Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro assessment of the factors that determine the activity of the rumen microbiota for further applications as inoculum.

BACKGROUND The rumen microbiota has been used as inoculum for in vitro studies and as a probiotic to improve productivity in young animals. However, great variability across studies has been noted depending on the inoculum considered. The present study aims to assess the relevance of different factors (microbial fraction, collection time, donor animal diet, fermentation substrate and inoculum preservation method) to maximize the rumen inoculum activity and set the standards for further in vitro and in vivo applications. RESULTS Rumen inoculum sampled at 3 h after feeding led to greater microbial growth and activity [+12% volatile fatty acid (VFA), +17% ammonia] compared to before feeding. Similar results were noted when rumen liquid or rumen content were used as inocula. Rumen inoculum adapted to concentrate diets increased microbial activity (+19% VFA) independently of the substrate used in vitro. Freezing-thawing the inoculum, in comparison to fresh inoculum, decreased microbial activity (-14% VFA, -96% ammonia), anaerobic fungi and protozoa, with holotrichs protozoa being particularly vulnerable. Inoculum lyophilization had a stronger negative effect on microbial activity (-51% VFA) and delayed re-activation of the microbes, leading to lower levels of methanogens and anaerobic fungi, as well as almost complete wipe out of rumen protozoa. CONCLUSIONS Fresh rumen fluid sampled at 3 h after feeding from donor animals that were fed concentrate diets should be chosen when the aim is to provide the most diverse and active rumen microbial inoculum. © 2018 Society of Chemical Industry.
Hierarchically aligned fibrin nanofiber hydrogel accelerated axonal regrowth and locomotor function recovery in rat spinal cord injury

Background Designing novel biomaterials that incorporate or mimic the functions of extracellular matrix to deliver precise regulatory signals for tissue regeneration is the focus of current intensive research efforts in tissue engineering and regenerative medicine. Methods and results To mimic the natural environment of the spinal cord tissue, a three-dimensional hierarchically aligned fibrin hydrogel (AFG) with oriented topography and soft stiffness has been fabricated by electrospinning and a concurrent molecular self-assembling process. In this study, the AFG was implanted into a rat dorsal hemisected spinal cord injury model to bridge the lesion site. Host cells invaded promptly along the aligned fibrin hydrogels to form aligned tissue cables in the first week, and then were followed by axonal regrowth. At 4 weeks after the surgery, neurofilament (NF)-positive staining fibers were detected near the rostral end as well as the middle site of defect, which aligned along the tissue cables. Abundant NF- and GAP-43-positive staining indicated new axon regrowth in the oriented tissue cables, which penetrated throughout the lesion site in 8 weeks. Additionally, the abundant blood vessels marked with RECA-1 had reconstructed within the lesion site at 4 weeks after surgery. Basso-Beattie-Bresnahan scoring showed that the locomotor performance of the AFG group recovered much faster than that of blank control group or the random fibrin hydrogel (RFG) group from 2 weeks after surgery. Furthermore, diffusion tensor imaging tractography of MRI confirmed the optimal axon fiber reconstruction compared with the RFG and control groups. Conclusion Taken together, our results suggested that the AFG scaffold provided an inductive matrix for accelerating directional host cell invasion, vascular system reconstruction, and axonal regrowth, which could promote and support extensive aligned axonal regrowth and locomotor function recovery.
Spillover from marine reserves and the replenishment of fished stocks

SUMMARY No-take marine reserves are widely recognized as an effective conservation tool for protecting marine resources. Despite considerable empirical evidence that abundance and biomass of fished species increase within marine reserve boundaries, the potential for reserves to provide fisheries and conservation benefits to adjacent waters remains heavily debated. This paper uses statistical and population models to evaluate published empirical data on adult spillover from marine reserves and shows that spillover is a common phenomenon for species that respond positively to reserve protection, but at relatively small scales, detectable on average up to 800 m from reserve boundaries. At these small scales, local fisheries around reserves were likely unsustainable in 12 of 14 cases without the reserve, and spillover partially or fully offsets losses in catch due to reserve closure in the other two cases. For reserves to play a role in sustaining and replenishing larger-scale fished stocks, networks of reserves may be necessary, but as few exist this is difficult to evaluate. The results suggest reserves can simultaneously meet conservation objectives and benefit local fisheries adjacent to their boundaries.
From Keys to Databases - Real-World Applications of Secure Multi-Party Computation

We discuss the widely increasing range of applications of a cryptographic technique called Multi-Party Computation. For many decades this was perceived to be of purely theoretical interest, but now it has started to ﬁnd application in a number of use cases. We highlight in this paper a number of these, ranging from securing small high value items such as cryptographic keys, through to securing an entire database.
The BesMan Learning Platform for Automated Robot Skill Learning

We describe the BesMan learning platform which allows learning robotic manipulation behavior. It is a stand-alone solution which can be combined with different robotic systems and applications. Behavior that is adaptive to task changes and different target platforms can be learned to solve unforeseen challenges and tasks, which can occur during deployment of a robot. The learning platform is composed of components that deal with preprocessing of human demonstrations, segmenting the demonstrated behavior into basic building blocks, imitation, refinement by means of reinforcement learning, and generalization to related tasks. The core components are evaluated in an empirical study with 10 participants with respect to automation level and time requirements. We show that most of the required steps for transferring skills from humans to robots can be automated and all steps can be performed in reasonable time allowing to apply the learning platform on demand.
Adenosine and Ticagrelor Plasma Levels in Patients With and Without Ticagrelor-Related Dyspnea.

Dyspnea is a common side effect of ticagrelor, leading to drug discontinuation in roughly one in every 20 treated patients.1, 2 Studies have suggested that ticagrelor inhibits the sodium-independent equilibrative nucleoside transporter-1, which may increase adenosine plasma levels and explain drug-related dyspnea.3 However, the identification of a pattern of periodic breathing associated to increased chemosensitivity to hypercapnia in patients with ticagrelor-related dyspnea4 has reinforced the hypothesis that this side effect may result from direct inhibition of P2Y12 receptors on neurons leading to purinergic stimulation of the chemoreflex system.3, 4 Simultaneous measurements of adenosine and ticagrelor plasma levels in patients with and without dyspnea while on treatment with ticagrelor may help unraveling the mechanism of this common and clinically relevant side effect.
Influence of inclination and permeability of solitary woody riparian plants on local hydraulic and sedimentary processes

The role of solitary woody riparian plants with respect to local erosion and deposition of sediments is investigated. A focus is laid on the characteristics ‘inclination’ and ‘permeability’ of the plant's projected frontal area. Therefore, two experimental studies using cylindrical obstacles were carried out in a laboratory flume, one aiming at inclination, the other at permeability. The first series revealed that the total amount of mobilized sediment around the cylinder on average decreased by 8–10% per 5° increasing inclination in streamwise direction. Locations of maximum scour depth simultaneously shifted downstream. A horseshoe vortex system, causing the frontal and lateral scouring, ceased to exist below inclinations of 25–30°. The second series revealed that with increasing permeability, frontal scour incision is delayed, and the eroded sediment volume is significantly reduced. With permeable obstacles, two system states were observed: first, frontal scouring with leeside deposition at higher flow velocities and, second, moderate leeside scouring at lower flow velocities. For up‐scaling and comparison, a field study focussing on fluvial obstacle marks at poplars and willows in secondary channels of the River Loire was additionally conducted. A modified analytical model enabled us to quantify the amount of deposited sediments leeside of the plants. Leeside sediment ridges are significantly stabilized and have a higher preservation potential when covered by pioneer vegetation. Under such conditions, they may indeed induce the development of stable islands. Eventually, ‘sediment ridge width’ turned out to be a suitable indicator for leeside deposited sediment volume, irrespective of spatial scale. Copyright © 2012 John Wiley & Sons, Ltd.
Bragg Gratings in Suspended-Core Photonic Microcells for High-Temperature Applications

We report a novel type-II photonic crystal fiber Bragg grating for high-temperature applications. The Bragg grating is inscribed in a low-loss in-fiber structure named suspended-core photonic microcell, which is postprocessed from a commercial pure-silica photonic crystal fiber. Grating samples with core diameters of about 4 μm were made by using a focused near-infrared femtosecond laser and a phase mask, and then tested in a tube furnace from room temperature to about 1200 °C. The thermal response of the Bragg resonant wavelength was measure to be about 12 and 16 pm/°C, respectively, at the temperature around 100 °C and 1000 °C. The grating spectrum remained stable in a 10-h isothermal annealing at 1000 °C and started decaying at about 1120 °C with the rate of about 0.02 dB/min. This type of grating possesses flexibilities in both waveguide and grating structure design, exhibits good high-temperature performance, hence would be promising platform for building wavelength-division-multiplexed fiber sensors and tunable devices with a wide working temperature range.
Lovasz Convolutional Networks

Semi-supervised learning on graph structured data has received significant attention with the recent introduction of Graph Convolution Networks (GCN). While traditional methods have focused on optimizing a loss augmented with Laplacian regularization framework, GCNs perform an implicit Laplacian type regularization to capture local graph structure. In this work, we propose Lovasz Convolutional Network (LCNs) which are capable of incorporating global graph properties. LCNs achieve this by utilizing Lovasz's orthonormal embeddings of the nodes. We analyse local and global properties of graphs and demonstrate settings where LCNs tend to work better than GCNs. We validate the proposed method on standard random graph models such as stochastic block models (SBM) and certain community structure based graphs where LCNs outperform GCNs and learn more intuitive embeddings. We also perform extensive binary and multi-class classification experiments on real world datasets to demonstrate LCN's effectiveness. In addition to simple graphs, we also demonstrate the use of LCNs on hyper-graphs by identifying settings where they are expected to work better than GCNs.
Study of population dynamics and impact of abiotic factors on thrips,Scirtothrips dorsalisof chilli,Capsicum annuumand comparative bio-efficacy of few novel pesticides against it

Field experiment to study the population dynamics and bio-efficacy of some newer pesticides at various test concentrations against chilli thrips, Scirtothrips dorsalis Hood, on chilli crop was tested in field conditions. The highest incidence of thrips was observed during first week of October. The population of thrips showed significant positive correlation with maximum temperature and negatively correlated with rainfall, relative humidity. The bio-efficacy results revealed that the mean per cent reduction in thrips population over the untreated-control in Pyridaben 20% WP 125g a.i/ha was significantly superior over other treatments; with highest per cent reduction of 74.47%; closely followed by Fenpyroximate 5% EC 20g a.i/ha (70.58%). Pyridaben 20% WP 100g a.i/ha and Propargite 57% EC both were less effective than previous two treatments and were at par with a reduction of 68.08% and 65.45% respectively. However, the lower doses of Pyridaben 20% WP 50g a.i/ha and 75g a.i/ha gave the lowest performance with a mean percent reduction of 56.66% and 59.85% respectively against control. Such studies are helpful in developing prediction models against thrips for its efficient management with combining both conventional and newer pesticides.
Effects of sample size on classifier design for computer-aided diagnosis

One of the important issues in the development of computer- aided diagnosis (CAD) algorithms is the design of classifiers. A classifier is designed with case samples drawn from the patient population. Generally, the sample size available for classifier design is limited, which introduces bias and variance into the performance of the trained classifier. Fukunaga showed that the bias on the probability of misclassification is proportional to 1/Nt, where Nt is the design (training) sample size, under conditions that the higher-order terms can be neglected. For CAD applications, a commonly used performance index for a classifier is the area, Az, under the receiver operating characteristic curve. We have studied the dependence of the bias in Az on sample size by computer simulation for a linear classifier and nonlinear classifiers such as the quadratic and the backpropagation neural network classifiers.
On Romeo and Juliet Problems: Minimizing Distance-to-Sight

We introduce a variant of the watchman route problem, which we call the quickest pair-visibility problem. Given two persons standing at points $s$ and $t$ in a simple polygon $P$ with no holes, we want to minimize the distance they travel in order to see each other in $P$. We solve two variants of this problem, one minimizing the longer distance the two persons travel (min-max) and one minimizing the total travel distance (min-sum), optimally in linear time. We also consider a query version of this problem for the min-max variant. We can preprocess a simple $n$-gon in linear time so that the minimum of the longer distance the two persons travel can be computed in $O(\log^2 n)$ time for any two query positions $s,t$ where the two persons start.
Visualizing and Exploring Dynamic Multichannel EEG Coherence Networks

An electroencephalography (EEG) coherence network represents functional brain connectivity, and is constructed by calculating the coherence between pairs of electrode signals as a function of frequency. Visualization of coherence networks can provide insight into unexpected patterns of cognitive processing and help neuroscientists to understand brain mechanisms. However, visualizing dynamic EEG coherence networks is a challenge for the analysis of brain connectivity, especially when the spatial structure of the network needs to be taken into account. In this paper, we present a design and implementation of a visualization framework for such dynamic networks. First, requirements for supporting typical tasks in the context of dynamic functional connectivity network analysis were collected from neuroscience researchers. In our design, we consider groups of network nodes and their corresponding spatial location for visualizing the evolution of the dynamic coherence network. We introduce an augmented timeline-based representation to provide an overview of the evolution of functional units (FUs) and their spatial location over time. This representation can help the viewer to identify relations between functional connectivity and brain regions, as well as to identify persistent or transient functional connectivity patterns across the whole timewindow. In addition, we modiﬁed the FU map representation to facilitate comparison of the behavior of nodes between consecutive FU maps. Our implementation also supports interactive exploration. The usefulness of our visualization design was evaluated by an informal user study. The feedback we received shows that our design supports exploratory analysis tasks well. The method can serve as an preprocessing step before a complete analysis of dynamic EEG coherence networks.
mmonia as a stimulant to ventilation in rainbow trout Oncorhynchus mykiss

Ammonia is the third most important respiratory gas in ammoniotelic fish after oxygen and carbon dioxide. We here investigated the effects of elevated plasma ammonia on ventilation in freshwater rainbow trout. Intact trout fitted with indwelling dorsal aortic catheters were given injections (over 5 min) of Cortland saline, isotonic high ammonia solutions (NH4HCO3, (NH4)2SO4, NH4OH at pH 8.0, and NH4OH at pH 9.0), and other solutions as controls for acid–base effects, while ventilatory rate (VR) and buccal pressure amplitude ( Pbuccal) were recorded. All high ammonia solutions resulted in immediate elevations of plasma Tamma, PaNH3 , and [NH4 ]a, and increases in ventilatory Pbuccal and VR to different degrees. However, while PaO2 remained constant, in every case there was a confounding change in one or more components of acid–base status (decreases in pHa or increases in [HCO3−]a or PaCO2 in different treatments), although the ventilatory responses to ammonia injections were generally larger than could be explained by changes in acid–base status. Therefore a series was performed in which normal blood perfusion of the gills was replaced by ventral aortic perfusion with either Cortland saline or Cortland saline plus high ammonia in which pH, [HCO3−], PCO2 , and PO2 remained unchanged. Although ventilation was depressed in these anaesthetized, spontaneously ventilating preparations, perfusion with high ammonia saline increased Pbuccal. In a final series, trout were infused for 24 h with Cortland saline, isotonic NH4HCO3, or isotonic (NH4)2SO4 solutions. The two ammonia solutions both caused persistent elevations in VR and Pbuccal, together with similar large increases in plasma Tamma, PaNH3 , and [NH4 ]a. As there was no changes in PaO2 , pHa, PaCO2 , or [HCO3 −]a in the (NH4)2SO4 infusion series, this, together with the ventral aortic perfusion experiment, provides the most convincing evidence that ammonia stimulates ventilation. We suggest several circumstances (post-feeding, post-exercise) where the role of ammonia as a ventilatory stimulant may have adaptive benefits for O2 uptake, and propose that ammonia-induced o faci hyperventilation may als
Regulation of RhoGEF proteins by G12/13‐coupled receptors

G protein‐coupled receptors (GPCRs) represent a large family of seven transmembrane receptors, which communicate extracellular signals into the cellular lumen. The human genome contains 720–800 GPCRs, and their diverse signal characteristics are determined by their specific tissue and subcellular expression profiles, as well as their coupling profile to the various G protein families (Gs, Gi, Gq, G12). The G protein coupling pattern links GPCR activation to the specific downstream effector pathways. G12/13 signalling of GPCRs has been studied only recently in more detail, and involves activation of RhoGTPase nucleotide exchange factors (RhoGEFs). Four mammalian RhoGEFs regulated by G12/13 proteins are known: p115‐RhoGEF, PSD‐95/Disc‐large/ZO‐1 homology‐RhoGEF, leukemia‐associated RhoGEF and lymphoid blast crisis‐RhoGEF. These link GPCRs to activation of the small monomeric GTPase RhoA, and other downstream effectors. Misregulated G12/13 signalling is involved in multiple pathophysiological conditions such as cancer, cardiovascular diseases, arterial and pulmonary hypertension, and bronchial asthma. Specific targeting of G12/13 signalling‐related diseases of GPCRs hence provides novel therapeutic approaches. Assays to quantitatively measure GPCR‐mediated activation of G12/13 are only emerging, and are required to understand the G12/13‐linked pharmacology. The review gives an overview of G12/13 signalling of GPCRs with a focus on RhoGEF proteins as the immediate mediators of G12/13 activation.
Fast Low-Complexity Triple-Error-Correcting BCH Decoding Architecture

An efficient decoding architecture for triple-error-correcting BCH codes is proposed by utilizing a lookup table (LUT) that stores the roots of the error locator polynomial instead of using the Chien search. Two roots of the polynomial equation are precomputed and stored in the LUT in order to relax the hardware complexity. To relax the complexity further, a new method to compress the LUT is additionally proposed. While a large portion of the LUT is filled with unnecessary information in the previous designs, this brief eliminates the redundant information by investigating an algebraic property of the equation. For BCH codes over GF(210), the LUT size is reduced to 18% of the previous work. As a result, the proposed decoding architecture reduces the decoding latency by 38% and the equivalent gate count by up to 40% compared to the previous work, achieving a fast low-complexity triple-error-correcting BCH decoder.
Molecular genetic variation in sheep of the central Volga area inhabited by Finno-Ugric peoples

Based on morphology, native northern European sheep breeds belong to the short tailed type, of which the Romanov is the only native example still distributed in northwest Russia. Besides this, there exist local sheep populations kept by Finno-Ugric peoples in the central Volga region, which represent additional genetic resources in the area. Four sheep populations from the central Volga region were genotyped for 20 microsatellites and compared with geographically proximate breeds (Estonian Whitehead and Blackhead, the Finnsheep and an exported and a native population of Russian Romanov) and with local populations in Estonia, Finland and Russian Karelia. Between-breed analyses including admixture analysis using molecular genetic markers and the phenotypic characteristics indicated that the Volgaic populations have not remained pure. The Viena population from Russian Karelia, the Romanov breed and, to some extent, the Komi population, have escaped extensive mixing, making them most attractive for conservation programmes. The study compared imported and native Romanov breed populations and the results suggest that the diversity parameters are markedly similar in these two populations. ;
Determination of antibiotic resistance of lactic acid bacteria isolated from traditional Turkish fermented dairy products.

In this study, the antibiotic resistance (AR) of lactic acid bacteria (LAB) isolated from traditional Turkish fermented dairy products was investigated. Yogurt, white cheese, tulum cheese, cokelek, camız cream and kefir as dairy products were collected from various supermarkets. Lactic acid bacteria such as Lactobacillus spp. , Streptococcus spp. , Bifidobacterium spp. , and Enterecoccus spp. were isolated from these dairy products. Lactobacillus spp. were resistant to vancomycin (58%), erythromycin (10.8%), tetracycline (4.3%), gentamicin (28%), and ciprofloxacin (26%). Streptococcus spp. were resistant to vancomycin (40%), erythromycin (10%), chloramphenicol (10%), gentamicin (20%), and ciprofloxacin (30%). Bifidobacterium spp. were resistant to vancomycin (60%), E 15 (6.6%), gentamicin (20%), and ciprofloxacin (33%). Enterococcus spp. were resistant to vancomycin (100%), erythromycin (100%), rifampin (100%), and ciprofloxacin (100%). As a result, LAB islated from dairy products in this study showed mostly resistance to vancomycin.