Miracle-dz/UniFAR-FTUs huggingface dataset:
The FastMap Algorithm for Shortest Path Computations

We present a new preprocessing algorithm for embedding the nodes of a given edge-weighted undirected graph into a Euclidean space. The Euclidean distance between any two nodes in this space approximates the length of the shortest path between them in the given graph. Later, at runtime, a shortest path between any two nodes can be computed with an A* search using the Euclidean distances as heuristic. Our preprocessing algorithm, called FastMap, is inspired by the data-mining algorithm of the same name and runs in near-linear time. Hence, FastMap is orders of magnitude faster than competing approaches that produce a Euclidean embedding using Semidefinite Programming. FastMap also produces admissible and consistent heuristics and therefore guarantees the generation of shortest paths. Moreover, FastMap applies to general undirected graphs for which many traditional heuristics, such as the Manhattan Distance heuristic, are not well defined. Empirically, we demonstrate that A* search using the FastMap heuristic is competitive with A* search using other state-of-the-art heuristics, such as the Differential heuristic.
Lactate dehydrogenase from Streptococcus mutans: purification, characterization, and crossed antigenicity with lactate dehydrogenases from Lactobacillus casei, Actinomyces viscosus, and Streptococcus sanguis

A cytoplasmic fructose-1,6-diphosphate-dependent lactate dehydrogenase (LDH; EC 1.1.1.27) from Streptococcus mutans OMZ175 was purified to homogeneity as judged by sodium dodecyl sulfate-gel electrophoresis. The purification consisted of ammonium sulfate precipitation of the cytoplasmic fraction, DEAE-Sephacel and Blue-Sepharose CL.6B chromatography, and Sephacryl S200 gel permeation. The catalytic activity of the purified enzyme required the presence of fructose-1,6-diphosphate with a broad optimum between pH 5 and 6.2. The concentration of fructose-1,6-diphosphate required for half-maximal velocity was around 0.02 mM and was affected by the pyruvate concentration. The enzyme seemed to have at least two binding sites for the activator which interact in a cooperative manner. Increasing concentrations of fructose-1,6-diphosphate up to 2 mM enhanced the relative affinity of the enzyme for pyruvate and modified the pyruvate saturation curve from sigmoidal to hyperbolic. The enzyme activity showed also a sigmoidal response to NADH, exhibiting two binding sites for the cofactor with a Hill coefficient of about 1.9. The molecular weight of the native enzyme was 150,000 as determined by gel permeation on Sephacryl S200. Monomers (38,000 daltons) and dimers (85,000 daltons) were observed by sodium dodecyl sulfate-gel electrophoresis; the latter form was dissociated after reduction with 2-mercaptoethanol, and the enzyme could be considered a tetramer. Antibodies obtained against the purified S. mutans OMZ175 LDH cross-reacted with the sodium dodecyl sulfate-dissociated forms of LDHs from different S. mutans serotypes, Streptococcus sanguis OMZ9, Lactobacillus casei ATCC 4646, and Actinomyces viscosus NY 1. A competitive enzyme-linked immunosorbent assay allowed us to detect a very close relationship between the native states of L-LDHs from S. mutans serotypes and S. sanguis. Cross-reactions were also observed with the LDHs from A. viscosus and L. casei, the latter being the least related. A very weak immunological relationship was obtained between the L-LDH from S. mutans OMZ175 and the D-LDH from Lactobacillus leichmannii, whereas no cross-reaction could be detected with mammal LDHs.
Optimizing HTTP-Based Adaptive Streaming in Vehicular Environment Using Markov Decision Process

Hypertext transfer protocol (HTTP) is the fundamental mechanics supporting web browsing on the Internet. An HTTP server stores large volumes of contents and delivers specific pieces to the clients when requested. There is a recent move to use HTTP for video streaming as well, which promises seamless integration of video delivery to existing HTTP-based server platforms. This is achieved by segmenting the video into many small chunks and storing these chunks as separate files on the server. For adaptive streaming, the server stores different quality versions of the same chunk in different files to allow real-time quality adaptation of the video due to network bandwidth variation experienced by a client. For each chunk of the video, which quality version to download, therefore, becomes a major decision-making challenge for the streaming client, especially in vehicular environment with significant uncertainty in mobile bandwidth. In this paper, we demonstrate that for such decision making, the Markov decision process (MDP) is superior to previously proposed non-MDP solutions. Using publicly available video and bandwidth datasets, we show that the MDP achieves up to a 15x reduction in playback deadline miss compared to a well-known non-MDP solution when the MDP has the prior knowledge of the bandwidth model. We also consider a model-free MDP implementation that uses Q-learning to gradually learn the optimal decisions by continuously observing the outcome of its decision making. We find that the MDP with Q-learning significantly outperforms the MDP that uses bandwidth models.
Ontology-Based Knowledge Retrieval

We deal with knowledge retrieval within the context of Virtual Learning Environment (VLE). A good VLE should deliver relevant learning materials to the learner at the most appropriate time to facilitate knowledge acquisition by Problem-Based Learning (PBL). In PBL, students should retrieve information about a problem by working in small groups with the guidance of a learning facilitator providing materials required through the problem solving process. The use of ontologies to represent domain knowledge improves the information management in a VLE because it enables automatic reasoning and facilitates the processes of knowledge searching and retrieving needed to promote the interest in problem solving. We propose an ontology-based for searching, discovering and publishing relevant learning materials as Learning Objects to help students in the PBL approach.
Transcriptional Modulation of Ethylene Response Factor Protein JERF3 in the Oxidative Stress Response Enhances Tolerance of Tobacco Seedlings to Salt, Drought, and Freezing1[C][W][OA]

Abiotic stresses such as drought, cold, and salinity affect normal growth and development in plants. The production and accumulation of reactive oxygen species (ROS) cause oxidative stress under these abiotic conditions. Recent research has elucidated the significant role of ethylene response factor (ERF) proteins in plant adaptation to abiotic stresses. Our earlier functional analysis of an ERF protein, JERF3, indicated that JERF3-expressing tobacco (Nicotiana tabacum) adapts better to salinity in vitro. This article extends that study by showing that transcriptional regulation of JERF3 in the oxidative stress response modulates the increased tolerance to abiotic stresses. First, we confirm that JERF3-expressing tobacco enhances adaptation to drought, freezing, and osmotic stress during germination and seedling development. Then we demonstrate that JERF3-expressing tobacco imparts not only higher expression of osmotic stress genes compared to wild-type tobacco, but also the activation of photosynthetic carbon assimilation/metabolism and oxidative genes. More importantly, this regulation of the expression of oxidative genes subsequently enhances the activities of superoxide dismutase but reduces the content of ROS in tobacco under drought, cold, salt, and abscisic acid treatments. This indicates that JERF3 also modulates the abiotic stress response via the regulation of the oxidative stress response. Further assays indicate that JERF3 activates the expression of reporter genes driven by the osmotic-responsive GCC box, DRE, and CE1 and by oxidative-responsive as-1 in transient assays, suggesting the transcriptional activation of JERF3 in the expression of genes involved in response to oxidative and osmotic stress. Our results therefore establish that JERF3 activates the expression of such genes through transcription, resulting in decreased accumulation of ROS and, in turn, enhanced adaptation to drought, freezing, and salt in tobacco.
Watching sexy displays improves hatching success and offspring growth through maternal allocation

Male attractiveness can have tremendous effects on the fitness of his offspring via good genes, but also via enhanced maternal allocation of resources. Yet the proximate mechanisms influencing differential maternal allocation in relation to male sexiness are poorly known. Here, we studied the importance of visual stimulation for maternal allocation in the Houbara bustard, a vulnerable bird species bred in captivity to support wild populations. Artificial insemination allowed controlling for potential confounding factors, such as a male's territory quality, social interactions or sperm quality/quantity, probably linked to mate attractiveness. We show that artificially inseminated females stimulated by highly displaying males increased their hatching success, owing to increased fertilization success. The females also increased the allocation of maternal androgens in their eggs, leading to an increase of circulating testosterone and growth rate in chicks. Hence, visual stimulation of the females can promote differential maternal allocation and favour offspring fitness. Our results further suggest that using artificial insemination for species conservation without appropriate stimulation of the breeding females probably has negative impacts on their breeding performance and therefore on population viability.
Roles of Aquaporins in Setaria viridis Stem Development and Sugar Storage

Setaria viridis is a C4 grass used as a model for bioenergy feedstocks. The elongating internodes in developing S. viridis stems grow from an intercalary meristem at the base, and progress acropetally toward fully expanded cells that store sugar. During stem development and maturation, water flow is a driver of cell expansion and sugar delivery. As aquaporin proteins are implicated in regulating water flow, we analyzed elongating and mature internode transcriptomes to identify putative aquaporin encoding genes that had particularly high transcript levels during the distinct stages of internode cell expansion and maturation. We observed that SvPIP2;1 was highly expressed in internode regions undergoing cell expansion, and SvNIP2;2 was highly expressed in mature sugar accumulating regions. Gene co-expression analysis revealed SvNIP2;2 expression was highly correlated with the expression of five putative sugar transporters expressed in the S. viridis internode. To explore the function of the proteins encoded by SvPIP2;1 and SvNIP2;2, we expressed them in Xenopus laevis oocytes and tested their permeability to water. SvPIP2;1 and SvNIP2;2 functioned as water channels in X. laevis oocytes and their permeability was gated by pH. Our results indicate that SvPIP2;1 may function as a water channel in developing stems undergoing cell expansion and SvNIP2;2 is a candidate for retrieving water and possibly a yet to be determined solute from mature internodes. Future research will investigate whether changing the function of these proteins influences stem growth and sugar yield in S. viridis.
An fMRI study on cortical responses during active self-touch and passive touch from others

Active, self-touch and the passive touch from an external source engage comparable afferent mechanoreceptors on the touched skin site. However, touch directed to glabrous skin compared to hairy skin will activate different types of afferent mechanoreceptors. Despite perceptual similarities between touch to different body sites, it is likely that the touch information is processed differently. In the present study, we used functional magnetic resonance imaging (fMRI) to elucidate the cortical differences in the neural signal of touch representations during active, self-touch and passive touch from another, to both glabrous (palm) and hairy (arm) skin, where a soft brush was used as the stimulus. There were two active touch conditions, where the participant used the brush in their right hand to stroke either their left palm or arm. There were two similar passive, touch conditions where the experimenter used an identical brush to stroke the same palm and arm areas on the participant. Touch on the left palm elicited a large, significant, positive blood-oxygenation level dependence (BOLD) signal in right sensorimotor areas. Less extensive activity was found for touch to the arm. Separate somatotopical palm and arm representations were found in Brodmann area (BA) 3 of the right primary somatosensory cortex (SI) and in both these areas, active stroking gave significantly higher signals than passive stroking. Active, self-touch elicited a positive BOLD signal in a network of sensorimotor cortical areas in the left hemisphere, compared to the resting baseline. In contrast, during passive touch, a significant negative BOLD signal was found in the left SI. Thus, each of the four conditions had a unique cortical signature despite similarities in afferent signaling or evoked perception. It is hypothesized that attentional mechanisms play a role in the modulation of the touch signal in the right SI, accounting for the differences found between active and passive touch.
Fusion of spectral and prosodic information using combined error optimization for keyword spotting

Incorporating prosodic information with spectral information at the feature level is challenging. In this paper, a method for feature level fusion of spectral and prosodic information is proposed. A pitch contour is first extracted from the frame blocked segments of the speech signal. These speech segments obtained herein are labeled as high pitch and low pitch segments. Both spectral and prosodic features are extracted from each segment class. An integrated feature set is obtained by concatenating spectral and prosodic features from each of these classes. In the next stage of fusion, the high and low pitch labeled features are further combined using joint error optimization approach. This optimization approach assumes that the mean of the high pitch segments can be obtained by an affine transformation on the mean of the low pitch segments. The parameters of the affine transformation are obtained using the gradient descent approach. The final integrated feature set is obtained after normalization of both sets of features thus obtained. This integrated feature set is used in a Hidden Markov Modeling (HMM) framework along with a novel sliding syllable protocol for keyword spotting. Keyword spotting experiments are conducted on the Hindi language database developed for this purpose. Experiments on keyword recognition and keyword spotting are conducted to evaluate the performance of the proposed fusion method. Experimental results obtained in terms of WER and receiver operating characteristics indicate a reasonable improvements over the use of a single feature set like the MFCC.
Comparison of Intracoronary Versus Intravenous Administration of Adenosine for Measurement of Coronary Fractional Flow Reserve

Background—Measurement of fractional flow reserve (FFR) constitutes the current gold standard to evaluate the hemodynamic significance of coronary stenoses. Limited data validate the intracoronary application of adenosine against standard intravenous infusion. We systematically compared FFR measurements during intracoronary and intravenous application of adenosine about agreement and reproducibility. Methods and Results—We included 114 patients with an intermediate degree of stenosis in coronary angiography. Two FFR measurements were performed during intracoronary bolus injection (40 &mgr;g for the right and 80 &mgr;g for the left coronary artery, FFRic), and 2 FFR measurements during continuous intravenous infusion of adenosine (140 &mgr;g/kg per minute, FFRiv). FFR value, the time to reach FFR and patient discomfort (on a subjective scale from 0 for no symptoms to 5 for maximal discomfort) were recorded for each measurement. Mean time to FFR was 100±27 s for continuous intravenous infusion versus 23±14 s for intracoronary bolus administration of adenosine (P<0.001). Reported discomfort after intracoronary application was significantly lower compared with intravenous adenosine (subjective scale >0 in 35.1% versus 87.7% of the patients; P<0.001). Correlation between FFRiv and FFRic was extremely close (r=0.99; P<0.001) with no systematic bias in Bland–Altman analysis (bias 0.002 [confidence interval, −0.001 to 0.005]) and low intermethod variability (1.56%). Intramethod variability was not different between intravenous and intracoronary administration (1.47% versus 1.33%; P=0.5). Conclusions—Intracoronary bolus injection of adenosine (40 &mgr;g for the right and 80 &mgr;g for the left coronary artery) yields identical FFR results compared with intravenous infusion (140 &mgr;g/kg per minute), while requiring less time and offering superior patient comfort.
Impact assessment of changes in land use / conservation practices on soil erosion in the PenedeÁs ± Anoia vineyard region ( NE Spain )

Soil erosion by water is one of the most important land degradation processes in the Mediterranean basin. In comparison with other typical crops in this region, vineyards are the agricultural land use that cause the highest soil losses. The changes in land use types and management that have involved the intensi®cation of agriculture from the 1950s have contributed to the increase of soil erosion. This paper presents an assessment of this impact in a vineyard region of fundamental concern in the NE Spain, the PenedeÁs±Anoia, mainly dedicated to the production of high quality wines and `̀ cavas''. The analysis is based on the comparison of the estimated soil loss rates in the period just before the mechanisation (1950s) and in the most recent past (1990s). Multitemporal data (aerial photographs and digital terrain models), the revised universal soil loss equation and GIS analysis were used for that purpose. The results show a clear negative soil loss balance, with 12.6% of the agricultural land having experienced major negative changes. This negative balance is associated with the increase of the area dedicated to vineyards, the transformation of old traditional vineyard plantations to modern trained plantations and to the removing of conservation practices to adopt plots to crop mechanisation. This leads to an unsustainable viticulture and soil degradation in mediumto long-term periods. # 2000 Elsevier Science B.V. All rights reserved.
Potential Transmission Pathways of Streptococcus gallolyticus subsp. gallolyticus

Streptococcus gallolyticus subsp. gallolyticus (S. gallolyticus subsp. gallolyticus), a member of group D streptococci, is an inhabitant of the animal and human gastrointestinal tract. Furthermore, it is a facultative pathogen which causes e.g. endocarditis, septicemia and mastitis. S. gallolyticus subsp. gallolyticus may be transmitted either directly or indirectly between animals and humans. However, the transmission routes are an unsolved issue. In this study, we present systematic analyses of an S. gallolyticus subsp. gallolyticus isolate of an infective endocarditis patient in relation to isolates of his laying hen flock. Isolates from pooled droppings of laying hens, pooled dust samples and human blood culture were characterized by using multilocus sequence typing (MLST) and DNA fingerprinting. MLST revealed the same allelic profile of isolates from the human blood culture and from the droppings of laying hens. In addition, these isolates showed clonal identity regarding a similar DNA fingerprinting pattern. For the first time, we received a hint that transmission of S. gallolyticus subsp. gallolyticus between poultry and humans may occur. This raises the question about the zoonotic potential of isolates from poultry and should be considered in future studies.
A modelling study of the permafrost carbon feedback to climate change: feedback strength, timing, and carbon cycle consequences

The recent quantification of the reservoir of carbon held in permafrost soils has rekindled the concern that the terrestrial biosphere will transition from a carbon sink to a carbon source during the 21st century. This dissertation is a compilation of four modelling studies that investigate the permafrost carbon feedback, its consequences for the projected future behaviour of the carbon cycle, and the origins of the proportionally between cumulative CO2 emissions and near surface temperature change. The dissertation is centred around five questions: 1) what is the strength and timing of the permafrost carbon feedback to climate change? 2) If anthropogenic CO2 emissions cease, will atmospheric CO2 concentration continue to increase? 3) Can climate warming be reversed using artificial atmospheric carbon-dioxide removal? 4) What are the underlying physical mechanisms that explain the existence in Earth system models of the proportionality between cumulative CO2 emissions and mean global near surface temperature change? And 5) can strong terrestrial carbon cycle feedbacks, such as the permafrost carbon feedback, disrupt this proportionality?
Smart linkers in polymer–drug conjugates for tumor-targeted delivery

Abstract To achieve effective chemotherapy, many types of drug delivery systems have been developed for the specific environments in tumor tissues. Polymer–drug conjugates are increasingly used in tumor therapy due to several significant advantages over traditional delivery systems. In the fabrication of polymer–drug conjugates, a smart linker is an important component that joins two fragments or molecules together and can be cleared by a specific stimulus, which results in targeted drug delivery and controlled release. By regulating the conjugation between the drug and the nanocarriers, stimulus-sensitive systems based on smart linkers can offer high payloads, certified stability, controlled release and targeted delivery. In this review, we summarize the current state of smart linkers (e.g. disulfide, hydrazone, peptide, azo) used recently in various polymer–drug conjugate-based delivery systems with a primary focus on their sophisticated design principles and drug delivery mechanisms as well as in vivo processes.
Malaria transmission indices of two dominant anopheles species in selected rural and urban communities in Benue state North Central, Nigeria

An entomological survey was piloted to generate baseline entomological data in some communities in Benue State where such information was not previously available. Indoor resting mosquitoes were captured using Pyrethrum Spray Catch (PSC) in 2015. Of the 1,734 mosquitoes captured 276 (16%), were Anopheles species. Molecular assays revealed the presence of Anopheles gambiae sensu. stricto and Anopheles arabiensis. Human blood meal source was within the range of 97% to 100% clearly expressing a high degree of human-vector contact. Circumsporozoite (CS) proteins infection status of engorged female species were determined by Enzyme Linked Immunosorbent Assay (ELISA). The calculated Sporozoite Infection Rate (SR) for rural was 1.9% and 0% for urban communities respectively. The Entomological Inoculation Rates (EIR) recorded was 0.4% per person per night culminating in an annual 146 infective bites per person per year. Our observed data highlights some malaria risk indices in the study communities.