Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Volatiles Induce Systemic Resistance in Arabidopsis1

Plant growth-promoting rhizobacteria, in association with plant roots, can trigger induced systemic resistance (ISR). Considering that low-molecular weight volatile hormone analogues such as methyl jasmonate and methyl salicylate can trigger defense responses in plants, we examined whether volatile organic compounds (VOCs) associated with rhizobacteria can initiate ISR. In Arabidopsis seedlings exposed to bacterial volatile blends from Bacillus subtilis GB03 and Bacillus amyloliquefaciens IN937a, disease severity by the bacterial pathogen Erwinia carotovora subsp. carotovora was significantly reduced compared with seedlings not exposed to bacterial volatiles before pathogen inoculation. Exposure to VOCs from rhizobacteria for as little as 4 d was sufficient to activate ISR in Arabidopsis seedlings. Chemical analysis of the bacterial volatile emissions revealed the release of a series of low-molecular weight hydrocarbons including the growth promoting VOC (2R,3R)-(-)-butanediol. Exogenous application of racemic mixture of (RR) and (SS) isomers of 2,3-butanediol was found to trigger ISR and transgenic lines of B. subtilis that emitted reduced levels of 2,3-butanediol and acetoin conferred reduced Arabidopsis protection to pathogen infection compared with seedlings exposed to VOCs from wild-type bacterial lines. Using transgenic and mutant lines of Arabidopsis, we provide evidence that the signaling pathway activated by volatiles from GB03 is dependent on ethylene, albeit independent of the salicylic acid or jasmonic acid signaling pathways. This study provides new insight into the role of bacteria VOCs as initiators of defense responses in plants.
Studies on chronic versus transient intestinal nematode infections in mice I. A comparison of responses to excretory/secretory (ES) products of Nippostrongylus brasiliensis and Nematospiroides dubius worms

Summary Previous reports have demonstrated that after implantation of intestinal worms or after exposure to infective third stage larvae, the duration of infection with Nematospiroides dubius is markedly prolonged in intact mice relative to infection with Nippostrongylus brasiliensis. The rapid rejection of N. brasiliensis adults appears T‐cell dependent in that adults persist for longer periods in hypothymic nude mice than in intact mice. Excretory/secretory (ES) products harvested from N. dubius or N. brasiliensis intestinal worms did not differ obviously in the following characteristics: rate of production and degree of complexity of proteins, in vitro mitogenicity, allergenicity, or in their abilities to induce or elicit delayed type hypersensitivity reactions in naive and infected mice, respectively. Two differences between N. brasiliensis‐ and N. dubius‐infected mice were an IgG1 hypergammaglobulinaemia and readily detected anti‐ES precipitating antibodies in the circulation; both responses were confined to the chronic N. dubius infection. One difference between N. brasiliensis and N. dubius ES products was that the former, but not the latter, induced protection against homologous infection when injected with Freund's complete adjuvant. By contrast, intraperitoneal implantation of either type of adult worm induced protection against homologous infection at least in female Balb/c mice. After intestinal implantation of both N. dubius and N. brasiliensis intestinal worms, the rejection of N. brasiliensis was not influenced by, nor did it alter, persistence of N. dubius adults. In support of conclusions drawn by others, the differences in persistence of infection between these two nematodes probably reflect differences in the ability to resist both specific and nonspecific components of the complex intestinal rejection process. The chronicity of N. dubius infection and nonpersistence of N. brasiliensis
“Specificity Determinants” Improve Therapeutic Indices of Two Antimicrobial Peptides Piscidin 1 and Dermaseptin S4 against the Gram-negative Pathogens Acinetobacter baumannii and Pseudomonas aeruginosa

A new class of antimicrobial agents with lower rates of resistance and different targets is urgently needed because of the rapidly increasing resistance to classical antibiotics. Amphipathic cationic α-helical antimicrobial peptides (AMPs) represent such a class of compounds. In our previous studies, using a 26-residue de novo designed antimicrobial peptide, we proposed the concept of “specificity determinant(s)”: positively charged residue(s) in the center of the non-polar face of AMPs that could decrease hemolytic activity/toxicity but increase or maintain the same level of antimicrobial activity to increase dramatically the therapeutic index. In the current study, we used d-enantiomers of two AMPs, Piscidin 1 isolated from fish and dermaseptin S4 isolated from frog. We substituted different positions in the center of the hydrophobic face with one or two lysine residue(s) (one or two “specificity determinant(s)”). This simple modification not only maintained or improved antimicrobial activity against Gram-negative pathogens Acinetobacter baumannii (11 strains) and Pseudomonas aeruginosa (6 strains), but also dramatically decreased hemolytic activity of human red blood cells, as predicted. Therapeutic indices improved by 55-fold and 730-fold for piscidin 1 (I9K) and dermaseptin S4 (L7K, A14K), respectively, against A. baumannii. Similarly, the therapeutic indices improved 32-fold and 980-fold for piscidin 1 (I9K) and dermaseptin S4 (L7K, A14K), respectively, against P. aeruginosa.
Carried baggage detection and recognition in video surveillance with foreground segmentation

Security cameras installed in public spaces or in private organizations continuously record video data with the aim of detecting and preventing crime. For that reason, video content analysis applications, either for real time (i.e. analytic) or post-event (i.e. forensic) analysis, have gained high interest in recent years. In this thesis, the primary focus is on two key aspects of video analysis, reliable moving object segmentation and carried object detection & identification. A novel moving object segmentation scheme by background subtraction is presented in this thesis. The scheme relies on background modelling which is based on multi-directional gradient and phase congruency. As a post processing step, the detected foreground contours are refined by classifying the edge segments as either belonging to the foreground or background. Further contour completion technique by anisotropic diffusion is first introduced in this area. The proposed method targets cast shadow removal, gradual illumination change invariance, and closed contour extraction. A state of the art carried object detection method is employed as a benchmark algorithm. This method includes silhouette analysis by comparing human temporal templates with unencumbered human models. The implementation aspects of the algorithm are improved by automatically estimating the viewing direction of the pedestrian and are extended by a carried luggage identification module. As the temporal template is a frequency template and the information that it provides is not sufficient, a colour temporal template is introduced. The standard steps followed by the state of the art algorithm are approached from a different extended (by colour information) perspective, resulting in more accurate carried object segmentation. The experiments conducted in this research show that the proposed closed foreground segmentation technique attains all the aforementioned goals. The incremental improvements applied to the state of the art carried object detection algorithm revealed the full potential of the scheme. The experiments demonstrate the ability of the proposed carried object detection algorithm to supersede the state of the art method.
Effect of Oral and Transdermal Estrogen Replacement Therapy on Hemostatic Variables Associated With Venous Thrombosis: A Randomized, Placebo-Controlled Study in Postmenopausal Women

Objective—The purpose of this study was to investigate whether the effect of transdermal estrogen therapy in postmenopausal women differs from that of oral therapy with regard to resistance to activated protein C (APC), an important risk factor for venous thrombosis, and levels of related proteins, such as protein S, protein C, and prothrombin. Methods and Results—In a randomized, double-blind, placebo-controlled study, 152 healthy hysterectomized postmenopausal women received daily either placebo (n=49), transdermal 17&bgr;-estradiol (E2) 50 &mgr;g (tE2 group, n=33), oral E2 1 mg (oE2 group, n=37), or oral E2 1 mg combined with gestodene 25 &mgr;g (oE2+G group, n=33) for 13 28-day treatment cycles, followed by 4 cycles of placebo for each group. Plasma samples were collected at baseline and in cycles 4, 13, and 17. In cycle 13, significant increases versus baseline and placebo were found in normalized APC sensitivity ratios (nAPCsr) in all treated groups (tE2, +26.9%; oE2, +102.7%; oE2+G, +69.9%). Increases in nAPCsr were significantly higher in the oral treatment groups than in the tE2 group. In addition, compared with baseline and placebo, after 13 cycles, decreases were observed in total protein S (tE2, −4.1%; oE2, −7.9%; oE2+G, −5.8%), free protein S (tE2, −7.1%; oE2, −8.4%; oE2+G, −5.2%), and protein C in the oE2+G group (−6.4%), but these changes did not explain the increase in nAPCsr. Changes in prothrombin were small and also did not affect the nAPCsr. Conclusions—Increases were observed in resistance to APC, which were more pronounced in the oral treatment groups than in the transdermal group. The increase in resistance to APC was not explained by changes in protein S, protein C, or prothrombin and may contribute to the increased incidence of venous thrombosis in users of hormone replacement therapy.
Diarrheal Diseases Hospitalization in Yemen before and after Rotavirus Vaccination

The study aims to assess the impact of rotavirus vaccine introduction on diarrheal diseases hospitalization and to identify the rotavirus genotypes most prevalent before and after vaccine introduction among children ≤ 5 years of age. Rotarix™ ® rotavirus vaccine is currently licensed for infants in Yemen and was introduced in 2012. The vaccination course consists of two doses. The first dose is administrated at 6 weeks of age and the second dose is completed by 10 weeks. Based on a longitudinal observational study, we assessed the impact of vaccination on rotavirus hospitalization before and after vaccination among children ≤ 5 years of age at the Yemeni-Swedish Hospital (YSH) in Taiz, Yemen. Prevaccination covered January 2009–July 2012 during which 2335 fecal samples were collected from children ≤ 5 years old. Postvaccination covered January 2013–December 2014 during which 1114 fecal samples were collected. Rotavirus was detected by Enzyme Linkage Immunosorbent Assay (ELISA). The incidence of rotavirus hospitalization decreased from 43.79% in 2009 to 10.54% in 2014. Hospitalization due to rotavirus diarrhea was reduced by 75.93%. Vaccine coverage increased from 23% in 2012 to 72% in 2014. Also, the results showed that the most predominant genotypes in prevaccination period were G2P[4] (55.0%), followed by G1P[8] (15.0%), while in postvaccination period G1P[8] (31%) was the predominant genotype, followed by G9P[8] (27.5%). In conclusion, rotavirus vaccination in Yemen resulted in sharp reduction in diarrheal hospitalization. A successful rotavirus vaccination program in Yemen will rely upon efficient vaccine delivery systems and sustained vaccine efficacy against diverse and evolving rotavirus strains.
Validating the Integrated Multisatellite Retrievals for Global Precipitation Measurement in Terms of Diurnal Variability With Hourly Gauge Observations Collected at 50,000 Stations in China

The diurnal cycle of precipitation is a key feature in the Earth system and related to multiscale physical processes. The Integrated Multi‐satellitE Retrievals for Global Precipitation Measurement (IMERG) data are expected to improve its presentation of diurnal cycle, but how it really performs remains poorly known. This study compares the diurnal characteristics of the half‐hourly IMERG V05 Final Run product with the hourly rain gauge data collected at approximately 50,000 automatic weather stations in China during a 3‐year period (2014–2016). Our results show that IMERG performs well in terms of the diurnal cycle of precipitation amount but less well in terms of frequency and even worse in terms of intensity. Ground observations show that the frequency and intensity are rather stable for the diurnal cycle; however, IMERG shows strong fluctuations. Significant inverse correlation is found between the diurnal cycles of IMERG precipitation frequency and intensity; thus, the biases of these two variables offset and result in a better estimate of amount. A low probability of detection (POD≈50%) and a high false alarm ratio (FAR≈50%) are the major reasons for the inaccurate diurnal cycles of precipitation intensity and frequency. In particular, IMERG presents a false peak of frequency at approximately 23:00–01:00 (Beijing Time) because a large proportion of the data sources at this time contain the indirect estimates from thermal infrared observations. The significant underestimation of the frequency and overestimation of the intensity at approximately 09:00–11:00 and 20:00–22:00 is because the estimates primarily come from less accurate cross‐track microwave sensors.
Skin Injuries Reduce Survival and Modulate Corticosterone, C-Reactive Protein, Complement Component 3, IgM, and Prostaglandin E2 after Whole-Body Reactor-Produced Mixed Field (n + γ-Photons) Irradiation

Skin injuries such as wounds or burns following whole-body γ-irradiation (radiation combined injury (RCI)) increase mortality more than whole-body γ-irradiation alone. Wound-induced decreases in survival after irradiation are triggered by sustained activation of inducible nitric oxide synthase pathways, persistent alteration of cytokine homeostasis, and increased susceptibility to systemic bacterial infection. Among these factors, radiation-induced increases in interleukin-6 (IL-6) concentrations in serum were amplified by skin wound trauma. Herein, the IL-6-induced stress proteins including C-reactive protein (CRP), complement 3 (C3), immunoglobulin M (IgM), and prostaglandin E2 (PGE2) were evaluated after skin injuries given following a mixed radiation environment that might be found after a nuclear incident. In this report, mice received 3 Gy of reactor-produced mixed field (n + γ-photons) radiations at 0.38 Gy/min followed by nonlethal skin wounding or burning. Both wounds and burns reduced survival and increased CRP, C3, and PGE2 in serum after radiation. Decreased IgM production along with an early rise in corticosterone followed by a subsequent decrease was noted for each RCI situation. These results suggest that RCI-induced alterations of corticosterone, CRP, C3, IgM, and PGE2 cause homeostatic imbalance and may contribute to reduced survival. Agents inhibiting these responses may prove to be therapeutic for RCI and improve related survival.
A classification-based methodology for planning audit strategies in fraud detection

Planning adequate audit strategies is a key success factor in a posterion’ fraud detection, e.g., in the fiscal and insurance domains, where audits are intended to detect tax evasion and fraudulent claims. A case study is presented in this paper, which illustrates how techniques based on classification can be used to support the task of planning audit strategies. The proposed approach is sensible to some conflicting issues of audit planning, e.g., the trade-off between maximizing audit benefits vs. minimizing audit costs. A methodological scenario, common to a whole class of similar applications, is then abstracted away from the case study. The limitations of available systems to support the identified overall KDD process, bring us to point out the key aspects of a logic-based database language, integrated with mining mechanisms, which is used to provide a uniform, highly expressive environment for the various steps in the construction of the considered case-study.
Distributed Maximum Matching in Bounded Degree Graphs

We present deterministic distributed algorithms for computing approximate maximum cardinality matchings and approximate maximum weight matchings. Our algorithm for the unweighted case computes a matching whose size is at least (1−ε) times the optimal in Δ O(1/ε) + O(1/ε2) · log* (n) rounds where n is the number of vertices in the graph and Δ is the maximum degree. Our algorithm for the edge-weighted case computes a matching whose weight is at least (1 − ε) times the optimal in log(min{1/ωmin, n/ε})O(1/ε). (Δ O(1/ε) + log*(n)) rounds for edge-weights in [wmin, 1]. The best previous algorithms for both the unweighted case and the weighted case are by Lotker, Patt-Shamir, and Pettie (SPAA 2008). For the unweighted case they give a randomized (1 − ε)-approximation algorithm that runs in O((log(n))ε3) rounds. For the weighted case they give a randomized (1/2 − ε)-approximation algorithm that runs in O(log(ε−1) · log(n)) rounds. Hence, our results improve on the previous ones when the parameters Δ, ε and wmin are constants (where we reduce the number of runs from O(log(n)) to O(log*(n))), and more generally when Δ, 1/ε and 1/wmin are sufficiently slowly increasing functions of n. Moreover, our algorithms are deterministic rather than randomized.
A Constraint-based Approach to Noun Phrase Coreference Resolution in German Newspaper Text

In this paper, we investigate the usefulness of a wide range of features for their usefulness in the resolution of nominal coreference, both as hard constraints (i.e. completely removing elements from the list of possible candidates) as well as soft constraints (where a cumulation of violations of soft constraints will make it less likely that a candidate is chosen as the antecedent). We present a state of the art system based on such constraints and weights estimated with a maximum entropy model, using lexical information to resolve cases of coreferent bridging.
The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range‐wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well‐supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74–0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal‐ and landscape‐level contexts, providing important insights into the conservation genetics of the California tiger salamander.
Meta-analyses of the association between cytochrome CYP2C19 loss- and gain-of-function polymorphisms and cardiovascular outcomes in patients with coronary artery disease treated with clopidogrel

Aims To perform a meta-analysis of the association between CYP2C19 loss- and gain-of-function variants and cardiovascular outcomes and bleeding in patients with coronary artery disease treated with clopidogrel, and to explore the causes of heterogeneity between studies. Methods A comprehensive literature search was conducted. A random-effects model was used to summarise the results. In the presence of between-study heterogeneity, a meta-regression analysis was performed to identify study characteristics explaining this heterogeneity. Results Patients who carried a loss-of-function allele, mainly CYP2C19*2, did not present an increased risk of a cardiovascular event, HR =1.23 (95% CI 0.97 to 1.55). Substantial heterogeneity was observed between studies (I2 =35.6), which was partially explained by the study sample size: the pooled HR was higher among studies with a sample size <500 patients (HR =3.55; 95% CI 1.66 to 7.56) and lower among studies with a sample size ≥500 (HR =1.06; 95% CI 0.89 to 1.26). CYP2C19*2 was associated with an increased risk of a stent thrombosis (HR =2.24; 95% CI 1.52 to 3.30). The gain-of-function allele, mainly CYP2C19*17, was associated with a lower risk of cardiovascular events (HR =0.75; 95% CI 0.66 to 0.87) and a higher risk of major bleeding (HR =1.26; 95% CI 1.05 to 1.50). Conclusions Not only CYP2C19 loss-of-function but also gain-of-function alleles should be considered to define the pharmacogenetic response to clopidogrel. The results question the relevance of the CYP2C19 loss-of-function alleles in the prediction of major cardiovascular events beyond stent thrombosis in coronary patients treated with clopidogrel. The gain-of-function variant is associated with a lower risk of cardiovascular events but a higher risk of bleeding.
Secondary caries detection by DIAGNOdent and radiography: a comparative in vitro study

DIAGNOdent is now well documented for detection of primary occlusal caries, but not as yet for secondary caries. The aim of this study was to investigate the application of DIAGNOdent for in vitro detection of secondary caries. The material comprised 66 extracted teeth: 48 with amalgam restorations and 18 with tooth‐colored restorations. Digital images of occlusal surfaces were captured for each specimen. The teeth were mounted in groups of 3 or 4 in plaster blocks simulating their anatomical positions. Bitewing radiographs of each block were assessed for secondary caries by 5 observers. The margins of each restoration were carefully scanned with DIAGNOdent; the site of the highest reading was localized in digital images; and the corresponding values were registered. Marginal integrity and staining were also documented. The restorations were then removed and the teeth were hemi‐sectioned. For verification, two observers working together examined all the cavities under a stereomicroscope at 16 x magnification followed by probing. Sensitivity and specificity for DIAGNOdent and conventional radiography were 0.77/0.81 and 0.65/0.81, respectively. Regarding ROC analyses, the A z values were 0.89 and 0.72 for DIAGNOdent and radiography. For DIAGNOdent, the false‐positive fraction included only stained teeth. Cohen's kappa statistics disclosed moderate agreement between the 2 methods, with an agreement of 56%. DIAGNOdent tended to give more positive diagnoses than bitewing radiography. The results indicate that DIAGNOdent may be a helpful tool for detecting secondary caries.