Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture

Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.
Hierarchically Distributed Peer-to-Peer Document Clustering and Cluster Summarization

In distributed data mining, adopting a flat node distribution model can affect scalability. To address the problem of modularity, flexibility and scalability, we propose a Hierarchically-distributed Peer-to-Peer (HP2PC) architecture and clustering algorithm. The architecture is based on a multi-layer overlay network of peer neighborhoods. Supernodes, which act as representatives of neighborhoods, are recursively grouped to form higher level neighborhoods. Within a certain level of the hierarchy, peers cooperate within their respective neighborhoods to perform P2P clustering. Using this model, we can partition the clustering problem in a modular way across neighborhoods, solve each part individually using a distributed K-means variant, then successively combine clusterings up the hierarchy where increasingly more global solutions are computed. In addition, for document clustering applications, we summarize the distributed document clusters using a distributed keyphrase extraction algorithm, thus providing interpretation of the clusters. Results show decent speedup, reaching 165 times faster than centralized clustering for a 250-node simulated network, with comparable clustering quality to the centralized approach. We also provide comparison to the P2P K-means algorithm and show that HP2PC accuracy is better for typical hierarchy heights. Results for distributed cluster summarization match those of their centralized counterparts with up to 88% accuracy.
The Contribution of Early Traumatic Events to Schizophrenia in Some Patients: A Traumagenic Neurodevelopmental Model

Abstract The current diathesis-stress model of schizophrenia proposes that a genetic deficit creates a predisposing vulnerability in the form of oversenstivity to stress. This model positions all psychosocial events on the stress side of the diathesis-stress equation. As an example of hypotheses that emerge when consideration is given to repositioning adverse life events as potential contributors to the diathesis, this article examines one possible explanation for the high prevalence of child abuse found in adults diagnosed schizophrenic. A traumagenic neurodevelopmental (TN) model of schizophrenia is presented, documenting the similarities between the effects of traumatic events on the developing brain and the biological abnormalities found in persons diagnosed with schizophrenia, including overreactivity of the hypothalamic-pituitary-adrenal (HPA) axis; dopamine, norepinephrine, and serotonin abnormalities; and structural changes to the brain such as hippocampal damage, cerebral atrophy, ventricular enlargement, and reversed cerebral asymmetry. The TN model offers potential explanations for other findings in schizophrenia research beyond oversensitivity to stress, including cognitive impairment, pathways to positive and negative symptoms, and the relationship between psychotic and dissociative symptomatology. It is recommended that clinicians and researchers explore the presence of early adverse life events in adults with psychotic symptoms in order to ensure comprehensive formulations and appropriate treatment plans, and to further investigate the hypotheses generated by the TN model.
Cost-Benefit Analysis and the Environment: Recent Developments

Environmental protection is now an integral part of public policies, at local, national and global levels. In all instances, the cost and benefits of policies and projects must be carefully weighed using a common monetary measuring rod. Yet, many different categories of benefits and cost must be evaluated, such as health impacts, property damage, ecosystem losses and other welfare effects. Furthermore, many of these benefits or damages occur over the long term, sometimes over several generations, or are irreversible (e.g. global warming, biodiversity losses). How can we evaluate these elements and give them a monetary value? How should we take into account impacts on future generations and of irreversible losses? How to deal with equity and sustainability issues? This book presents an in-depth assessment of the most recent conceptual and methodological developments in this area. It should provide a valuable reference and tool for environmental economists and policy analysts.
Intracranial arterial variations: A comprehensive evaluation using CT angiography

Background Intracranial arterial variations are a frequent finding in the general population. Knowledge of these vascular variations has significant clinical impact because some of them predispose patients to development of an aneurysm or cerebrovascular ischemic disease. The purpose of this study was to evaluate the frequency of intracranial vascular variations and associated vascular lesions on computed tomography angiography (CTA) examinations. Material/Methods CTA examinations performed by 16-detector computed tomography were prospectively reviewed in 455 patients for the presence of fenestrations, duplications, hypoplasia, aplasia, aneurysms, and other vascular lesions. Results Arterial fenestrations were found in 2.4% of patients, with the vertebrobasilar system as the most common location. The remaining fenestrations were located on the middle cerebral artery M1 segment (0.2%), anterior communicating artery (0.4%), and anterior cerebral artery A1 segment (0.6%). No associated aneurysms were noted in these patients. The prevalence of an azygos anterior cerebral artery was 1.5%. Bihemispheric anterior cerebral artery was found in 0.9%, hypoplastic A1 segment in 17.6%, and congenital absence of A1 segment in 0.4% of patients. Fetal origin of the posterior cerebral artery was found in 37% of cases. Hypoplastic vertebral artery terminating as posterior inferior cerebellar artery was observed in 9 patients, while transversal anastomosis between vertebral arteries was seen in only 1 patient. Conclusions CTA precisely demonstrates the diversity of intracranial arterial variations, whose overall frequency in this study is similar to previous radiological reports. Furthermore, our results do not show significant association between the frequency of aneurysms and cerebral arterial anomalies.
Plasma adrenomedullin during acute changes in intravascular volume in hemodialysis patients.

BACKGROUND Adrenomedullin, is a potent vasorelaxant that is highly expressed in the adrenal medulla, kidney, heart and lung. Since there is indirect evidence that hypervolemia enhances the release of this peptide, we measured plasma adrenomedullin in 9 uremic patients on chronic dialysis treatment and in 10 healthy subjects matched for age and gender. METHODS Measurements were performed in baseline conditions, after isotonic fluid subtraction (by isolated ultrafiltration) and during a 70 degrees tilt. Tilt was performed in volume-depleted state, that is, after isolated ultrafiltration (UF). In the control experiment patients underwent sham UF (UF = 0) followed by a period of supine resting identical to the one they had spent in tilted position in the active experiment. Adrenomedullin was measured on pre-extracted plasma samples (Sep-Pak C-18 cartridges) by a specific RIA for human adrenomedullin 1-52. RESULTS The average plasma adrenomedullin was 2.6 times higher (P < 0.01) in uremic patients (103 +/- 8 pg/ml) than in healthy subjects (39 +/- 7 pg/ml). After fluid subtraction (-2.6 +/- 0.2 liter) adrenomedullin fell to 79. +/- 8 pg/ml (P = 0.02) but remained well above the upper limit of the 95% CI in normal subjects (52 pg/ml). There was no relationship between adrenomedullin and ANF changes. In the control experiment sham UF did not modify plasma adrenomedullin. Tilt did not significantly change plasma adrenomedullin either in dialysis patients or healthy subjects. CONCLUSIONS Plasma adrenomedullin is markedly raised in uremic patients on dialysis, which confirms that the kidney has a major role in the clearance of this peptide. However, the fall in plasma adrenomedullin after isolated UF indicates that the plasma concentration of this peptide is influenced by the body fluid volume status. Whether or not adrenomedullin participates in the counter-regulatory response to fluid subtraction in uremic patients remains to be explored by specific antagonists of this substance.
Plasticity in epithelial cell phenotype: modulation by expression of different cadherin cell adhesion molecules

A primary function of cadherins is to regulate cell adhesion. Here, we demonstrate a broader function of cadherins in the differentiation of specialized epithelial cell phenotypes. In situ, the rat retinal pigment epithelium (RPE) forms cell-cell contacts within its monolayer, and at the apical membrane with the neural retina; Na+, K(+)-ATPase and the membrane cytoskeleton are restricted to the apical membrane. In vitro, RPE cells (RPE-J cell line) express an endogenous cadherin, form adherens junctions and a tight monolayer, but Na+,K(+)-ATPase is localized to both apical and basal-lateral membranes. Expression of E- cadherin in RPE-J cells results in restriction and accumulation of both Na+,K(+)-ATPase and the membrane cytoskeleton at the lateral membrane; these changes correlate with the synthesis of a different ankyrin isoform. In contrast to both RPE in situ and RPE-J cells that do not form desmosomes, E-cadherin expression in RPE-J cells induces accumulation of desmoglein mRNA, and assembly of desmosome-keratin complexes at cell-cell contacts. These results demonstrate that cadherins directly affect epithelial cell phenotype by remodeling the distributions of constitutively expressed proteins and by induced accumulation of specific proteins, which together lead to the generation of structurally and functionally distinct epithelial cell types.
Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X

The prevalence of obesity (body mass index (BMI) ≥30 kg/m2) is higher in African Americans than in European Americans, even after adjustment for socioeconomic factors, suggesting that genetic factors may explain some of the difference. To identify genetic loci influencing BMI, we carried out a pooled analysis of genome-wide admixture mapping scans in 15,280 African Americans from 14 epidemiologic studies. Samples were genotyped at a median of 1,411 ancestry-informative markers. After adjusting for age, sex, and study, BMI was analyzed both as a dichotomized (top 20% versus bottom 20%) and a continuous trait. We found that a higher percentage of European ancestry was significantly correlated with lower BMI (ρ = −0.042, P = 1.6×10−7). In the dichotomized analysis, we detected two loci on chromosome X as associated with increased African ancestry: the first at Xq25 (locus-specific LOD = 5.94; genome-wide score = 3.22; case-control Z = −3.94); and the second at Xq13.1 (locus-specific LOD = 2.22; case-control Z = −4.62). Quantitative analysis identified a third locus at 5q13.3 where higher BMI was highly significantly associated with greater European ancestry (locus-specific LOD = 6.27; genome-wide score = 3.46). Further mapping studies with dense sets of markers will be necessary to identify the alleles in these regions of chromosomes X and 5 that may be associated with variation in BMI.
The Construction of cubature rules for multivariate highly oscillatory integrals

We present an efficient approach to evaluate multivariate highly oscillatory integrals on piecewise analytic integration domains. Cubature rules are developed that only require the evaluation of the integrand and its derivatives in a limited set of points. A general method is presented to identify these points and to compute the weights of the corresponding rule. The accuracy of the constructed rules increases with increasing frequency of the integrand. For a fixed frequency, the accuracy can be improved by incorporating more derivatives of the integrand. The results are illustrated numerically for Fourier integrals on a circle and on the unit sphere, and for more general oscillators on a rectangular domain.
Twenty-Seven Years Experience With Transvenous Pacemaker Implantation in Children Weighing <10 kg

Background—Epicardial pacemaker implantation is the favored approach in children weighing <10 kg in many units. The high incidence of premature failure and fractures with earlier epicardial leads led our unit to undertake transvenous pacemaker implantation in neonates and infants from 1987. To date there have been no long-term follow-up reports of what is for many a controversial strategy. Methods and Results—Between 1987 and 2003, 37 neonates and infants—median age 6.7 months (1 day to 3 years) and median weight 4.6 kg (2.7–10 kg)—had a permanent transvenous pacing system implanted. Pacing leads were placed into the right ventricular apex/outflow tract through a subclavian vein puncture with a redundant loop in the atrium. Three patients were lost to follow-up, 4 patients died from complications of cardiac surgery, and 2 patients had their system removed. At long-term follow-up in 28 patients at a median of 17.2 (range, 11.2–27.4) years, 10 patients have a single chamber ventricular pacemaker, 14 a dual chamber pacemaker, 3 a biventricular pacemaker, and 1 has a single chamber implantable cardioverter defibrillator. Subclavian vein patency was assessed in 26 patients. The overall subclavian vein occlusion rate was 10 of 13 (77%) <5 kg and 2 of 13 (15%) >5 kg during long-term follow-up. After a median of 14.3 (range, 13.4–17.6) years of pacing, 7 patients continue with their original lead. Conclusions—Transvenous pacing in infants <10 kg results in encouraging short- and long-term clinical outcomes. Subclavian vein occlusion remains an important complication, occurring predominantly in those weighing <5 kg.
Investigation of multiphase fluid imbibition in shale through synchrotron‐based dynamic micro‐CT imaging

While substantial advances were made in pore system characterization in shale in the past decade, understanding of fundamentals of multiphase fluid flow in shale remains limited. The complexity of multiphase fluid flow in shale is related to many factors including nanoscale to submicron‐scale pore systems, differences in mineralogy and associated surface wettability, heterogeneity of these properties at different scales, and possible existence of microfractures. Previous work related to fluid flow, such as permeability measurement, spontaneous imbibition, and wettability analysis, includes many simplified assumptions/hypotheses with limited consideration of small‐scale details. In addition, these studies were mostly focused on single‐phase phenomena. Direct observation of multiphase fluid flow in shale showing small‐scale details is highly desired. In this study, dynamic imaging using synchrotron‐based micro‐CT (computed microtomography) was conducted on two shale samples to investigate multiphase (oil and water) spontaneous imbibition. The results revealed many details of multiphase flow in shale, including pore connectivity, porosity and permeability layered distribution, and wettability of microfractures and pores. At the same time, results illustrate the complexity of multiphase flow in shale and gaps in understanding that need further investigation.
Ultrasound Stimulation Attenuates CRS-Induced Depressive Behavior by Modulating Dopamine Release in the Prefrontal Cortex

Depression is one of the most serious mental disorders affecting modern human life and is often caused by chronic stress. Dopamine system dysfunction is proposed to contribute to the pathophysiology of chronic stress, especially the ventral tegmental area (VTA) which mainly consists of dopaminergic neurons. Focused ultrasound stimulation (FUS) is a promising neuromodulation modality and multiple studies have demonstrated effective ultrasonic activation of cortical, subcortical, and related networks. However, the effects of FUS on the dopamine system and the potential link to chronic stress-induced depressive behaviors are relatively unknown. Here, we measured the effects of FUS targeting VTA on the improvement of depression-like behavior and evaluated the dopamine concentration in the downstream region - medial prefrontal cortex (mPFC). We found that targeting VTA FUS treatment alleviated chronic restraint stress (CRS) -induced anhedonia and despair behavior. Using an in vivo photometry approach, we analyzed the dopamine signal of mPFC and revealed a significant increase following the FUS, positively associated with the improvement of anhedonia behavior. FUS also protected the dopaminergic neurons in VTA from the damage caused by CRS exposure. Thus, these results demonstrated that targeting VTA FUS treatment significantly rescued the depressive-like behavior and declined dopamine level of mPFC induced by CRS. These beneficial effects of FUS might be due to protection in the DA neuron of VTA. Our findings suggest that FUS treatment could serve as a new therapeutic strategy for the treatment of stress-related disorders.
The dexamethasone suppression test and suicide prediction.

OBJECTIVE Despite the substantial risks of eventual suicide associated with major depressive disorder, clinicians lack robust predictors with which to quantify these risks. This study compared the validity of demographic and historical risk factors with that of the dexamethasone suppression test (DST), a clinically practical measure of hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis. METHOD Seventy-eight inpatients with Research Diagnostic Criteria major depressive disorder or schizoaffective disorder, depressed type, entered a long-term follow-up study between 1978 and 1981, and, in addition, underwent a 1-mg DST. The number of suicides in this group during a 15-year follow-up period was determined, and the predictive validity of four demographic and historical risk factors reported in the literature to be consistently predictive of suicide in depressed patients was compared to the predictive validity of the DST results. RESULTS Thirty-two of the 78 patients had abnormal DST results. Survival analyses showed that the estimated risk for eventual suicide in this group was 26.8%, compared to only 2.9% among patients who had normal DST results. None of the demographic and historical risk factors examined in the study significantly distinguished those who later committed suicide from those who did not. CONCLUSIONS In efforts to predict and prevent suicidal behavior in patients with major depressive disorder, HPA-axis hyperactivity, as reflected in DST results, may provide a tool that is considerably more powerful than the clinical predictors currently in use. Research on the pathophysiology of suicidal behavior in major depressive disorder should emphasize the HPA axis and its interplay with the serotonin system.
Prediction of response to salvage radiation therapy in patients with prostate cancer recurrence after radical prostatectomy.

PURPOSE To identify factors predictive of local recurrence as defined by a complete response to salvage radiation therapy in patients whose disease recurs after radical prostatectomy. PATIENTS AND METHODS Ninety-five patients with recurrence after radical prostatectomy who were evaluated by prostatic fossa biopsies, and a subset of 49 of these patients treated with radiation for control of presumed or biopsy-proven local recurrence, were studied. RESULTS Biopsies were positive in 40 (42%) of the 95 biopsied patients. Multivariate analysis revealed that prebiopsy prostate-specific antigen (PSA) level, postrecurrence PSA doubling time, and positive digital rectal examination (DRE) of the prostatic fossa were all statistically significant predictors of a positive biopsy. For the 49 patients subsequently treated with salvage radiation therapy, the overall actuarial 3- and 5-year PSA relapse-free probabilities were 43% and 24%, respectively. Univariate analysis showed no differences in the PSA relapse-free probabilities associated with any pathologic features of the radical prostatectomy specimen, biopsy confirmation of local recurrence, or DRE of the prostatic fossa. In multivariate analysis, controlling for all other variables, preradiation PSA and postrecurrence PSA doubling time measured before radiation were the only statistically significant predictors of outcome. CONCLUSION DRE of the prostatic fossa, prebiopsy PSA, and postrecurrence PSA doubling time predict which patients will have biopsy-proven local recurrence. However, response to salvage radiation therapy is associated with postrecurrence PSA doubling time and with preradiation PSA level only. DRE of the prostatic fossa and biopsy confirmation of local recurrence are not associated with salvage radiation outcome.
Data-Defined Kernels for Parse Reranking Derived from Probabilistic Models

Previous research applying kernel methods to natural language parsing have focussed on proposing kernels over parse trees, which are hand-crafted based on domain knowledge and computational considerations. In this paper we propose a method for defining kernels in terms of a probabilistic model of parsing. This model is then trained, so that the parameters of the probabilistic model reflect the generalizations in the training data. The method we propose then uses these trained parameters to define a kernel for reranking parse trees. In experiments, we use a neural network based statistical parser as the probabilistic model, and use the resulting kernel with the Voted Perceptron algorithm to rerank the top 20 parses from the probabilistic model. This method achieves a significant improvement over the accuracy of the probabilistic model.