Miracle-dz/UniFAR-FTUs huggingface dataset:
Ergodicity for SDEs and approximations: locally Lipschitz vector (elds and degenerate noise

The ergodic properties of SDEs, and various time discretizations for SDEs, are studied. The ergodicity of SDEs is established by using techniques from the theory of Markov chains on general state spaces, such as that expounded by Meyn–Tweedie. Application of these Markov chain results leads to straightforward proofs of geometric ergodicity for a variety of SDEs, including problems with degenerate noise and for problems with locally Lipschitz vector (elds. Applications where this theory can be usefully applied include damped-driven Hamiltonian problems (the Langevin equation), the Lorenz equation with degenerate noise and gradient systems. The same Markov chain theory is then used to study time-discrete approximations of these SDEs. The two primary ingredients for ergodicity are a minorization condition and a Lyapunov condition. It is shown that the minorization condition is robust under approximation. For globally Lipschitz vector (elds this is also true of the Lyapunov condition. However in the locally Lipschitz case the Lyapunov condition fails for explicit methods such as Euler–Maruyama; for pathwise approximations it is, in general, only inherited by specially constructed implicit discretizations. Examples of such discretization based on backward Euler methods are given, and approximation of the Langevin equation studied in some detail. c © 2002 Elsevier Science B.V. All rights reserved.
FACE SPOOFING DETECTION USING MACHINE LEARNING WITH COLOR FEATURES

-The non-intrusive software based face spoofing detection schemes mainly focuses on the analysis of the luminance information of the face images. It discards the chroma component which can be very useful for discriminating fake faces from genuine ones. This project introduces a novel and appealing approach for detecting face spoofing using colour texture analysis. It exploit the joint colour-texture information from the luminance and the chrominance channels by extracting complementary low-level feature descriptions from different colour spaces. By using these features the colour texture is analyzed and extracted by face descriptors from different colour bands. In final the feature vector is fed into a binary classifier and the output score value describes whether it is a real or a fake image.
Mechanisms Associated With Decline of Woody Species in Riparian Ecosystems of the Southwestern U.S.

Throughout western North America, riparian ecosystem function has been transformed by anthropogenic influences on riverine environments. Modified flood frequency, duration, or intensity; depressed floodplain water tables; and increased alluvium salinity have contributed to change in riparian forest communities formerly dominated by Populus fremontii and Salix gooddingii. The invasion of the naturalized arborescent shrub, Tamarix ramosissima, potentially alters competitive hierarchies and disturbance regimes in these riparian ecosystems. We evaluated the structure and function of two southwestern riparian communities that differed in the degree of streamflow perturbation to which they had been subjected: the highly regulated lower Colorado River and the less tightly regulated Bill Williams River. Ordination analyses provided evidence that these riparian communities are structured along gradients relating to moisture, salinity, disturbance from fire, and community maturity, with Colorado River sites being more xeric and saline than those on the Bill Williams River. Foliar elemental analyses revealed high sodium concentrations in Tamarix (Na:K ratio = 1.87) and in the native shrub Tessaria sericea (Na:K = 1.56). Evaluation of tissue water relations parameters showed that Tamarix had lower osmotic potentials than sympatric woody taxa, helping to confirm that Tamarix is halophytic and probably capable of greater osmotic adjustment than native species. Carbon isotopic discrimination (△) provided evidence for higher water use efficiency in Tamaris than in Populus, Salix, and Tessaria. Tamarix △ averaged over 1% less than that of the other riparian taxa. Experimental removal of Tamarix from stands where Salix was codominant resulted in growth augmentation, less negative water potentials, and higher leaf conductance in Salix, all providing evidence of interspecific competition. The persistence of Salix, but not Populus, on the Colorado River appears to be due to greater water— and salinity stress tolerance in Salix than in Populus. A preponderance of senescent Populus along the Colorado River is an indication that this formerly dominant species is effectively approaching local extinction in parts of this ecosystem.
Choosing alternatives: Using Bayesian Networks and memory-based learning to study the dative alternation

Abstract In existing research on syntactic alternations such as the dative alternation, (give her the apple vs. give the apple to her), the linguistic data is often analysed with the help of logistic regression models. In this article, we evaluate the use of logistic regression for this type of research, and present two different approaches: Bayesian Networks and Memory-based learning. For the Bayesian Network, we use the higher-level semantic features suggested in the literature, while we limit ourselves to lexical items in the memory-based approach. We evaluate the suitability of the three approaches by applying them to a large data set (>11,000 instances) extracted from the British National Corpus, and comparing their quality in terms of classification accuracy, their interpretability in the context of linguistic research, and their actual classification of individual cases. Our main finding is that the classifications are very similar across the three approaches, also when employing lexical items instead of the higher-level features, because most of the alternation is determined by the verb and the length of the two objects (here: her and the apple).
The structure–activity relationships of the triketone class of HPPD herbicides†

The 2-benzoylcyclohexane-1,3-diones, the triketones, are a novel class of bleaching herbicides whose mode of action is the inhibition of the enzyme p-hydroxyphenylpyruvate dioxygenase. The structure–activity relationships of this chemical class are elucidated. An ortho-substituent on the aryl ring is an absolute requirement for herbicidal activity. Beyond that, the herbicidal activity of these compounds is best correlated with the overall electron deficiency of the benzoyl group induced by 2,4-disubstitution of the aryl ring, with the most electron-deficient analogs being the most active. Moreover, the degree of electron deficiency of the benzoyl group is outwardly manifested in the acidity of the molecule. The activity of these compounds is further enhanced through additional aromatic substitution in the 3-position of the aryl ring. The greater activity of these 2,3,4-trisubstituted aryl analogs over the 2,4-disubstituted aryl analogs is due to increased intrinsic activity. © 1998 Society of Chemical Industry
Defensins: A Double-Edged Sword in Host Immunity

Defensins are a major family of host defense peptides expressed predominantly in neutrophils and epithelial cells. Their broad antimicrobial activities and multifaceted immunomodulatory functions have been extensively studied, cementing their role in innate immunity as a core host-protective component against bacterial, viral and fungal infections. More recent studies, however, paint defensins in a bad light such that they are “alleged” to promote viral and bacterial infections in certain biological settings. This mini review summarizes the latest findings on the potential pathogenic properties of defensins against the backdrop of their protective roles in antiviral and antibacterial immunity. Further, a succinct description of both tumor-proliferative and -suppressive activities of defensins is also given to highlight their functional and mechanistic complexity in antitumor immunity. We posit that given an enabling environment defensins, widely heralded as the “Swiss army knife,” can function as a “double−edged sword” in host immunity.
Harvesting-Aware Optimal Communication Scheme for Infrastructure-Less Sensing

Sensing systems for long-term monitoring constitute an important part of the emerging Internet of Things. In this domain, energy harvesting and infrastructure-less communication enable truly autonomous and maintenance-free operation of sensor nodes gathering long-term environmental data. Due to the infrastructure-less nature of the communication, receivers are not always available. The variable energy provided by the environment and the receiver’s mobility lead to non-deterministic node availability. In this work, we study infrastructure-less data transmission schemes to optimize communication when both senders and receivers exhibit intermittent behavior. We rely on the notion of data utility, describing the importance of sensed data to the receiver, to determine an optimal communication scheme. Deriving the communication policy that maximizes the utility of the received data is shown to be a convex optimization problem. The resulting scheme is implemented and validated on a batteryless Bluetooth Low Energy sensor node that communicates to commodity smartphones. Our evaluation demonstrates that the model accurately captures the application scenario with a maximum root-mean-square error of less than 0.016 in data reception probability. The communication scheme’s adaptiveness to variable harvesting conditions is experimentally demonstrated under varying harvesting conditions and is shown to significantly increase the data utility.
Growth and Morphological Responses to Irradiance in Three Forest Understory Species of the C4 Grass Genus Muhlenbergia

Three species of the C4 grass genus Muhlenbergia-M. frondosa, M. sobolifera, and M. schreberi-were collected from forest understory sites in northeastern Kansas and grown in a growth chamber at 1,500, 150, and 15-25 μmol m-2 s-1 photosynthetic photon flux density (PPFD). Leaf, stem, root, and total biomasses and several morphological and anatomical characteristics were measured after 35-38 days. Results were compared with similar measurements for M. cuspidata collected from exposed prairie sites. Although all species grew maximally at the highest PPFD, M. sobolifera grew equally well at medium PPFD. Few anatomical changes were correlated with changes in PPFD except leaf thickness, which increased with increasing PPFD. The results indicate that, while the understory species of Muhlenbergia can adjust morphologically to some extent to shaded environments, they produce more biomass at higher PPFD.
Phenotypic Plasticity in Sympatric Diploid and Autotetraploid Dactylis glomerata

It is often supposed that increased heterozygosity of autopolyploids provides a greater stability of phenotypic expression compared with related diploids and, hence, a greater ability to survive in marginal diploid environments or the ability to colonize new environments. The aim of this study was to compare the phenotypic plasticity of fitness‐related characters in diploid and derivative autotetraploid Dactylis glomerata from genotypes sampled in their zone of natural sympatric occurrence in northern Spain. To achieve this aim, nine genotypes were grown in a range of controlled environments. We found no evidence for consistent differences in plasticity between diploids and related tetraploids. We did find, however, consistent differences between diploids and tetraploids in the mean values of the set of examined fitness‐related characters. Such differences could be critical for the maintenance and evolutionary success of polyploids.
Effects of Temperature on Embryonic Development of Banana Weevil Cosmopolites Sordidus germar

Developemental threshold and thermal requirements for eggs of banana weevil, Cosmopolites sordidus Germar, were determined under laboratory conditions at constant temperatures of 15,18,25,27,30,32 and 34 °C and a photoperiod of 12:12 L/D. The duration of the egg stage decreased from 34.9 days at 15° C to 4.9 days at 30° C, then increased again to 5.3 days at 32° C. Eggs did not hatch above the latter temperature although signs of embryonic development, such as formation of the head capsule, could be observed. Simple linear regression revealed a developmental threshold of 12° C and a thermal requirement of 89 days-degrees average. Highest rates of eclosion occurred between 25° C and 30° C. Keywords: Banana weevil, Cosmopolites sordidus, development, thermal requirements
Effects of dietary inclusion of cassava peel meal on functional properties of chicken egg in duration of storage

Effect of dietary inclusion of cassava peel meal on functional properties of chicken eggs in days of storage was evaluated. Issa Brown layers (n=2400), aged 36 weeks were randomly allotted to two dietary treatments of 1200 birds each. Control (T1) was corn-soya diet while T2 had 5% corn replaced with cassava peel mash and were fed ad libitum to respective birds for six weeks. Eggs (n=150) were sampled, stored at ambient conditions and functional properties as well as lipid oxidation monitored at days 0, 7, 14, and 21. Bulk density (9.75±0.94-10.00±1.42), emulsion activity (51.83±1.0052.00±1.41), lipid oxidation (0.91±0.14-0.96±0.06) increased while foaming capacity (15.17±5.784.17±4.26), foaming stability (8.00±6.63-3.75±2.72), water absorption capacity (1.53±0.781.441±0.89), water retention capacity (1.66±1.06-1.48±0.90), oil absorption capacity (1.39±0.891.38±0.93), oil retention capacity (0.99±0.74-1.16±0.73) decreased in days of storage (DOS). Interaction of DOS and diets affected (P<0.05) foaming capacity and stability of eggs. Dietary cassava peel meal enhanced foaming capacity and lipid oxidation in chicken eggs.
Seasonal and long-term responses of host trees to microbial associates of the pine engraver, Ipspini

Within-season responses of Pinusresinosa and Pinusbanksiana to fungi vectored by the pine engraver, Ipspini, are strongly influenced by the month of inoculation. The seasonal pattern is a characteristic of the host-fungus interaction, rather than being indicative of either host-or fungal-specific properties alone. The most consistent trend was that early season inoculation resulted in more rapid lesion formation in sapwood than in phloem and that this difference declined as the growing season progressed. Prior inoculation had no effect on necrotic lesion formation. Inoculated trees were examined for three growing seasons. No significant damage related to treatment occurred to either P. resinosa or P. banksiana during this interval. However, Ceratocystisips persisted in living hosts for a longer period than did Ceratocystisnigrocarpa and showed signs of radial and vertical progression throughout the first and beginning of the second growing season. This was especially true in P. resinosa, the host in which.
Escherichia coli proteomics analysis and protein structure identification with bioinformatics analysis

In order to separate Escherichia coli proteins we have developed a two-dimensional electrophoresis system. For the iso-electric focusing, immobilised pH gradient, dehydrated polyacrylamide gels cast on solid films was used as a supporting matrix. Protein complexes are an intrinsic aspect of life in the membrane. Knowing which proteins are assembled in these complexes is therefore essential to understanding protein function(s). Unfortunately, recent high throughput protein interaction studies have failed to deliver any significant information on proteins embedded in the membrane
Is a Simple Sensorimotor Reaction Really Simple?

The simple sensorimotor reaction (SSR) is widely used in psychophysiological research. It was previously shown, that the SSR latency is not constant. We studied changes in the SSR latency as a function of the waiting time from the moment of the previous response to the moment of the start of the stimulation. We performed the stimulation using light, sound and air impulse. As a response, we used a “labial sound”, a finger touch and blinking of the eyes. In all cases, where the objects of the study were humans, the SSR latency had constant and variable components. The constant SSR component was the shortest in response to closing the eyes to sound (120 ms). For “lip reaction” and finger response to sound it was 174–178 ms and 178–182 ms, respectively, but for “lip reaction” and finger response to light it was 220–226 ms. The variable SSR component represented exponential latency decay with an increase in the waiting time interval. In this case, the decay consisted of at least two components, with an apparent relaxation time in the range 30–150 ms and 600–1300 ms. Alternating stimulation of paired organs of the reception or alternating fingers reduced the apparent relaxation time of the SSR latency decay. Moreover, the latency of the human corneal reflex during eye stimulation with an air pulse also had the latency decay with three components of apparent relaxation time 9.5, 68.2 and 1,086 ms and the constant latency of 34.2 ms. The latency of the corneal reflex in a young cat was constant and had a value of 14.6 ms. Thus, it has been shown, that the SSR latency has a complex structure and, like any conditioned reflex, is strongly influenced by the cortex. We believe that a choice is made in the centers for analysis of receiving signals from reception organs and centers sending signals to reacting organs, i.e. essentially, the SSR is also a choice reaction.
Determinants of Selective Fidelity in Diversity-Generating Retroelements

Diversity-generating retroelements (DGRs) diversify proteins to the greatest extent known in the natural world. These elements are found in a wide variety of microbes, including constituents of the microbial ‘dark matter’ and the human microbiome. Diversification occurs through selective fidelity, in which genetic information in RNA is reverse transcribed to cDNA faithfully for all bases but adenine. We investigated the determinants of selective fidelity in the prototypical Bordetella bacteriophage DGR using an in vitro system that recapitulates this process. We found that the DGR reverse transcriptase bRT and associated protein Avd, along with a specific DGR RNA that contains a template region and flanking functional elements, had a markedly low catalytic efficiency across a template adenine. This was the case even for the correct base pair with an incoming TTP, in agreement with results from other low fidelity polymerases. We identified the C6 substituent of a template purine as a major determinant of selective fidelity, and also identified two bRT amino acids with counterparts in HIV RT based on an in silico model, R74 and I181, whose substitution led to increased fidelity. Our results provide the first elucidation of nucleobase and protein determinants of selective fidelity in DGRs.
Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing

MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in disease such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin primary microRNAs are challenging to study in clinical samples where input material is limited. Here, we present a high-sensitivity targeted method to determine processing efficiency of several hundred primary microRNAs from total RNA using as little as 500 thousand Illumina HiSeq sequencing reads. We validate the method using RNA from HeLa cells and show the applicability to clinical samples by analyzing RNA from normal liver and hepatocellular carcinoma. We identify 24 primary microRNAs with significant changes in processing efficiency from normal liver to hepatocellular carcinoma, among those the highly expressed miRNA-122 and miRNA-21, demonstrating that differential processing of primary microRNAs is occurring and could be involved in disease. With our method presented here we provide means to study pri-miRNA processing in disease from clinical samples.
Formation of Biomolecular Condensates in Bacteria by Tuning Protein Electrostatics

Biomolecular condensates provide a strategy for cellular organization without a physical membrane barrier while allowing for dynamic, responsive organization of the cell. To date, very few biomolecular condensates have been identified in prokaryotes, presenting an obstacle to engineering these compartments in bacteria. As a novel strategy for bacterial compartmentalization, protein supercharging and complex coacervation were employed to engineer liquid-like condensates in E. coli. A simple model for the phase separation of supercharged proteins was developed and used to predict intracellular condensate formation. Herein, we demonstrate that GFP-dense condensates formed by expressing GFP variants of sufficient charge in cells are dynamic and enrich specific nucleic acid and protein components. This study provides a fundamental characterization of intracellular phase separation in E. coli driven by protein supercharging and highlights future utility in designing functional synthetic membraneless organelles.
Invasive freshwater snails form novel microbial relationships

Resident microbes (microbiota) can shape host organismal function and adaptation in the face of environmental change. Invasion of new habitats exposes hosts to novel selection pressures, but little is known about the impact of invasion on microbiota and the host-microbiome relationship after this transition (e.g., how rapidly symbioses are formed, whether microbes influence invasion success). We used high-throughput 16S rRNA sequencing of New Zealand (native) and European (invasive) populations of the freshwater snail Potamopyrgus antipodarum and found that while invaders do carry over some core microbial taxa from New Zealand, most of their microbial community is distinct. This finding highlights that invasions can result in the formation of novel symbioses. We further show that the native microbiome is composed of fewer core microbes than the microbiome of invasive snails, suggesting that the microbiota is streamlined to essential members. Together, our findings demonstrate that microbiota comparisons across native and invasive populations can reveal the impact of a long coevolutionary history and specialization of microbes in the native host range, as well as new associations occurring after invasion. We lay essential groundwork for understanding how microbial relationships affect invasion success and how microbes may be utilized in the control of invasive hosts.
Dietary S. maltophilia promotes fat storage by enhancing lipogenesis and ER-LD contacts in C. elegans

Dietary and symbiotic bacteria can exert powerful influence on metazoan lipid metabolism. Here, we demonstrate that feeding Caenorhabditis elegans (C. elegans) with the opportunistic pathogenic bacteria Stenotrophomonas maltophilia (S. maltophilia) retards growth and promotes excessive fat storage. Gene expression analysis reveals that dietary S. maltophilia induces a lipogenic transcriptional response that includes the SREBP ortholog SBP-1, and fatty acid desaturases FAT-6 and FAT-7. Live imaging and ultrastructural analysis suggest that excess fat is stored in greatly expanded lipid droplets (LDs), as a result of enhanced endoplasmic reticulum-LD interaction. We also report that loss of function mutations in cyp-35B1 or dpy-9 in C. elegans confers resistance to S. maltophilia. Our work delineates a new model for understanding microbial regulation of metazoan physiology.