation is among the most important uses of water. The sustainibility and performance of irrigation canals can be greatly affected by sediment transport and deposition. In our previous works, we proposed a Lattice Boltzmann model for simulating a free surface flow in an irrigation canal, as an alternative to more traditional models mainly based on shallow water equations. Here we introduce the sedimentation phenomenon into our model by adding a new algorithm, based on the earlier work by B. Chopard, A. Dupuis and A. Masselot [9,11,12,27]. Transport, erosion, deposition and toppling of sediments are taken into account and enable the global sedimentation algorithm to simulate different transport modes such as bed load and suspended load. In the present work, we study both the behaviour of a sediment deposit located at an underflow submerged gate (depending on the gate opening and the flow discharge) and the influence of the presence of such a deposit on the flow. Both numerical and experimental validations have been performed. The [. ] MARCOU, Olivier, et al. A Lattice Boltzmann Model to Study Sedimentation Phenomena in Irrigation Canals. Communications in Computational Physics, 2013, vol. 13, no. 3, p.
Steganalysis of Inactive Voice-Over-IP Frames Based on Poker Test

This paper concentrates on the detection of steganography in inactive frames of low bit rate audio streams in Voice over Internet Protocol (VoIP) scenarios. Both theoretical and experimental analyses demonstrate that the distribution of 0 and 1 in encoding parameter bits becomes symmetric after a steganographic process. Moreover, this symmetry affects the frequency of each subsequence of parameter bits, and accordingly changes the poker test statistical features of encoding parameter bits. Employing the poker test statistics of each type of encoding parameter bits as detection features, we present a steganalysis method based on a support vector machine. We evaluate the proposed method with a large quantity of speech samples encoded by G.723. 1 and compare it with the entropy test. The experimental results show that the proposed method is effective, and largely outperforms the entropy test in any cases.
Electrospun polycaprolactone nanofiber scaffolds for tissue engineering

Stem cell and tissue engineering offer us with a unique opportunity to research and develop new therapies for treating various diseases that are otherwise incurable using traditional medicines. However, development of these new therapies replies upon the establishment of in vitro cell culture and differentiation systems that mimic in vivo microenvironments required for cell-cell and cell-ECM interaction. The development of these cell culture systems depends upon the identification of appropriate biomaterials and cell sources. Biomaterials should be carefully selected and fabricated into scaffolds for supporting cell growth and differentiation. In this study, we explored the fabrication of 3D electrospun nanofiber scaffolds and demonstrated the feasibility of using these scaffolds for supporting cell growth. The material that we used for scaffold fabrication is a polymer, polycaprolactone (PCL). We discovered that the electrospun PCL nanofibers are highly hydrophobic, unsuitable for cell growth. The treatment of PCL electrospun nanofibers with oxygen plasma treatment endowed the fibers with hydrophilic property, making them suitable for cell growth. Our studies suggested that the length of oxygen plasma treatment considerably influences the water contact degree of the nanofibers and their hydrophilicity. The optimization of oxygen plasma treatment resulted in significant improvement of cell proliferation within the electrospun nanofiber scaffolds. Our results provide insight into plasma treatment effects on electrospun PCL as they relate to material properties and cell growth. This thesis is approved for recommendation to the Graduate Council
INVERSE DESIGN OF DIELECTRIC MATERIALS BY TOPOLOGY OPTIMIZATION

The capabilities and operation of electromagnetic devices can be dramatically enhanced if artiflcial materials that provide certain prescribed properties can be designed and fabricated. This paper presents a systematic methodology for the design of dielectric materials with prescribed electric permittivity. A gradient-based topology optimization method is used to flnd the distribution of dielectric material for the unit cell of a periodic microstructure composed of one or two dielectric materials. The optimization problem is formulated as a problem to minimize the square of the difierence between the efiective permittivity and a prescribed value. The optimization algorithm uses the adjoint variable method (AVM) for the sensitivity analysis and the flnite element method (FEM) for solving the equilibrium and adjoint equations, respectively. A Heaviside projection fllter is used to obtain clear optimized conflgurations. Several design problems show that clear optimized unit cell conflgurations that provide the prescribed electric permittivity can be obtained for all the presented cases. These include the design of isotropic material, anisotropic material, anisotropic material with a non-zero ofi-diagonal terms, and anisotropic material with loss. The results show that the optimized values are in agreement with theoretical bounds, conflrming that our method yields appropriate and useful solutions.
No Change in Lower Limb Extension Power during a Hospital Stay in Geriatric Patients, Despite Improved Functional Level

The aim of the current study was to evaluate changes in lower limb extension power (LLEP) during hospitalization in older medical patients. LLEP was measured in a PowerRig at admission (day 2 to 4; mean ± SD: day 2.5 ± 0.8) and before discharge (day 5-11; mean ± SD: day 8.4 ± 2.2) in 33 older medical patients (age ≥ 65 years, mean age 86.7 years). “High” asymmetry was defined as >10% difference in LLEP between the lower limbs. Functional performance was measured with the De Morton Mobility Index (DEMMI-test) and 30 second chair stand test (30-s CST). The patients were characterized by very low LLEP (0.95 ± 0.37 watt/kg for men, 0.68 ± 0.27 watt/kg for women; mean ± SD) and a high prevalence of asymmetry. LLEP did not change during hospital stay while the prevalence of “high” asymmetry seemed to increase. Significant improvements in the DEMMI-test and 30-s CST was observed, but did not correlate with changes in LLEP. The patient’s activity level (measured with ActivPal) was not related to LLEP at admission, and could not explain the individual changes in LLEP during the hospital stay. Conclusion: Although LLEP is related to function, the current results suggest that the functional improvements in older geriatric patients occur in the absence of improvements in LLEP. Individual changes in LLEP were not related to the changes in function or to the daily activity level in the patients.