Miracle-dz/UniFAR-FTUs huggingface dataset:
Photorespiration and Carbon Limitation Determine Productivity in Temperate Seagrasses

The gross primary productivity of two seagrasses, Zostera marina and Ruppia maritima, and one green macroalga, Ulva intestinalis, was assessed in laboratory and field experiments to determine whether the photorespiratory pathway operates at a substantial level in these macrophytes and to what extent it is enhanced by naturally occurring shifts in dissolved inorganic carbon (DIC) and O2 in dense vegetation. To achieve these conditions in laboratory experiments, seawater was incubated with U. intestinalis in light to obtain a range of higher pH and O2 levels and lower DIC levels. Gross photosynthetic O2 evolution was then measured in this pretreated seawater (pH, 7.8–9.8; high to low DIC:O2 ratio) at both natural and low O2 concentrations (adjusted by N2 bubbling). The presence of photorespiration was indicated by a lower gross O2 evolution rate under natural O2 conditions than when O2 was reduced. In all three macrophytes, gross photosynthetic rates were negatively affected by higher pH and lower DIC. However, while both seagrasses exhibited significant photorespiratory activity at increasing pH values, the macroalga U. intestinalis exhibited no such activity. Rates of seagrass photosynthesis were then assessed in seawater collected from the natural habitats (i.e., shallow bays characterized by high macrophyte cover and by low DIC and high pH during daytime) and compared with open baymouth water conditions (where seawater DIC is in equilibrium with air, normal DIC, and pH). The gross photosynthetic rates of both seagrasses were significantly higher when incubated in the baymouth water, indicating that these grasses can be significantly carbon limited in shallow bays. Photorespiration was also detected in both seagrasses under shallow bay water conditions. Our findings indicate that natural carbon limitations caused by high community photosynthesis can enhance photorespiration and cause a significant decline in seagrass primary production in shallow waters.
Adaptive Opportunistic Routing for Wireless Ad Hoc Networks

A distributed adaptive opportunistic routing scheme for multihop wireless ad hoc networks is proposed. The proposed scheme utilizes a reinforcement learning framework to opportunistically route the packets even in the absence of reliable knowledge about channel statistics and network model. This scheme is shown to be optimal with respect to an expected average per-packet reward criterion. The proposed routing scheme jointly addresses the issues of learning and routing in an opportunistic context, where the network structure is characterized by the transmission success probabilities. In particular, this learning framework leads to a stochastic routing scheme that optimally “explores” and “exploits” the opportunities in the network.
Presence and Effects of Pituitary Adenylate Cyclase Activating Polypeptide Under Physiological and Pathological Conditions in the Stomach

Pituitary adenylate cyclase activating polypeptide (PACAP) is a multifunctional neuropeptide with widespread occurrence throughout the body including the gastrointestinal system. In the small and large intestine, effects of PACAP on cell proliferation, secretion, motility, gut immunology and blood flow, as well as its importance in bowel inflammatory reactions and cancer development have been shown and reviewed earlier. However, no current review is available on the actions of PACAP in the stomach in spite of numerous data published on the gastric presence and actions of the peptide. Therefore, the aim of the present review is to summarize currently available data on the distribution and effects of PACAP in the stomach. We review data on the localization of PACAP and its receptors in the stomach wall of various mammalian and non-mammalian species, we then give an overview on PACAP’s effects on secretion of gastric acid and various hormones. Effects on cell proliferation, differentiation, blood flow and gastric motility are also reviewed. Finally, we outline PACAP’s involvement and changes in various human pathological conditions.
Accuracy improvement in human detection using HOG features on train-mounted camera

Nowadays, researches on accident prevention using train-mounted cameras had been progressing. Our proposed method considers temporal continuity between frames by using motion vectors in addition to conventional thresholding on similarity values obtained by a human detection method using HOG features. Experiments show the effectiveness of our method as compared with a previous method using only HOG features.
Effect of temporal averaging of meteorological data on predictions of groundwater recharge

Abstract Accurate estimates of infiltration and groundwater recharge are critical for many hydrologic, agricultural and environmental applications. Anticipated climate change in many regions of the world, especially in tropical areas, is expected to increase the frequency of high-intensity, short-duration precipitation events, which in turn will affect the groundwater recharge rate. Estimates of recharge are often obtained using monthly or even annually averaged meteorological time series data. In this study we employed the HYDRUS-1D software package to assess the sensitivity of groundwater recharge calculations to using meteorological time series of different temporal resolutions (i.e., hourly, daily, weekly, monthly and yearly averaged precipitation and potential evaporation rates). Calculations were applied to three sites in Brazil having different climatological conditions: a tropical savanna (the Cerrado), a humid subtropical area (the temperate southern part of Brazil), and a very wet tropical area (Amazonia). To simplify our current analysis, we did not consider any land use effects by ignoring root water uptake. Temporal averaging of meteorological data was found to lead to significant bias in predictions of groundwater recharge, with much greater estimated recharge rates in case of very uneven temporal rainfall distributions during the year involving distinct wet and dry seasons. For example, at the Cerrado site, using daily averaged data produced recharge rates of up to 9 times greater than using yearly averaged data. In all cases, an increase in the time of averaging of meteorological data led to lower estimates of groundwater recharge, especially at sites having coarse-textured soils. Our results show that temporal averaging limits the ability of simulations to predict deep penetration of moisture in response to precipitation, so that water remains in the upper part of the vadose zone subject to upward flow and evaporation.
Amplitude and phase dereverberation of monocomponent signals

While most dereverberation methods focus on how to estimate the amplitude of an anechoic signal, we propose a method which also takes the phase into account. By applying a sinusoidal model to the anechoic signal, we derive a formulation to compute the amplitude and phase of each sinusoid. These parameters are then estimated by our method in the reverberant case. As we jointly estimate the amplitude and phase of the clean signal, we achieve a very strong dereverberation, resulting in a significant improvement of objective dereverberation measures over the state-of-the-art.
The potential of Chrysoperla rufilabris and Doru taeniatum as agents for dispersal of Spodoptera frugiperda nucleopolyhedrovirus in maize

The behaviour of two abundant predators in Mesoamerican maize crops, Chrysoperla rufilabris larvae and Doru taeniatum adults, towards healthy and nucleopolyhedrovirus‐infected Spodoptera frugiperda larvae was compared. C. rufilabris did not discriminate between healthy and virus‐infected prey, although the mean search time was approximately two times longer towards virus‐infected larvae. In contrast, D. taeniatum directed a greater proportion of their attacks towards virus‐infected prey but there was no significant difference in the search time. Prey consumption time did not differ significantly for each type of prey by either predator, although prey consumption was much faster in D. taeniatum. Viable virus was detected in D. taeniatum faeces up to 3 d after feeding on infected S. frugiperda larvae, whereas virus was inactivated in the gut of C. rufilabris. Both predators were shown to have acidic guts. A field experiment demonstrated that D. taeniatum that had fed on infected prey could contaminate foliage resulting in the transmission of the disease at a low prevalence (4.7%) to S. frugiperda larvae in a field maize crop.
Caractérisation par analyse d'images de l'angiogenèse sur des coupes histologiques

New image processing algorithms for the detection and measurement of a vascular network from images of histological sections obtained by optical microscopy are presented. After extraction of the blood vessels, the resulting binary images are registered and stacked to reconstruct the tridimensional vascular network image. The developed method evaluates quantitatively different parameters of the vascular geometry from images at two and three dimensions. These measurements allow characterizing the process of stimulation/inhibition of the vascular structure.
Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups (“pheasants” and “partridges”) is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.
System for robust bronchoscopic video distortion correction

Bronchoscopes contain wide-angle lenses that produce a large field of view but suffer from radial distortion. For image-guided bronchoscopy, geometric calibration including distortion correction is essential for comparing video images to renderings developed from 3D computed-tomography (CT) images. This paper describes an easy-to-use system for bronchoscopic video-distortion correction and studies the robustness of the resulting calibration over a wide range of conditions. The internal calibration method integrated into the system incorporates a well-known camera calibration framework devised for general camera-distortion correction. The robustness study considers the calibration results as follows: (1) varying lighting during video capture, (2) using different number of captured images for parameter estimation, (3) changing camera pose with respect to the calibration pattern, (4) recording temporal changes in estimated parameters, and (5) comparing parameters between different bronchoscopes of a same model. Multiple bronchoscopes were successfully calibrated under a variety of conditions.
Parameterized Low-distortion Embeddings - Graph metrics into lines and trees

We revisit the issue of low-distortion embedding of metric spaces into the line, and more generally, into the shortest path metric of trees, from the parameterized complexity perspective.Let $M=M(G)$ be the shortest path metric of an edge weighted graph $G=(V,E)$ on $n$ vertices. We describe algorithms for the problem of finding a low distortion non-contracting embedding of $M$ into line and tree metrics. We give an $O(nd^4(2d+1)^{2d})$ time algorithm that for an unweighted graph metric $M$ and integer $d$ either constructs an embedding of $M$ into the line with distortion at most $d$, or concludes that no such embedding exists. We find the result surprising, because the considered problem bears a strong resemblance to the notoriously hard Bandwidth Minimization problem which does not admit any FPT algorithm unless an unlikely collapse of parameterized complexity classes occurs. We show that our algorithm can also be applied to construct small distortion embeddings of weighted graph metrics. The running time of our algorithm is $O(n(dW)^4(2d+1)^{2dW})$ where $W$ is the largest edge weight of the input graph. We also show that deciding whether a weighted graph metric $M(G)$ with maximum weight $W < |V(G)|$ can be embedded into the line with distortion at most $d$ is NP-Complete for every fixed rational $d \geq 2$. This rules out any possibility of an algorithm with running time $O((nW)^{h(d)})$ where $h$ is a function of $d$ alone. We generalize the result on embedding into the line by proving that for any tree $T$ with maximum degree $\Delta$, embedding of $M$ into a shortest path metric of $T$ is FPT, parameterized by $(\Delta,d)$.
New Generation of Social Networks Based on Semantic Web Technologies

This article investigates several well-known social network applications such as Last.fm, Flickr and identifies social data portability as one of the main technical issues that need to be addressed in the future. We argue that this issue can be addressed by building social networks as Semantic Web applications with FOAF, SIOC, and Linked Data technologies, and prove it by implementing a prototype application using Java and core Semantic Web standards. Furthermore, the developed prototype shows how features from semantic websites such as Freebase and DBpedia can be reused in social applications and lead to more relevant content and stronger social connections.
Associations between earliness, Ascochyta response, and grain yield in chickpea

Evidence from an array of dryland systems suggests that chickpea (Cicer arietinum L.) grain yield could be improved through better phenological adaptation. However, information on the relationship between phenology and Ascochyta response genes, and their possible interaction with biomass and grain yield, is missing. Accordingly, the aim of the present study was to determine the associations between the above factors and biomass and grain yield in chickpea. To that end, standard Israeli cultivars and advanced generation bulked progeny from the cv. Hadas × ICC5810 cross were used. Hadas is a late-flowering, high-yielding Israeli kabuli (0.45 g/seed) cultivar with moderate field resistance to Ascochyta blight, whereas ICC5810 is a day-neutral desi (0.15 g/seed) genotype with a strong temperature response, from India. Higher yields were observed among the late-flowering bulks of the Hadas × ICC5810 progeny. No relationship between the Ascochyta response and biomass and grain yield was observed. No interaction between the phenology and Ascochyta response grouping on biomass and grain yield was observed. The results demonstrate the feasibility of combining Ascochyta resistance with earlier flowering and its potential to improve chickpea adaptation to dryland systems.
Microplate-Test for the Rapid Determination of Bacteriophage-Susceptibility of Campylobacter Isolates—Development and Validation

A simple susceptibility test using 800 isolates of one Campylobacter strain with different degrees of susceptibility and four bacteriophages of the British phage typing scheme was developed and examined for its suitability. The test presented is economically cheaper and less time consuming than the conventional agar overlay plate assay and therefore enables the monitoring of changes in the susceptibility pattern during phage therapy under practical field conditions. The main objective of this study was to compare the simplified test with the conventional agar overlay plate assay. The conventional test describes for a population of Campylobacter: i. the rate of resistant isolates (0 plaques) and ii. the degree of susceptibility, also called relative efficiency of plating (EOP), for the remaining isolates. The simplified test divides the isolates into four susceptibility ranks, which are easily distinguishable to the naked eye. Ten Campylobacter isolates out of each rank were subjected to the conventional method for validation of the simplified test. Each resistance rank contained isolates showing certain degrees of susceptibility, reflecting decreasing susceptibility by an increase of the rank. Thus, the simplified test correlated well with the conventional method. Nevertheless, it can be suggested for a clear cut to summarise the first thee ranks as “high susceptible” and to mark out the fourth rank as reduced susceptible. Further test improvements will enable the monitoring of the degree of susceptibility and potentially also of resistance during phage therapy in the field. To ensure a long-lasting successful use of phage therapy, further studies on both the loss of susceptibility and the development of resistance of Campylobacter against phages combined with their impact on phage therapy will be necessary.
A thermodynamical framework for the solidification of molten polymers and its application to fiber extrusion

A Thermodynamical Framework for the Solidification of Molten Polymers and Its Application to Fiber Extrusion. (December 2004) Krishna Kannan, B.E. , PSG Tech, India; M.S., Texas A&M University Chair of Advisory Committee: Dr. K.R. Rajagopal A thermodynamical framework is presented that describes the solidification of molten polymers to an amorphous as well as to a semicrystalline solid-like state. This framework fits into a general structure developed for materials undergoing a large class of entropy producing processes. The molten polymers are usually isotropic in nature and certain polymers crystallize, with the exception of largely atactic polymers, which solidify to an amorphous solid, to an anisotropic solid. The symmetry of the crystalline structures in the semicrystalline polymers is dependent upon the thermomechanical process to which the polymer is subjected to. The framework presented takes into account that the natural configurations associated with the polymer melt (associated with the breaking and reforming of the polymer network) and the solid evolve in addition to the evolving material symmetry associated with these natural configurations. The functional form of the various primitives such as how the material stores, dissipates energy and produces entropy are prescribed. Entropy may be produced by a variety of mechanisms such as conduction, dissipation, solidification, rearragement of crystalline structures due to annealing and so forth. The manner in which the natural configurations evolve is dictated by the maximization of the rate of dissipation. Similarly, the crystallization and glass transition kinetics may be obtained by maximization of their corresponding entropy productions. The restrictions
Identification of Functional mob Regions in Rhizobium etli: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d

ABSTRACT An approach originally designed to identify functional origins of conjugative transfer (oriT or mob) in a bacterial genome (J. A. Herrera-Cervera, J. M. Sanjuán-Pinilla, J. Olivares, and J. Sanjuán, J. Bacteriol. 180:4583-4590, 1998) was modified to improve its reliability and prevent selection of undesired false mob clones. By following this modified approach, we were able to identify two functional mob regions in the genome of Rhizobium etli CFN42. One corresponds to the recently characterized transfer region of the nonsymbiotic, self-transmissible plasmid pRetCFN42a (C. Tun-Garrido, P. Bustos, V. González, and S. Brom, J. Bacteriol. 185:1681-1692, 2003), whereas the second mob region belongs to the symbiotic plasmid pRetCFN42d. The new transfer region identified contains a putative oriT and a typical conjugative (tra) gene cluster organization. Although pRetCFN42d had not previously been shown to be self-transmissible, mobilization of cosmids containing this tra region required the presence of a wild-type pRetCFN42d in the donor cell; the presence of multiple copies of this mob region in CFN42 also promoted conjugal transfer of the Sym plasmid pRetCFN42d. The overexpression of a small open reading frame, named yp028, located downstream of the putative relaxase gene traA, appeared to be responsible for promoting the conjugal transfer of the R. etli pSym under laboratory conditions. This yp028-dependent conjugal transfer required a wild-type pRetCFN42d traA gene. Our results suggest for the first time that the R. etli symbiotic plasmid is self-transmissible and that its transfer is subject to regulation. In wild-type CFN42, pRetCFN42d tra gene expression appears to be insufficient to promote plasmid transfer under standard laboratory conditions; gene yp028 may play some role in the activation of conjugal transfer in response to as-yet-unknown environmental conditions.
Use of strong opioids for chronic pain in osteoarthritis: an insight into the Latin American reality

ABSTRACT Introduction: Osteoarthritis is the most common cause of arthritis and one of the main causes of chronic pain. Although opioids are frequently employed for chronic pain treatment, their usage for osteoarthritis pain remains controversial due to the associated adverse effects. Most guidelines reserve their use for refractory pain in patients with hip and knee osteoarthritis. The situation is even more complex in Latin America, where the prevalence of insufficient pain treatment is high because of the limited availability and use of strong opioids. Areas covered: In this article we review the epidemiology of osteoarthritis, its socioeconomic burden, its impact as a chronic pain cause and the pharmacological treatment options, giving emphasis to the role of strong opioids, their safety and efficacy, especially in Latin American countries, where restrictions regulate their usage. Expert commentary: Usage of strong opioids is safe and effective in the short-term management of osteoarthritis with moderate to severe pain, when other pharmacological treatments are inadequate and surgery is contraindicated, provided their use adheres to existing guidelines. Educational programs for patients and physicians and further research on treating chronic pain with opioids should be implemented to reduce adverse effects and improve care quality.
Screening for Lung Cancer

Lung cancer is the leading cause of cancer related deaths in the United States. The estimated number of lung cancer deaths in 2012 was higher than the total combined number of deaths from breast, prostate and colon cancer. In 2012, according to the published data from the American Cancer Society, a total of 226,160 new cases of lung cancer had been diagnosed with a total death of 160,340 secondary to lung cancer . It was estimated that about 1 person out of 2000 in the US died because of lung cancer in 2012 [1-2].