Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen Reserve Pools in Two Miscanthus × giganteus Genotypes under Contrasting N Managements

Nitrogen (N) reserves in vegetative tissues contribute N to regrowth of Miscanthus × giganteus shoots in spring, but our understanding of how N fertilization and plant genotype affect this process is incomplete. Our specific objectives were to: (1) determine how N fertilizer management impacts accumulation of dry matter and N among aboveground and belowground tissues and organs; (2) understand how changes in N management and tissue N concentration influence seasonal fluctuations in concentrations of buffer-soluble proteins and amino acids in putative storage organs including rhizomes and roots; and (3) characterize genotypic variability and genotype × N interactions for N reserve accumulation and use among Miscanthus × giganteus genotypes. Established plots of the IL Clone and Nagara-sib population were fertilized with 0–0, 0–150, 75–75, 150–0, and 150–150 kg N ha-1 where the first numeral denotes the N rate applied in 2011 (Year 1) and the second number denotes the N rate applied in 2012 (Year 2). Rhizomes, roots, stembases, and shoots were sampled at 6-week intervals between March and August and then in November at dormancy. Concentrations of N, soluble protein and amino-N increased in all tissues with fertilizer N application. With the exception of rhizome amino-N, concentrations of these N pools in roots and rhizomes declined as plants resumed growth in spring and increased sharply between August and November as growth slowed. Losses in shoot and stembase N mass between August and November were similar to total N accumulation in roots and rhizomes during this interval. Compared to the unfertilized control, specific N managements enhanced growth of above- and belowground tissues. The IL Clone generally had greater biomass yield of all organs than the Nagara-sib; the exception being shoot biomass in November when extensive leaf senescence reduce yield of the IL Clone. High biomass yields were obtained with 75 kg N ha-1 applied annually rather than semi-annual N applications of 150 kg N-1 ha that depended on N recycling from roots/rhizomes as a supplemental N source.
Evidence for Conserved Function of γ–Glutamyltranspeptidase in Helicobacter Genus

The confounding consequences of Helicobacter bilis infection in experimental mice populations are well recognized, but the role of this bacterium in human diseases is less known. Limited data are available on virulence determinants of this species. In Helicobacter pylori, γ-glutamyltranspeptidase (γGT) contributes to the colonization of the gastric mucosa and to the pathogenesis of peptic ulcer. The role of γGT in H. bilis infections remains unknown. The annotated genome sequence of H. bilis revealed two putative ggt genes and our aim was to characterize these H. bilis γGT paralogues. We performed a phylogenetic analysis to understand the evolution of Helicobacter γGTs and to predict functional activities of these two genes. In addition, both copies of H. bilis γGTs were expressed as recombinant proteins and their biochemical characteristics were analysed. Functional complementation of Esherichia coli deficient in γGT activity and deletion of γGT in H. bilis were performed. Finally, the inhibitory effect of T-cell and gastric cell proliferation by H. bilis γGT was assessed. Our results indicated that one gene is responsible for γGT activity, while the other showed no γGT activity due to lack of autoprocessing. Although both H. bilis and H. pylori γGTs exhibited a similar affinity to L-Glutamine and γ-Glutamyl-p-nitroanilide, the H. bilis γGT was significantly less active. Nevertheless, H. bilis γGT inhibited T-cell proliferation at a similar level to that observed for H. pylori. Finally, we showed a similar suppressive influence of both H. bilis and H. pylori γGTs on AGS cell proliferation mediated by an apoptosis-independent mechanism. Our data suggest a conserved function of γGT in the Helicobacter genus. Since γGT is present only in a few enterohepatic Helicobacter species, its expression appears not to be essential for colonization of the lower gastrointestinal tract, but it could provide metabolic advantages in colonization capability of different niches.
Contrast enhanced ultrasound and magnetic resonance imaging in hepatocellular carcinoma diagnosis.

BACKGROUND The new developments in imaging technology, including contrast enhanced ultrasound (CEUS), computed tomography (CT), and magnetic resonance imaging (MRI), allow a better diagnosis of both malignant and benign liver lesions. MATERIAL AND METHODS A retrospective trial of 126 patients was conducted in the Gastroenterology and Imaging Departments of the University of Medicine and Pharmacy Craiova, Romania. CEUS and MRI were the imaging techniques used for diagnosis of focal liver lesions (FLL), especially for hepatocellular carcinoma (HCC). Histopathology was used only in 15 cases. For each method of investigation we calculated the sensitivity, specificity, positive and negative predictive values (PPV and NPV), positive and negative likelihood ratio (+LR, -LR), accuracy and we compared the ROC curves. Statistical analysis also included the Chi-square and Kappa tests. RESULTS Seventy six cases were diagnosed as HCC, with average size of 5.2±3.3 cm in diameter. The sensitivity and specificity were 71.4% and 95.6% for CEUS and 91.4%, 98.9% respectively, for MRI. When comparing the ROC curves, we found a higher area under curve for MRI (0.952) then for CEUS (0.835) (p=0.005), and 95% confidence interval of 0.0343 to 0.199. No statistically significant difference in diagnosis of FLL was found between CEUS and MRI (p > 0.05) and the agreement between the two imaging techniques was good (k = 0.78). CONCLUSIONS CEUS can be used as the first step in the diagnosis of liver lesions, but MRI remains the gold standard diagnostic method for liver tumors.
Cortical Attractor Network Dynamics with Diluted Connectivity

The connectivity of the cerebral cortex is diluted, with the probability of excitatory connections between even nearby pyramidal cells rarely more than 0.1, and in the hippocampus 0.04. To investigate the extent to which this diluted connectivity affects the dynamics of attractor networks in the cerebral cortex, we simulated an integrate-and-fire attractor network taking decisions between competing inputs with diluted connectivity of 0.25 or 0.1, and with the same number of synaptic connections per neuron for the recurrent collateral synapses within an attractor population as for full connectivity. The results indicated that there was less spiking-related noise with the diluted connectivity in that the stability of the network when in the spontaneous state of firing increased, and the accuracy of the correct decisions increased. The decision times were a little slower with diluted than with complete connectivity. Given that the capacity of the network is set by the number of recurrent collateral synaptic connections per neuron, on which there is a biological limit, the findings indicate that the stability of cortical networks, and the accuracy of their correct decisions or memory recall operations, can be increased by utilizing diluted connectivity and correspondingly increasing the number of neurons in the network, with little impact on the speed of processing of the cortex. Thus diluted connectivity can decrease cortical spiking-related noise. In addition, we show that the Fano factor for the trial-to-trial variability of the neuronal firing decreases from the spontaneous firing state value when the attractor network makes a decision.
Automated Speech Act Classification For Online Chat

In this paper, we present our investigation on using supervised machine learning methods to automatically classify online chat posts into speech act categories, which are semantic categories indicating speakers’ intentions. Supervised machine learning methods presuppose the existence of annotated training data based on which machine learning algorithms can be used to learn the parameters of some model that was proposed to solve the task at hand. In our case, we used the annotated Linguistic Data Consortium chat corpus to tune our model which is based on the assumption that the first few tokens/words in each chat post are very predictive of the post’s speech act category. We present results for predicting the speech act category of chat posts that were obtained using two machine learning algorithms, Naive Bayes and Decision Trees, in conjunction with several variants of the basic model that include the first 2 to 6 words and their part-of-speech tags as features. The results support the validity of our initial assumption that the first words in an utterance can be used to predict its speech act category with very good accuracy.
Cow’s Milk Allergy: A Complex Disorder

Cow’s milk allergy (CMA) is a complex disorder. Numerous milk proteins have been implicated in allergic responses and most of these have been shown to contain multiple allergenic epitopes. There is considerable heterogeneity amongst allergic individuals for the particular proteins and epitopes to which they react, and to further complicate matters, allergic reactions to cow’s milk are driven by more than one immunological mechanism. Finally, the incidence and dominant allergic mechanisms change with age, with IgE-mediated reactions common in infancy and non-IgE-mediated reactions dominating in adults. The complexity of CMA has lead to many public misconceptions about this disorder, including confusion with lactose intolerance and frequent self-misdiagnosis. Indeed, the prevalence of self-diagnosed CMA in the community is 10-fold higher than the clinically proven incidence, suggesting a sizable population is unnecessarily eschewing dairy products. Avoidance of dairy foods, whether for true or perceived CMA, carries with it nutritional consequences and the provision of appropriate nutritional advice is important. In this review, the epidemiology and natural course of CMA is discussed along with our current understanding of its triggers and immunological mechanisms. We examine current strategies for the primary and secondary prevention of allergic sensitization and the ongoing search for effective therapies to ultimately cure CMA.
AgentP classifier system: self-adjusting vs. gradual approach

Learning classifier systems belong to the class of algorithms based on the principle of self-organization and evolution and have frequently been applied to mazes, an important type of reinforcement learning problem. Mazes may contain aliasing cells, i.e. squares in a different location that look identical to an agent with limited perceptive power. Mazes with aliasing squares present a particular difficult learning problem. As a possible approach to the problem, AgentP, a learning classifier system with associative perception, was recently introduced. AgentP is based on the psychological model of associative perception learning and operates explicitly imprinted images of the environment states. Two types of learning mode are described: the first, self-adjusting AgentP, is more flexible and adapts rapidly to changing information; the second, gradual AgentP, is more conservative in drawing conclusions and rigid when it comes to revising strategy. The performance of both systems is tested on existing and new aliasing environments. The results show that AgentP often outperforms (and always at least matches) the performance of other techniques and, on the large majority of mazes used, learns optimal or near optimal solutions with fewer trials and a smaller classifier population.
Incremental prognostic value of post-stress left ventricular ejection fraction and volume by gated myocardial perfusion single photon emission computed tomography.

BACKGROUND The incremental prognostic value of post-stress left ventricular ejection fraction (EF) and volume over perfusion has not been investigated. METHODS AND RESULTS We identified 1680 consecutive patients who underwent rest Tl-201/stress Tc-99m sestamibi gated single photon emission computed tomography (SPECT) and who were followed-up for 569+/-106 days. Receiver-operator characteristics analysis defined an EF<45%, an end-systolic volume (ESV) >70 mL, and an end-diastolic volume >120 mL as optimal thresholds, yielding moderate sensitivity and high specificity in the prediction of cardiac death. Patients with an EF> or = 45% had mortality rates <1%/year, despite severe perfusion abnormalities, whereas patients with an EF<45% had high mortality rates, even with only mild/moderate perfusion abnormalities (9.2%/year; P<0.00001). Similarly, an ESV< or = 70 mL was related to a low cardiac death rate (<1.2%/year), even for patients with severe perfusion abnormalities, whereas patients with an ESV>70 mL and only mild/moderate perfusion abnormalities had high death rates (8.2%/year; P<0.00001). Patients with an EF<45% and an ESV< or = 70 mL had low cardiac death rates (1.7%/year); those with an EF<45% but an ESV>70 mL had high death rates (7.9%/year; P<0.02). Multivariate Cox proportional hazards regression showed that perfusion variables and ESV were independent predictors of overall coronary events, whereas EF and ESV demonstrated incremental prognostic values over prescan and perfusion information in predicting cardiac death and cardiac death or myocardial infarction. CONCLUSIONS Post-stress EF and ESV by gated-SPECT have incremental prognostic values over prescan and perfusion information in predicting cardiac death, and they provide clinically useful risk stratification.
Impact of anthropogenic climate change on wildfire across western US forests

Significance Increased forest fire activity across the western United States in recent decades has contributed to widespread forest mortality, carbon emissions, periods of degraded air quality, and substantial fire suppression expenditures. Although numerous factors aided the recent rise in fire activity, observed warming and drying have significantly increased fire-season fuel aridity, fostering a more favorable fire environment across forested systems. We demonstrate that human-caused climate change caused over half of the documented increases in fuel aridity since the 1970s and doubled the cumulative forest fire area since 1984. This analysis suggests that anthropogenic climate change will continue to chronically enhance the potential for western US forest fire activity while fuels are not limiting. Increased forest fire activity across the western continental United States (US) in recent decades has likely been enabled by a number of factors, including the legacy of fire suppression and human settlement, natural climate variability, and human-caused climate change. We use modeled climate projections to estimate the contribution of anthropogenic climate change to observed increases in eight fuel aridity metrics and forest fire area across the western United States. Anthropogenic increases in temperature and vapor pressure deficit significantly enhanced fuel aridity across western US forests over the past several decades and, during 2000–2015, contributed to 75% more forested area experiencing high (>1 σ) fire-season fuel aridity and an average of nine additional days per year of high fire potential. Anthropogenic climate change accounted for ∼55% of observed increases in fuel aridity from 1979 to 2015 across western US forests, highlighting both anthropogenic climate change and natural climate variability as important contributors to increased wildfire potential in recent decades. We estimate that human-caused climate change contributed to an additional 4.2 million ha of forest fire area during 1984–2015, nearly doubling the forest fire area expected in its absence. Natural climate variability will continue to alternate between modulating and compounding anthropogenic increases in fuel aridity, but anthropogenic climate change has emerged as a driver of increased forest fire activity and should continue to do so while fuels are not limiting.
Lycopene Increases Urokinase Receptor and Fails to Inhibit Growth or Connexin Expression in a Metastatically Passaged Prostate Cancer Cell Line: A Brief Communication

The carotenoid lycopene, found in tomatoes, has been associated with decreasing prostate cancer risk. Potential mechanisms for this risk reduction include lycopene's status as a potent antioxidant, its inhibitory effect on cell proliferation, and its ability to increase intercellular gap junctional communication. Presently, in the United States, almost 200,000 men are diagnosed with prostate cancer and approximately 30,000 succumb to its metastatic effects. Therefore, novel treatment strategies are needed for patients who currently have the disease, especially those in advanced, i.e., metastatic status. In this study, we sought to determine if lycopene's inhibitory properties on premalignancy could be extended to advanced prostate cancer by assessing effects on a cell line derived through metastatic passage, the PC-3MM2. We report that in this cell line, lycopene has a potentially unwanted effect of upregulating expression of the urokinase plasminogen activator receptor and facilitating invasion while falling to significantly inhibit proliferation or to induce detectable levels of the gap junctional protein connexin 43 expression. Our results indicate that some caution should be taken with regard to use of lycopene to treat potentially advanced and metastatic prostate cancers.
Microstructure of Water At the Level of Three-particle Correlation Functions As Predicted by Classical Intermolecular Models

We compared the microscopic structure of liquid water at ambient conditions predicted by six classical intermolecular potential models. Applying their accepted acronyms were the SPC (Simple Point Charge), SPC/E (SPC extended), MSPC/E (SPC/E modified), TIP4P (Transferable Intermolecular Potential, four point charges), TIP5P (TIP, five point charges), and the PPC (Polarizable Point Charge) intermolecular potential models. Configurations of computer simulations were used to study the structure at the level of partial three-particle correlation functions. We created contour maps for visual evaluation, calculated overlap integrals of the three-particle correlation functions of the models to quantify their similarity, and determined their distance-dependent three-particle entropy contribution. The SPC/E and the TIP4P water models generate quite similar structures, while the SPC and the MSPC/E pair exhibit the largest discrepancies. The structure of the PPC is the most ordered and the SPC structure is the most disordered among the studied interaction models.
Pericyte MyD88 and IRAK4 control inflammatory and fibrotic responses to tissue injury

Fibrotic disease is associated with matrix deposition that results in the loss of organ function. Pericytes, the precursors of myofibroblasts, are a source of pathological matrix collagens and may be promising targets for treating fibrogenesis. Here, we have shown that pericytes activate a TLR2/4- and MyD88-dependent proinflammatory program in response to tissue injury. Similarly to classic immune cells, pericytes activate the NLRP3 inflammasome, leading to IL-1&bgr; and IL-18 secretion. Released IL-1&bgr; signals through pericyte MyD88 to amplify this response. Unexpectedly, we found that MyD88 and its downstream effector kinase IRAK4 intrinsically control pericyte migration and conversion to myofibroblasts. Specific ablation of MyD88 in pericytes or pharmacological inhibition of MyD88 signaling by an IRAK4 inhibitor in vivo protected against kidney injury by profoundly attenuating tissue injury, activation, and differentiation of myofibroblasts. Our data show that in pericytes, MyD88 and IRAK4 are key regulators of 2 major injury responses: inflammatory and fibrogenic. Moreover, these findings suggest that disruption of this MyD88-dependent pathway in pericytes might be a potential therapeutic approach to inhibit fibrogenesis and promote regeneration.
THE THICKNESS OF THE HUMAN CORNEA AS DETERMINED BY A SPECULAR METHOD

The thickness of the human cornea was measured by a simple accurate method which entails measurement of the distance between the anterior and the posterior corneal reflections when the cornea is illuminated at an angle. As compared to methods measuring the width of the optical section, the advantage of the method is that end‐points of measurement are clearly defined, providing a better basis for an exact estimation of the corneal thickness. The optical principle of the specular method is presented in a general form. The influence of physiological variation in corneal curvature and index of refracation is analysed and shown to cause an insignificant error on the standard thickness estimate. Using this method, the corneal thickness was measured in a random population sample of 115 normal subjects, aged 10–90 years. The corneal thickness was found to approximate a normal distribution with a mean value (± SD) of 0.515 mm (± 0.033). Asignificant decrease in corneal thickness with age of 0.0045 mm per decade was found.
Influence of the Biotope on the Tick Infestation of Cattle and on the Tick-Borne Pathogen Repertoire of Cattle Ticks in Ethiopia

Background The majority of vector-borne infections occur in the tropics, including Africa, but molecular eco-epidemiological studies are seldom reported from these regions. In particular, most previously published data on ticks in Ethiopia focus on species distribution, and only a few molecular studies on the occurrence of tick-borne pathogens or on ecological factors influencing these. The present study was undertaken to evaluate, if ticks collected from cattle in different Ethiopian biotopes harbour (had access to) different pathogens. Methods In South-Western Ethiopia 1032 hard ticks were removed from cattle grazing in three kinds of tick biotopes. DNA was individually extracted from one specimen of both sexes of each tick species per cattle. These samples were molecularly analysed for the presence of tick-borne pathogens. Results Amblyomma variegatum was significantly more abundant on mid highland, than on moist highland. Rhipicephalus decoloratus was absent from savannah lowland, where virtually only A. cohaerens was found. In the ticks Coxiella burnetii had the highest prevalence on savannah lowland. PCR positivity to Theileria spp. did not appear to depend on the biotope, but some genotypes were unique to certain tick species. Significantly more A. variegatum specimens were rickettsia-positive, than those of other tick species. The presence of rickettsiae (R. africae) appeared to be associated with mid highland in case of A. variegatum and A. cohaerens. The low level of haemoplasma positivity seemed to be equally distributed among the tick species, but was restricted to one biotope type. Conclusions The tick biotope, in which cattle are grazed, will influence not only the tick burden of these hosts, but also the spectrum of pathogens in their ticks. Thus, the presence of pathogens with alternative (non-tick-borne) transmission routes, with transstadial or with transovarial transmission by ticks appeared to be associated with the biotope type, with the tick species, or both, respectively.