Miracle-dz/UniFAR-FTUs huggingface dataset:
Equilibrium and nonequilibrium quantum correlations between two accelerated detectors

An accelerated detector will see thermal radiation around with temperature T which is termed as Unruh effect. The two accelerated observers can detect quantum correlations between them through the vacuum field. A natural question arises: is this equilibrium quantum correlation equivalent to the one between the two stationary detectors under a thermal bath? A further question is what if the two accelerations or the couplings between the detectors and vacuum field are different and how this nonequilibrium effect can influence the quantum correlations. In this study, we examine the above scenarios. We found that as the acceleration of the detectors increase, the quantum correlations (entanglement, mutual information, discord) will increase first and eventually decay depending on the redshift effect. The temperature and acceleration characterizing the equivalent space-time curvature show different impacts on the global quantum correlations in this equilibrium (equal temperatures or accelerations of the two detectors) scenario. When the equal acceleration is in the opposite direction, as the distance increases, the correlation will decay, and the entanglement appears to be more robust than the quantum mutual information and discord. Importantly, we have uncovered that the nonequilibriumness characterized by the degree of the detailed balance breaking due to the different couplings of the detectors to the vacuum field can increase the quantum correlations. We also uncovered both the nonequilibrium (different accelerations of the two detectors) and distance effects on quantum correlations between the detectors.
Failures of model-dependent generalization bounds for least-norm interpolation

We consider bounds on the generalization performance of the least-norm linear regressor, in the over-parameterized regime where it can interpolate the data. We describe a sense in which any generalization bound of a type that is commonly proved in statistical learning theory must sometimes be very loose when applied to analyze the least-norm interpolant. In particular, for a variety of natural joint distributions on training examples, any valid generalization bound that depends only on the output of the learning algorithm, the number of training examples, and the confidence parameter, and that satisfies a mild condition (substantially weaker than monotonicity in sample size), must sometimes be very loose---it can be bounded below by a constant when the true excess risk goes to zero.
Reduced-Order Simulation of Flexible Meta-Materials

We propose a reduced-order simulation and optimization technique for a type of digital materials which we denote as geometric meta-materials. They are planar cellular structures, which can be fabricated in 2d and folded in 3d space and thus well shaped into sophisticated 3d surfaces. They obtain their elasticity attributes mainly from the geometry of their cellular elements and their connections. While the physical properties of the base material (i.e., the physical substance) of course influence the behavior as well, our goal is to factor them out. However, the simulation of such complex structures still comes with a high computational cost. We propose an approach to reduce this computational cost by abstracting the meso-structures and encoding the properties of their elastic deformation behavior into a different set of material parameters. We can thus obtain an approximation of the deformed pattern by simulating a simplified version of the pattern using the computed material parameters.
New moult pattern in diurnal raptors: primary moult pattern of the Japanese Sparrowhawk Accipiter gularis

ABSTRACT In the family Accipitridae, the primary feathers (p) are moulted sequentially from p1 (innermost primary) outwards to p10. In comparison, the primaries are moulted divergently in the family Falconidae, starting from p4 (and sometimes p5), and simultaneously ascending towards p1 and descending towards p10. This moulting process is considered to be representative across diurnal raptors. Here, the moult pattern of the Japanese Sparrowhawk Accipiter gularis was examined from museum specimens and from direct observations of live birds. Two types of moult patterns were detected, with 13.2% of birds exhibiting a ‘normal-type’ moult and 59.4% of birds exhibiting a ‘new-type’ moult, while patterns could not be detected in the remaining 27.4%. During the non-breeding season, the primary feathers generally moulted outwards in the normal-type moult, starting from p1 and ending at mostly p8. In contrast, the intensity of the new-type moult varied among individuals, with most individuals moulting feathers between p4 and p8 and replacing their primaries between p3 and p10.
Response of Internal Conductance to Soil Drought in Sun and Shade Leaves of Adult Fagus crenata

The internal conductance to CO2 (gi) is an important constraint of photosynthesis, and its acclimation to environmental factors varies widely within plant functional groups, genera and even species. We measured photosynthesis and chlorophyll fluorescence response curves to intercellular CO2 concentrations simultaneously in attached sun and shade leaves of 90-year-old Fagus creneta Blume trees to determine (1) how gi varies within the crown and (2) whether soil drought affects gi. Internal conductance to CO2 was found to be 0.058 and 0.185 mol m-2 s-1 in lower and upper crowns, respectively, resulting in a decrease of about 70 μmol mol-1 in CO2 concentration from the intercellular space (Ci) to the site of carboxylation inside the chloroplast stroma (Cc). The results suggest that gi is as important as stomatal conductance for photosynthetic efficiency in F. crenata. If this large decrease from Ci to Cc was not accounted for, the maximum rate of carboxylation (Vcmax) in sun and shade leaves was underestimated ca 36% and 24%, respectively. When soil water supply was sufficient, leaf water potential dropped to a daily minimum in early morning, facilitating CO2 transfer and thus photosynthesis. When soil water potential at 25 cm depth fell to –0.015 MPa, gi and stomatal conductance decreased by 20–40% in comparison with their respective values under sufficient soil water supply. In contrast, Vcmax decreased by 7% in sun leaves, but there was no change in this parameter in shade leaves. Ignoring the effect of gi on Cc under stressed conditions would lead to up to 22% underestimates of Vcmax, and consequently overestimates of biochemical limitations. These results suggest that CO2 diffusional limitations have more significant effects than biochemical limitations on the rate of photosynthesis in F. crenata during soil drought.
Phenotypic Detection of Carbapenemases and β-lactamases induced Carbapenem Resistance in Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae has challenged the therapeutic efficacy and raised the most worrisome global issue of public health importance. The study was conducted to determine the burden of carbapenem resistant isolates of Enterobacteriaceae producing different types of β-lactamases. During the study period, a total of 310 enterobacterial pathogens were isolated and identified from the clinical specimens obtained from the patients visiting Kanti Children Hospital. By Kirby Bauer disc diffusion method, β-lactamase producers and multidrug resistant isolates were detected and ESBLs and carbapenemase producers were screened among them. Phenotypic detection of ESBLs was done by Combination disc test. Modified Hodge test was employed for detection of carbapenemase producers and they were typified by inhibitor based combination disk tests. A total of 251 (81.0%) isolates were β-lactamase producers and 213 (68.7%) were multidrug resistance among the Enterobacteriaceae. Typification of β-lactamases from 23 (7.4%) Modified Hodge Test positive isolates assorts 4 as KPC producers, 11 as MBL producers, 3 as AmpC β-lactamase producers and 1 with both KPC and MBL enzyme while 4 remained unclassified. The majority of carbapenem resistants were E. coli (52.1%) followed by K. pneumoniae (34.8%) and most of the CRE were resistant (56.52%) to all the combinations of ESBL test. Various classes of carbapenemases were found to have emerged among Enterobacteriaceae in Nepal. Since, the profound variation is found in β-lactamases of CRE, to reduce the risk of severe calamity effective detection procedures are mandatory in all clinical laboratories.
Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster

Long-range interactions between the 5*and 3*endsofmRNAmoleculeshavebeensuggestedtoplayarole in the initiation of translation and the regulation of gene expression. To identify such interactions and to study their molecularevolution,weusedphylogeneticanalysistogenerate amodelofmRNAhigher-orderstructureintheAdhtranscript of Drosophila melanogaster. This model predicts long-range, tertiary contacts between a region of the protein-encoding sequence just downstream of the start codon and a conserved sequence in the 3* untranslated region (UTR). To further examine the proposed structure, site-directed mutations were generatedinvitroinaclonedD.melanogasterAdhgene,andthe mutant constructs were introduced into theDrosophilagerm line through P-element mediated transformation. Transfor- mants were spectrophotometrically assayed for alcohol dehy- drogenase activity. Our results indicate that transformants containing a silent mutation near the start of the protein- encoding sequence show an '15% reduction in alcohol dehy- drogenase activity relative to wild-type transformants. This activity can be restored to wild-type levels by a second, compensatorymutationinthe3*UTR.Theseobservationsare consistent with a higher-order structure model that includes long-range interactions between the 5*and 3*ends of theAdh mRNA. However, our results do not fit the classical compen- satory substitution model because the second mutation by itself (in the 3*UTR) did not show a measurable reduction in gene expression.
The Influence of Probiotic Lactobacilli and Flaxseed on the Health of Weaned Piglets and Metabolism of Polyunsaturated Fatty Acids (PUFAs)

Abstract This study investigated for 14 days post-weaning, the influence of dietary supplementation of synbiotics in the form of probiotic cheeses containing cultures of L. plantarum and L. fermentum and crushed flaxseed (source of ω-3 polyunsaturated fatty acids — PUFAs and fibre) on 36 commercial piglets originating from an infected herd (Coronavirus and E. coli) during the critical period of weaning. We focused on the health and metabolism of PUFAs in this critical period of a piglet’s life. The dietary supplementation positively affected: the overall health state of weaners, reduced diarrhoea by 29 % by 14 days post-weaning and significantly increased the counts of lactic acid bacteria, bifidobacteria and the production of volatile fatty acids. The PUFA concentrations in the m. biceps femoris of the piglets were analysed by gas chromatography. High levels of ω-3 alpha-linolenic acid (ALA) in flaxseed increased significantly the level of ALA, eicosapentaenic acid (EPA) and docosahexaenic acid (DHA) in the pig muscles on days 7 and 14 post-weaning. The levels of ω-6 linolenic acid (LA) were less affected by the diet, but were increased on day 14 post-weaning, while the conversion products of LA, and arachidonic acid (AA), were decreased on days 7 and 14. The increased level of dietary ALA favoured the activity of Δ-6-desaturase for the conversion of ALA to EPA and DHA, at the expense of AA synthesis from LA. The ability of synbiotics to incorporate high levels of DHA in the pig muscles appear prospective for improving the nutritional properties of pork and reducing the occurrence of civilization diseases in consumers of this product of animal origin.
Glucocorticoid Signature in a Neuronal Genomic Context

During this research we wanted to gain more insight into the potential gene repertoire that is involved in the hippocampus when coping with stress and regulating learning and memory processes. To investigate this further we aimed to answer the question:""What are the primary genomic binding sites of the by stress and thus cortisol stimulated protein receptors MR and GR in the hippocampus? " To answer this question, new methods have been applied to determine where exactly MR and GR bind to the DNA, to find out which genes are potentially involved during stress management. As a result we have identified thousands of GR-binding sites at the DNA of which we have analyzed a selection in further detail. One of the identified pathways that have been found to be sensitive for activated GR and corticosteroids is the mTOR pathway. This pathway is involved in neuronal plasticity, which is the fundament for resilience. We have found that expression of the mTOR protein is decreased after exposure to acute stress when the organism has a history of chronic stress. Our results indicate that the reduced resilience after experiencing chronic stress is likely to be mediated by mTOR.
Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

Evolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep‐level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep‐level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP‐EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well‐resolved gene trees are critical for the effectiveness of coalescent‐based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of new methods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable.
Stability Comparison of Free and Encapsulated Lactobacilus casei ATCC 393 in Yoghurt for Long Time Storage

An innovative method of L. casei ATCC 393 encapsulation has been reported in the present study using pectin combined with alginate. The aim of this study was to investigate the effect of encapsulation on the survival of L. casei ATCC 393 in yoghurt during long time storage, free or encapsulated in alginate and alginate pectin microspheres, and influence over yoghurt properties, particularly acidification. Over 35 days of storage in yoghurt, the encapsulated probiotic cells proved a higher viability compared with free probiotic cells. An even higher viability and stability was observed for the samples where pectin was used. Pectin acts as prebiotic during encapsulation of L. casei ATCC 393.
GENERAL MODEL OF THE INNATE IMMUNE RESPONSE FROM A MECHANICAL ENGINEERING POINT OF VIEW

The continuous fight between bacteria and the phagocytes that belong to the innate immune system has attracted a cross-disciplinary interest. Different authors had developed different models of phagocytosis in the past. This paper extended the mathematical population model of Reed et al (2011) by investigating the dynamic energy flow associated with the neutrophils phagocytosis of bacteria. Reed et al (2011) had studied the stability properties of trivial and nontrivial equilibrium of their population model using the Jacobian matrix. This paper arrived at same conclusion regarding stability by following a different approach that involved expanding the non-linear system in Taylor series and studying the stability properties after the non-linear terms were truncated. Energy equation model of phagocytosis is then derived in this paper to augment the population model of Reed et al (2011). The derivation of the energy equation aims to bridge the gap between biological sciences (immunology) and mechanical engineering. Solution of the energy equation reveals that as time elapses, the graphs for which the engulfment parameter, , is negative gets more negative. This implies progression of phagocytosis. That is to say that more bacteria are being engulfed and more energy released with time (exothermic process). Propensity of engulfment to occur is considered to be higher for more negative final values of energy of engulfment on the real number line.
Association of allele variants of gene Rf with red fruit color of apple cultivars of ukrainian breeding

Apple is one of the most relevant fruit crop in Ukraine, the consumption of apple fruit by the population is prioritized among all the fruit and small-fruit crops. The prominent place in the Register of cultivars of Ukraine is taken by apple cultivars, created by the Institute of Horticulture (IH) NAAS and its network. Our studies have proven that these cultivars are valuable genetic material, which is insuf ciently characterized from the standpoint of relevant allele variants of genes, responsible for economically valuable traits. Their identi cation will expand the possibilities of involving the mentioned cultivars to MAS programs, in particular, by fruit skin color. The fruit of Ukrainian apple cultivars have different colors – from green color, like that of Papirovka cultivar, to dark red, like that of cultivars Rubinove Duky or Amulet. Fruit skin of many cultivars is of uneven color, it has stripes or “blush”, which may be manifested differently even among fruit of the same cultivar. Apple fruit color is not only a remarkable trait of the cultivar, but also a relevant criterion, affecting the consumer’s choice. In particular, buyers often prefer cultivars with red fruit color, which is associated with better ripeness and thus better taste and aroma [5]. Red color of apple fruit is mainly determined by the presence of secondary metabolites – anthocyanins [6, 7]. The intensity of red color of fruit skin is directly dependent on the accumulation degree of these natural antioxidants, which varies in a wide range and changes depending on the ripeness degree and environmental conditions. The ripest fruit, well lit by the sun during their growth, have the richest color and thus higher content of anthocyanins in their skin compared to not ripe, insuf ciently lit fruit of the same cultivar [8]. It is noteworthy that in ISSN: 2312-3370, Agricultural Science and Practice, 2016, Vol. 3, No. 3
Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics

It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of the study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced and determine if the data are comparable on different platforms. In this study, we perform ultra-deep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We validated the sequencing and analysis methods using different Illumina platform, and with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are more highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome, and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.
Characterizing the Role of Elongation Factor 1A and Other Cellular Proteins in the Yeast Rapid tRNA Decay Pathway

The structural and functional integrity of tRNA is crucial for translation, and is in part maintained by post-transcriptional modifications to the tRNA. In the yeast Saccharomyces cerevisiae, certain mature tRNAs are subject to rapid tRNA decay (RTD) if they are appropriately hypomodified or bear specific destabilizing mutations, leading to 5'-3' exonucleolytic degradation by Rat1 or Xrn1. Thus, trm8- trm4- strains are temperature sensitive due to lack of mG46 and m C and the consequent RTD of tRNA, and tan1- trm44- strains are temperature sensitive due to lack of acC12 and Um44 and RTD of tRNA Ser(CGA) and tRNA. It was unknown how generally the RTD pathway acts on hypomodified tRNAs, and how this pathway interacts with translation and other cellular components. It is shown here that RTD acts widely on tRNAs lacking modifications, since trm1 trm4- mutants are subject to RTD of tRNA and tRNA due to lack of mG26 and m C, and since trm8-, tan1-, and trm1- single mutants are each subject to RTD. Evidence is also presented that elongation factor 1A (eEF1A) competes with the RTD pathway for substrate tRNAs, since reduced eEF1A exacerbates the growth defect of all known RTD-susceptible strains, and exacerbates tRNA degradation in all RTDsusceptible strains tested. Conversely, eEF1A overexpression suppresses RTD. To further explore the effect of eEF1A on tRNA binding and RTD, I have set up a genetic screen and a biochemical assay.
The noisy underwater world: The effect of sound on behaviour of captive zebrafish

Over the past few decades, public attention, activities in the field of conservation and animal welfare by nongovernmental organizations (NGOs), and scientific exploration are raising awareness on the potential effects of sounds on marine mammals and fish species. The aim of this thesis was to explore sound-induced behavioral changes in fish using captive zebrafish as a model species. I explored behavioural parameters as potential indicators of sound-related stress, disturbance and deterrence. In four different studies, I examined various sound exposure treatments to provide insights that may be useful for future explorations for indoor and outdoor sound impact studies as well as for assessing animal welfare and productivity in captive situations. Furthermore, my findings may also raise awareness for sound levels in laboratories and the potential effect on reliability for fish as a model species for medical and pharmaceutical studies. I also explored the complexity of sound fields in indoor fish tanks by selecting a different set-up for each study, which makes behavioural analyses and direct comparisons not only relevant within each study, but also provides insight into the role of fish tank acoustics on ‘natural’ and experimental exposure condition.