Miracle-dz/UniFAR-FTUs huggingface dataset:
Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad-Spectrum and Strain-Specific Quantitative Trait Loci

Bacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen’s extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) × resistant AG91-25 (R). ERs1 was originally found to control three strains from phylotype I, while being totally ineffective against a virulent strain from the same phylotype. We tested this population against four additional RSSC strains, representing phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of phylotypes I, IIA, III and strains of phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene.
Recent research on aetiology, development and phenomenology of self-injurious behaviour in people with intellectual disabilities: a systematic review and implications for treatment.

BACKGROUND Behavioural interventions conceptualise self-injurious behaviour (SIB) as developing from early repetitive behaviours through acquisition of homeostatic functions in regulating stimulation and subsequent shaping into SIB through socially mediated or automatic operant reinforcement. Despite high success rates, such interventions rarely completely eliminate SIB, and overall effectiveness has not increased since the 1960s. METHODS Research (excluding studies of single genetic syndromes) on the early development, functional properties and phenomenology of SIB in persons with intellectual disabilities (IDs) published from 1999 to 2010 inclusive is reviewed. RESULTS Despite evidence to support the operant shaping hypothesis, in some cases tissue-damaging SIB, especially head-banging, emerges at a similar or younger age than stereotyped behaviours or 'proto-SIB', often associated with tantrums following frustrative non-reward and/or abrupt situational transitions. Many young children show undifferentiated patterns of responding in functional analyses of SIB, and SIB is associated with aggression and impulsivity as well as with repetitive behaviour. CONCLUSIONS One dynamic in the development of SIB may be Pavlovian conditioning of aggression, originally elicited by aversive events or frustrative non-reward, to stimuli associated with such situations. Integration into operant technology of interventions based on Pavlovian principles such as graduated exposure (with or without counterconditioning) to aversive stimuli may enhance the effectiveness of behavioural interventions.
Radius-Margin Bound on the Leave-One-Out Error of the LLW-M-SVM

To set the values of the hyperparameters of a support vector machine (SVM), one can use cross-validation. Its leave-one-out variant produces an estimator of the generalization error which is almost unbiased. Its major drawback rests in its time requirement. To overcome this difficulty, several upper bounds on the leave-one-out error of the pattern recognition SVM have been derived. The most popular one is the radius-margin bound. In this article, we introduce a generalized radius-margin bound dedicated to the multi-class SVM of Lee, Lin and Wahba.
Tonoplast Intrinsic Protein Isoforms as Markers for Vacuolar Functions

Plant cell vacuoles may have storage or lytic functions, but biochemical markers specific for the tonoplasts of functionally distinct vacuoles are poorly defined. Here, we use antipeptide antibodies specific for the tonoplast intrinsic proteins α-TIP, γ-TIP, and δ-TIP in confocal immunofluorescence experiments to test the hypothesis that different TIP isoforms may define different vacuole functions. Organelles labeled with these antibodies were also labeled with antipyrophosphatase antibodies, demonstrating that regardless of their size, they had the expected characteristics of vacuoles. Our results demonstrate that the storage vacuole tonoplast contains δ-TIP, protein storage vacuoles containing seed-type storage proteins are marked by α- and δ- or α- and δ-plus γ-TIP, whereas vacuoles storing vegetative storage proteins and pigments are marked by δ-TIP alone or δ-plus γ-TIP. In contrast, those marked by γ-TIP alone have characteristics of lytic vacuoles, and results from other researchers indicate that α-TIP alone is a marker for autophagic vacuoles. In root tips, relatively undifferentiated cells that contain vacuoles labeled separately for each of the three TIPs have been identified. These results argue that plant cells have the ability to generate and maintain three separate vacuole organelles, with each being marked by a different TIP, and that the functional diversity of the vacuolar system may be generated from different combinations of the three basic types.
General considerations for skin test procedures in the diagnosis of drug hypersensitivity

K. Brockow, A. Romano, M. Blanca, J. Ring, W. Pichler, P. Demoly Klinik und Poliklinik fur Dermatologie und Allergologie, Muenchen, Germany; Department of Internal Medicine and Geriatrics, UCSC, Allergy Unit, CI Columbus, Rome and IRCS Oasi Maria SS, Troina, Italy; Research Unit for Allergic Diseases, Carlos Haya Hospital, Malaga, Spain; Clinic for Rheumatology and Clinical Immunology/Allergology, Inselspital, Bern, Switzerland; Maladies Respiratoires, Hopital Arnaud de Villeneuve, Montpellier, France
Small-space encoding LCE data structure with constant-time queries

The \emph{longest common extension} (\emph{LCE}) problem is to preprocess a given string $w$ of length $n$ so that the length of the longest common prefix between suffixes of $w$ that start at any two given positions is answered quickly. In this paper, we present a data structure of $O(z \tau^2 + \frac{n}{\tau})$ words of space which answers LCE queries in $O(1)$ time and can be built in $O(n \log \sigma)$ time, where $1 \leq \tau \leq \sqrt{n}$ is a parameter, $z$ is the size of the Lempel-Ziv 77 factorization of $w$ and $\sigma$ is the alphabet size. This is an \emph{encoding} data structure, i.e., it does not access the input string $w$ when answering queries and thus $w$ can be deleted after preprocessing. On top of this main result, we obtain further results using (variants of) our LCE data structure, which include the following: - For highly repetitive strings where the $z\tau^2$ term is dominated by $\frac{n}{\tau}$, we obtain a \emph{constant-time and sub-linear space} LCE query data structure. - Even when the input string is not well compressible via Lempel-Ziv 77 factorization, we still can obtain a \emph{constant-time and sub-linear space} LCE data structure for suitable $\tau$ and for $\sigma \leq 2^{o(\log n)}$. - The time-space trade-off lower bounds for the LCE problem by Bille et al. [J. Discrete Algorithms, 25:42-50, 2014] and by Kosolobov [CoRR, abs/1611.02891, 2016] can be "surpassed" in some cases with our LCE data structure.
Stability Properties of the Perona-Malik Scheme

The Perona--Malik scheme is a numerical technique for denoising digital images without blurring object boundaries (edges). In general, solutions generated by this scheme do not satisfy a comparison principle. We identify conditions under which two solutions initially ordered remain ordered, and we state (restricted) comparison principles. These allow us to study stability properties of the scheme. We also explore what these results say in the limit as the discretization size goes to 0.
Behavioral flexibility impairment with negative feedback in refractory temporal lobe epileptic patients with unilateral amygdala and hippocampal resection.

INTRODUCTION Patients with amygdala dysfunction generally have behavioral impairment. Temporal lobe surgery might be a model of study of unilateral amygdala resection. The objective of this study was to evaluate behavioral flexibility in epileptic patients who undergo amygdala resection for epilepsy surgery and evaluate its relationship with their neuropsychiatric symptoms. MATERIAL AND METHODS Ten epileptic patients who underwent amygdala and hippocampal resection (6 left and 4 right) matched by age and educational level with 10 healthy controls were tested with an extensive neuropsychological and neuropsychiatric battery. Psychiatric symptomatology was measured with the positive and negative syndrome scale (PANSS) and the Beck depression inventory. To assess behavioral flexibility the emotion-related visual reversal-learning task (O'Doherty et al., 2001) and the gambling task (Bechara et al., 1994) were used. RESULTS Patient's mean scores were: Beck: 8 +/- 1.5; PANSS positive: 10 +/- 1.3, and negative: 14.4 +/- 2.2; intellectual quotient (IQ): 101.4 +/- 6.3; category number in Wisconsin card sorting test: 4.6 +/- 2.4. The emotion-related visual reversal-learning task showed significance differences in the number of reversion: healthy controls: 9.3; epileptic patients: 4.23 (p < 0.001); in the number of trials to the first reversion: healthy controls: 5; epileptic patients: 23.42 (p < 0.05). There was no correlation between reversion and depression, PANSS and IQ. CONCLUSIONS Patients with epilepsy who undergo unilateral hippocampal and amygdala resection appear to have alterations in the reversion capacity with an emotional component that would explain the lack of behavior flexibility that they sometimes have and that are not related with either the isolated presence of executive alterations or low intellectual quotient.
Rapid phase advance of the 24-h melatonin profile in response to afternoon dark exposure.

To investigate the adaptation of melatonin secretion to an abrupt time shift and the effects of sleep facilitation with a hypnotic, eight subjects were submitted to an 8-h advance shift achieved by advancing bedtimes from 2300-0700 to 1500-2300. Each subject participated in two studies (i.e., placebo and zolpidem). Each study included a baseline period with dim light during waking hours and 2300-0700 bedtimes in total darkness. Blood samples for determination of plasma melatonin were obtained at 20-min intervals for 68 h. Advanced exposure to sleep and darkness resulted in a nearly 2-h advance of melatonin onset, which appeared within 6 h after lights-out during the first shifted night, and an almost 1-h advance of the melatonin offset. No further adaptation occurred during the second shifted sleep period. Zolpidem had no beneficial effects on the adaptation of the melatonin profile. There was no relationship between sleep parameters and the magnitude of the melatonin shifts. Thus the overall advance of melatonin profiles was primarily achieved during the initial exposure to an 8-h period of darkness. The present data suggest that exposure to dark affects human circadian phase.
Predictable Markets? A News-Driven Model of the Stock Market

We attempt to explain stock market dynamics in terms of the interaction among three variables: market price, investor opinion and information flow. We propose a framework for such interaction and apply it to build a model of stock market dynamics which we study both empirically and theoretically. We demonstrate that this model replicates observed market behavior on all relevant timescales (from days to years) reasonably well. Using the model, we obtain and discuss a number of results that pose implications for current market theory and offer potential practical applications.
Dietary proteins improve endothelial function under fasting conditions but not in the postprandial state, with no effects on markers of low-grade inflammation

Abstract Endothelial dysfunction (ED) and low-grade inflammation (LGI) have a role in the development of CVD. The two studies reported here explored the effects of dietary proteins and carbohydrates on markers of ED and LGI in overweight/obese individuals with untreated elevated blood pressure. In the first study, fifty-two participants consumed a protein mix or maltodextrin (3×20 g/d) for 4 weeks. Fasting levels and 12 h postprandial responses of markers of ED (soluble intercellular adhesion molecule 1 (sICAM), soluble vascular cell adhesion molecule 1 (sVCAM), soluble endothelial selectin and von Willebrand factor) and markers of LGI (serum amyloid A, C-reactive protein and sICAM) were evaluated before and after intervention. Biomarkers were also combined into mean Z-scores of ED and LGI. The second study compared 4 h postprandial responses of ED and LGI markers in forty-eight participants after ingestion of 0·6 g/kg pea protein, milk protein and egg-white protein. In addition, postprandial responses after maltodextrin intake were compared with a protein mix and sucrose. The first study showed significantly lower fasting ED Z-scores and sICAM after 4 weeks on the high-protein diet (P≤0·02). The postprandial studies found no clear differences of ED and LGI between test meals. However, postprandial sVCAM decreased more after the protein mix compared with maltodextrin in both studies (P≤0·04). In conclusion, dietary protein is beneficial for fasting ED, but not for fasting LGI, after 4 weeks of supplementation. On the basis of Z-scores, postprandial ED and LGI were not differentially affected by protein sources or carbohydrates.
Statistical evaluation of alternative models of human evolution

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species ≈141 thousand years ago (Kya), an exit out-of-Africa ≈51 Kya, and a recent colonization of the Americas ≈10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.
3‐D Modeling of Irregular Volcanic Sources Using Sparsity‐Promoting Inversions of Geodetic Data and Boundary Element Method

Geodetic observations of surface deformation associated with volcanic activities can be used to constrain volcanic source parameters and their kinematics. Simple analytical models, such as point and spherical sources, are widely used to model deformation data. The inherent nature of oversimplified model geometries makes them unable to explain fine details of surface deformation. Current nonparametric, geometry‐free inversion approaches resolve the distributed volume change, assuming it varies smoothly in space, which may detect artificial volume change outside magmatic source regions. To obtain a physically meaningful representation of an irregular volcanic source, we devise a new sparsity‐promoting modeling scheme assuming active magma bodies are well‐localized melt accumulations, namely, outliers in the background crust. First, surface deformation data are inverted using a hybrid L1‐ and L2‐norm regularization scheme to solve for sparse volume change distributions. Next, a boundary element method is implemented to solve for the displacement discontinuity distribution of the reservoir, which satisfies a uniform pressure boundary condition. The inversion approach is thoroughly validated using benchmark and synthetic tests, of which the results show that source dimension, depth, and shape can be recovered appropriately. We apply this modeling scheme to deformation observed at Kilauea summit for periods of uplift and subsidence leading to and following the 2007 Father's Day event. We find that the magmatic source geometries for these periods are statistically distinct, which may be an indicator that magma is released from isolated compartments due to large differential pressure leading to the rift intrusion.
Sugar-sweetened beverage intake and cardiovascular risk factor profile in youth with type 1 diabetes: application of measurement error methodology in the SEARCH Nutrition Ancillary Study

The SEARCH Nutrition Ancillary Study aims to investigate the role of dietary intake on the development of long-term complications of type 1 diabetes in youth, and capitalise on measurement error (ME) adjustment methodology. Using the National Cancer Institute (NCI) method for episodically consumed foods, we evaluated the relationship between sugar-sweetened beverage (SSB) intake and cardiovascular risk factor profile, with the application of ME adjustment methodology. The calibration sample included 166 youth with two FFQ and three 24 h dietary recall data within 1 month. The full sample included 2286 youth with type 1 diabetes. SSB intake was significantly associated with higher TAG, total and LDL-cholesterol concentrations, after adjusting for energy, age, diabetes duration, race/ethnicity, sex and education. The estimated effect size was larger (model coefficients increased approximately 3-fold) after the application of the NCI method than without adjustment for ME. Compared with individuals consuming one serving of SSB every 2 weeks, those who consumed one serving of SSB every 2 d had 3·7 mg/dl (0·04 mmol/l) higher TAG concentrations and 4·0 mg/dl (0·10 mmol/l) higher total cholesterol and LDL-cholesterol concentrations, after adjusting for ME and covariates. SSB intake was not associated with measures of adiposity and blood pressure. Our findings suggest that SSB intake is significantly related to increased lipid levels in youth with type 1 diabetes, and that estimates of the effect size of SSB on lipid levels are severely attenuated in the presence of ME. Future studies in youth with diabetes should consider a design that will allow for the adjustment for ME when studying the influence of diet on health status.
Using preoperative UFT to predict sensitivity to fluoropyrimidines in colorectal cancer.

This study was designed to determine if histopathologic evaluation of patients with resectable colorectal cancer following preoperative chemotherapy with uracil and tegafur with a molar ratio of 4:1 (UFT) could predict chemosensitivity to postoperative fluoropyrimidines to prevent recurrence of disease. In this prospective randomized study involving 152 colorectal cancer patients, UFT 600 mg/day was administered for 10 days prior to surgery. Histopathology of the resected tumor was assessed, including the amount of necrosis or disappearance of tumor, and patients were thereafter stratified into two groups according to tumor response to preoperative therapy--grade > or = 2 (sensitive) vs those with grade < or = 1B (not sensitive). The patients were then randomly assigned to postoperative adjuvant UFT (400 mg/day for 12 months) or no treatment. At the time of this evaluation, the mean total preoperative UFT dose per patient was 7.76 g +/- 3.27 g. Thirteen patients were considered ineligible; therefore, 139 patients were included in the analysis. Stratification resulted in 22 (15.8%) cases in the sensitive group, of which 13 received adjuvant chemotherapy and nine were assigned to no treatment; 117 (84.2%) patients were considered nonsensitive, 60 of whom received adjuvant chemotherapy, and 57 of whom received no adjuvant therapy. Among nonsensitive patients, 3-year survival rates were 87.6% with adjuvant chemotherapy and 84.9% with no therapy, indicating no significant difference between groups. Among responders, however, there was a significant difference in 3-year survival rates: 100% for the adjuvant group and 62.5% for the no-treatment group (P = .0351). These findings suggest that histopathologic assessment following preoperative UFT chemotherapy provides information to predict fluoropyrimidine sensitivity. We believe grade 1B patients (19.8%) may respond to modulated fluorouracil. We also recommend the use of other drugs, such as irinotecan (CPT-11 [Camptosar]) and oxaliplatin, for patients with tumor responses of grades 0 and 1A.
Fracture behavior and mechanical characterization of a composite orthopedic use in the two direction of flow molding

A standard tensile test was carried out on prismatic specimens of glass-perlon reinforced acrylic resin laminate composite material of orthopedic use, developed by the National Office Equipments and Accessories for People with Disabilities, ONAAPH Annaba (Algeria). The measurement results of the Young's modulus and the fracture strength show a large scatter characteristic of these materials and are influenced by the cutting direction of the samples compared to the direction of molding. The use of the probabilistic two parameters Weibull's model made it possible to characterize brittleness and the fracture behavior of these materials and quantitatively to describe the probabilistic aspect of the latter. A report of the principal mechanisms responsible of the fracture is drawed up according to microscopic observations of the fracture topographies of the broken samples.