Miracle-dz/UniFAR-FTUs huggingface dataset:
Auditing the multiply-related concepts within the UMLS.

OBJECTIVE This work focuses on multiply-related Unified Medical Language System (UMLS) concepts, that is, concepts associated through multiple relations. The relations involved in such situations are audited to determine whether they are provided by source vocabularies or result from the integration of these vocabularies within the UMLS. METHODS We study the compatibility of the multiple relations which associate the concepts under investigation and try to explain the reason why they co-occur. Towards this end, we analyze the relations both at the concept and term levels. In addition, we randomly select 288 concepts associated through contradictory relations and manually analyze them. RESULTS At the UMLS scale, only 0.7% of combinations of relations are contradictory, while homogeneous combinations are observed in one-third of situations. At the scale of source vocabularies, one-third do not contain more than one relation between the concepts under investigation. Among the remaining source vocabularies, seven of them mainly present multiple non-homogeneous relations between terms. Analysis at the term level also shows that only in a quarter of cases are the source vocabularies responsible for the presence of multiply-related concepts in the UMLS. These results are available at: http://www.isped. u-bordeaux2.fr/ArticleJAMIA/results_multiply_related_concepts. aspx. DISCUSSION Manual analysis was useful to explain the conceptualization difference in relations between terms across source vocabularies. The exploitation of source relations was helpful for understanding why some source vocabularies describe multiple relations between a given pair of terms.
L-SHAPED LINEAR PROGRAMS WITH APPLICATIONS TO OPTIMAL CONTROL AND STOCHASTIC PROGRAMMING.

This paper gives an algorithm for L-shaped linear programs which arise naturally in optimal control problems with state constraints and stochastic linear programs (which can be represented in this form with an infinite number of linear constraints). The first section describes a cutting hyperplane algorithm which is shown to be equivalent to a partial decomposition algorithm of the dual program. The two last sections are devoted to applications of the cutting hyperplane algorithm to a linear optimal control problem and stochastic programming problems.
Uptake, Release, and Metabolism of Citrate in Neurons and Astrocytes in Primary Cultures

Abstract: Synthesis, uptake, release, and oxidative metabolism of citrate were investigated in neurons and astrocytes cultured from cerebral cortex or cerebellum. In addition, the possible role of citrate as a donor of the carbon skeleton for biosynthesis of neurotransmitter glutamate was studied. All cell types expressed the enzyme citrate synthase at a high activity, the cerebellar granule neurons containing the enzyme at a higher activity than that found in the astrocytes from the two brain regions or the cortical neurons. Saturable citrate uptake could not be detected in any of the cell types, but the astrocytes, and, in particular, those of cerebellar origin, had a very active de novo synthesis and release of citrate (∼70 nmol × h−1× mg of protein−1). The rate of release of citrate from neurons was <5% of this value. Using [14C]citrate it could be shown that citrate was oxidatively metabolized to 14CO2 at a modest rate (∼1 nmol × n−1× mg−1 of protein) with slightly higher rates in astrocytes compared with neurons. Experiments designed to investigate the ability of exogenously supplied citrate to serve as a precursor for synthesis of transmitter glutamate in cerebellar granule neurons failed to demonstrate this. Rather than citrate serving this purpose it may be suggested that astrocytically released citrate may regulate the extracellular concentration of Ca2+ and Mg2+ by chelation, thereby modulating neuronal excitability.
T-DNA-genome junctions form early after infection and are influenced by the chromatin state of the host genome

Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected. Analysis of the epigenetic landscape of previously isolated sites of T-DNA integration in Kanamycin-selected transgenic plants showed an association with extremely low methylation and nucleosome occupancy. Conversely, non-selected junctions from this study showed no correlation with methylation and had chromatin marks, such as high nucleosome occupancy and high H3K27me3, that correspond to three-dimensional-interacting heterochromatin islands embedded within euchromatin. Such structures may play a role in capturing and silencing invading T-DNA.
Photonic band gap structures for ITU-T G 694.1 systems

The range of the structural parameter values required to design the optical devices for ITU-T G 694.1 Dense Wavelength Division Multiplexing (DWDM) systems are numerically examined over the wavelength range of DWDM from 1470 nm to 1610 nm. The Photonic Band Gap structure is employed to know the required values. Further, the change in PBG in accordance with radius of the rod, lattice constant or period, refractive index difference, total number of rods used in the structure and arrangement of rods or phipattern are investigated through simulation. The Bandsolve simulator of Rsoft is utilized to calculate PBG which is derived using Plane Wave Expansion (PWE) method.
Experimental periodontitis induced by Porphyromonas gingivalis does not alter the onset or severity of diabetes in mice.

BACKGROUND AND OBJECTIVE Diabetes mellitus is believed to increase the risk and severity of periodontitis. However, less evidence is available on the converse effects of periodontitis on diabetes. The objective of the study was to investigate to what degree experimental periodontitis induced by Porphyromonas gingivalis might influence the onset and severity of diabetes in different mouse models. MATERIAL AND METHODS Twenty-eight male Tallyho/JngJ mice (type 2 diabetes), 20 male streptozotocin-induced diabetes C57BL/6J mice (type 1 diabetes) and 20 male C57BL/6J mice at 4 wks of age were evenly divided into two groups: periodontal infection and sham infection. Periodontitis was induced by Porphyromonas gingivalis W50 (P. gingivalis) oral inoculation before the development of diabetes. Sham-infected mice received vehicle as control. P. gingivalis in the oral cavity were identified by quantitative polymerase chain reaction. Fasting glucose, body weight and food intake levels were monitored and glucose tolerance tests were performed to assess glucose homeostasis for the onset and progression of diabetes. The level of alveolar bone loss and tumor necrosis factor-alpha were determined in week 20 when mice were killed. RESULTS Mice in the infection groups developed more alveolar bone loss than those in sham-infection groups (Tallyho p = 0.021; C57-STZ p = 0.014; C57 p = 0.035). Hyperglycemic mice exhibited significantly more bone loss compared to those normal glucose mice (Tallyho vs. C57 p = 0.029; C57-STZ vs. C57 p = 0.024). The level of tumor necrosis factor-alpha was consistent with that of periodontal bone loss and hyperglycemia. There was no significant effect of mouse species on the amount of bone loss at the same level of blood glucose. No statistically significant difference or trend in glucose metabolism was found between the infection and sham-infection group. CONCLUSION Diabetes enhanced the risk for periodontal disease induced by P. gingivalis. However, no converse impact was found between this periodontal infection and onset and severity of diabetes in both type 1 and 2 diabetes mice.
Multiobjective MILP model for optimal allocation of automated switching devices in electric power distribution systems

This paper presents an analytical mixed-integer linear programming model to improve reliability of distribution networks through the optimal allocation of automated switching devices. Optimal reliability is formulated as a multi-objective problem of minimizing customers' interruptions and the investment costs related to devices' acquisition, relocation and operation. In order to establish the optimal trade-off between these conflicting objectives the Goal Programming approach is proposed. The presented model considers post-fault restoration constraints which limit load transfers and thereby the system reconfiguration capability. Restoration feasibility is ensured by a linear formulation of power flow equations as functions of geographical locations of automated switching devices in the feeder. Therefore, the model's solutions provide a more effective and economic application of automated switching devices, so that voltage and system capacity constraints are taken into account in selecting optimal locations of devices. The proposed methodology was validated using the IEEE 123-bus test feeder.
Real-Time Monitoring of Nuclear Factor κB Activity in Cultured Cells and in Animal Models

Nuclear factor κB (NF-κB) is a transcription factor that plays a major role in many human disorders, including immune diseases and cancer. We designed a reporter system based on NF-κB responsive promoter elements driving expression of the secreted Gaussia princeps luciferase (Gluc). We show that this bioluminescent reporter is a highly sensitive tool for noninvasive monitoring of the kinetics of NF-κB activation and inhibition over time, both in conditioned medium of cultured cells and in the blood and urine of animals. NF-κB activation was successfully monitored in real time in endothelial cells in response to tumor angiogenic signaling, as well as in monocytes in response to inflammation. Further, we demonstrated dual blood monitoring of both NF-κB activation during tumor development as correlated to tumor formation using the NF-κB Gluc reporter, as well as the secreted alkaline phosphatase reporter. This NF-κB reporter system provides a powerful tool for monitoring NF-κB activity in real time in vitro and in vivo.
Etude et modélisation des sources froides de neutron

La these comporte cinq parties: 1 - Une presentation de "etat de l'art concernant les sources froides: la physique des sources, les types, les moderateurs froids, l'aspect thermique. Elle expose aussi plusieurs domaines connexes aux sources froides tel que la surete, la cryogenie, la circulation des fluides, etc. 2 - Les implementations realisees: la simulation des sources froides demande des outils informatiques adequates. Le code Monte Carlo TRIPOLl-4 a ete choisi pour developper une chaine de calcul complete propre a ces etudes. La chaine de calcul comprend une methode de decouplage, des systemes de ponderation, un couplage avec le code Monte Carlo MCSTAS (simulateur de guide de neutron). Grace a la technique de decouplage, il est possible de seulement simuler la partie interessante du reacteur. Un score de " flux ponctuel" sur une surface permet d'obtenir les flux entrants dans les guides de neutrons et d'enregistrer les evenements. Le couplage avec MCSTAS permet de simuler les guides de neutrons et d'obtenir les flux prevus arrivant sur les echantillons. Ceci reduit le temps de calcul de 90 mois a 26 heures pour le flux en entree de guide. 3 et 4 - Les etudes des sources froides dans les reacteurs de recherche Orphee (CEA-Saclay) et RHF (ILL Grenoble). Les resultats de ces etudes permettent de valider la chaine de calcul, de faire l'etude thermique des sources froides, et d'etudier l'impact des sources froides sur le vieillissement des structures des reacteurs qui sont proches des sources. 5 - La derniere partie est consacree a l'exposition des concepts directeurs dans la conception des sources froides. Elle presente aussi des ameliorations des sources froides.
MRI based dementia classification using semi-supervised learning and domain adaptation

We propose a method for dementia classification based brain magnetic resonance images (MRIs). The method learns to recognize patients with Alzheimer’s disease or Mild Cognitive Impairment from healthy controls. The features used are extracted with sparse logistic regression from a large pool of voxel-wise gray matter densities computed based on MRIs registered to stereotactic space. The classifier uses a Low Density Separation algorithm, which can take advantage of both labeled and unlabeled samples. The differences between the training and test sets are compensated based on an algorithm for unsupervised domain adaptation. The method is fully automatic. The proposed method participated in the 2014 CADDementia competition, with an estimated accuracy of 0.767 for the public test data. The training data was extracted from ADNI database.
Deep gray matter maturation in very preterm neonates: regional variations and pathology-related age-dependent changes in magnetization transfer ratio.

PURPOSE To elucidate the relationship between gestational age, pathologic findings, and magnetic resonance (MR) imaging measures of tissue maturation-myelination in deep gray matter areas in very preterm neonates imaged at birth. MATERIALS AND METHODS The study was approved by the research ethics board. Written informed consent was given by the infants' parents. Forty-two preterm neonates (19 boys; median gestational age, 28.7 weeks) with normal-appearing gray matter structures at presentation underwent MR imaging within 2 weeks of birth that included T1- and T2-weighted, magnetization transfer, and T1 relaxometry sequences. Neonates were separated into the following groups: those with normal findings (n = 23), those with white matter injury (WMI) (n = 9), those with grade I germinal matrix hemorrhage (GMH) (n = 3), and those with grade II GMH and WMI (n = 7). Analysis of covariance was used to determine regional effects of age and pathologic findings on magnetization transfer ratio (MTR) and to assess the relationship between MTR and T1. RESULTS MTR increased linearly with age (P ≤ .0265), with a similar rate of change of 0.32% per week (95% confidence interval [CI]: 0.16, 0.49) in the basal ganglia (BG) and thalami. A lower trend (0.11% per week; 95% CI: -0.05, 0.28) was seen in the pons. Higher MTRs were seen in the thalami and pons than in the BG (P < .05), indicating earlier maturation. Accordingly, higher T1 values were observed in the BG relative to the thalami (P < .0001). Higher MTRs in the BG were observed in the group of neonates with normal findings at presentation than in the group with WMI (P = .02). CONCLUSION MTR measurements can be used to monitor early myelination in the developing brain and to help detect changes in tissue that are not shown on T1- and T2-weighted MR images.
Differential power analysis: Simulated versus experimental attacks

This paper presents differences and similarities between experimental and simulated differential power analysis (DPA) based security attacks. DPA attacks are known for many years and experimental attacks have been performed on a large number of hardware and/or software implementations of various cryptographic algorithms (RSA, AES, etc.). Vulnerabilities are mostly discovered after the product has been released to the market making it quasi impossible to fix them. Therefore, a new approach to detecting security vulnerabilities is needed; one that detects flaws early in the design process, before the circuit is manufactured. This method relies on digital simulations rather than on experimental measurements. Simulations are the foundation of functional verification of digital circuits. Using a specifically for this purpose developed software framework, called Power Analysis Toolkit, a comparison between simulated and experimental DPA attacks was performed. The attacked circuit is a hardware implementation of the well-known AES cryptographic algorithm. Results show that, using the correct assumptions, digital simulations can be used to uncover security vulnerabilities.
Sentiment classification by a hybrid method of greedy search and multinomial naïve bayes algorithm

In this paper, we proposed sentiment classification framework focusing on the hybrid method of greedy and multinomial naive bayes algorithm. We found greedy search feature selection most effective in our experiments with multinomial naive bayes algorithm. We also discovered that the multinomial naive bayes is suitable for combination with the greedy method. The hybrid method of greedy and multinomial naive bayes algorithm yielded the best performance with the accuracy over all traditional algorithms. Based on our experiments, the multinomial naive bayes algorithm with the greedy search feature selection yielded the best performance with the accuracy of 85.00 %. Our experimental results also reveal that hybrid methods have a positive effect on sentiment classification framework.
Design of an optimal layout RF passive polyphase filter for large image rejection

This article presents the design and implementation of a multi-stage radio-frequency (RF) passive polyphase filter (PPF). The layout parasitics and mismatch which deteriorate significantly the RF filter performance are analyzed and modeled. To reduce this parasitic degradation, a novel optimal layout technique is proposed. It is based on reproducing the same optimized PPF stage layout for the different stages while the desired bandwidth is ensured due to an optimal sizing of the inter-stages connections. This approach has been validated with on chip measurements. Using the proposed techniques more than 55 dB of image rejection over the [1.5; 3.3] GHz bandwidth is demonstrated while achieving zero power consumption and small silicon area in 130nm CMOS technology.
Surface radiation budgets in support of the GEWEX Continental‐Scale International Project (GCIP) and the GEWEX Americas Prediction Project (GAPP), including the North American Land Data Assimilation System (NLDAS) project

[1] In support of the World Climate Research Program GEWEX Continental-Scale International Project (GCIP) and the GEWEX Americas Prediction Project (GAPP), real-time estimates of shortwave radiative fluxes, both at the surface and at the top of the atmosphere, are being produced operationally by the National Oceanic and Atmospheric Administration (NOAA)/National Environmental Satellite Data and Information Service using observations from GOES images. The inference scheme has been developed at the Department of Meteorology, University of Maryland, and the atmospheric and surface model input parameters are produced and provided by the NOAA/National Centers for Environmental Prediction. The radiative fluxes are being evaluated on hourly, daily, and monthly timescales using observations at about 50 stations. The satellite estimates have been found to be within acceptable limits during snow-free periods, but the difficulty in detecting clouds over snow affects the accuracy during the winter season. In what follows, this activity is discussed, and evaluation results of the derived fluxes against ground observations for time periods of 1–2 years are presented.
Development and Standardization of a New Cognitive Assessment Test Battery for Chinese Aphasic Patients: A Preliminary Study

Background: Nonlinguistic cognitive impairment has become an important issue for aphasic patients, but currently there are few neuropsychological cognitive assessment tests for it. To get more information on cognitive impairment of aphasic patients, this study aimed to develop a new cognitive assessment test battery for aphasic patients, the Non-language-based Cognitive Assessment (NLCA), and evaluate its utility in Chinese-speaking patients with aphasia. Methods: The NLCA consists of five nonverbal tests, which could assess five nonlinguistic cognitive domains such as visuospatial functions, attention test, memory, reasoning, and executive functions of aphasic patients. All tests are modified from the nonverbal items of the current existed tests with some changes to the characteristics of Chinese culture. The NLCA was tested in 157 participants (including 57 aphasic patients, 50 mild cognitive impairment (MCI) patients, and 50 normal controls), and was compared with other well-established relative neuropsychological tests on the reliability, validity, and utility. Results: The NLCA was fully applicable in the MCI patients and the normal controls, almost working in the aphasic patients (57/62 patients, 91.9%). The NLCA scores were 66.70 ± 6.30, 48.67 ± 15.04, and 77.58 ± 2.56 for the MCI group, the aphasic group, and the control group, respectively, and a significant difference was found among three groups (F = 118.446, P < 0.001). The Cronbach's alpha of the NLCA as an index of internal consistency was 0.805, and the test-retest and interrater reliability was adequate (r=0.977 and r= 0.970, respectively). The correlations of the cognitive subtests and their validation instruments were between 0.540 and 0.670 (all P < 0.05). Spearman's correlation analysis indicated that the coefficient of internal consistency of each subtest itself was higher than other subtests. When choosing the Montreal Cognitive Assessment score of <26 as the diagnostic criteria of cognitive impairment, the area under the curve for all participants in the control and MCI groups was 0.942 (95% confidence interval: 0.895–0.989), and an optimal cutoff point of 75.00 seemed to provide the best balance between sensitivity and specificity. Age (r = −0.406, P < 0.001) was the main influence factor for the NLCA. Conclusions: The NLCA could efficiently differentiate the cognitive impairment patients from the normal controls and is a reliable and valid cognitive assessment test battery to specially find nonlinguistic cognitive function for aphasic patients.
ELECTROCHEMICAL SENSORS FOR DIRECT DETERMINATION OF SIMVASTATIN IN PHARMACEUTICAL FORMULATIONS AND BIOLOGICAL FLUIDS

The construction and performance characteristics of simvastatin (SIM) selective electrodes were developed. Three types of electrodes: plastic membrane I, coated wire II, and coated graphite rod III were constructed based on the incorporation of simvastatin with phosphotungstic (PTA) or phosphomolybdic (PMA) acids and mixed ion pair (PTA/PMA) for the three electrodes, respectively. The influence of membrane composition, kind of plasticizer, type of ion-pair, pH of the test solution, soaking time, and foreign ions on the electrodes was investigated. The electrodes showed a Nernstain response with a mean calibration graph slope of 56.24±0.43, 55.44±0.14 and 58.93±0.34 mV decade-1 at 25oC over simvastatin concentration range from 1.0 x 10-6-5.0 x 10-2, 9.0 x 10-6-5.0 x 10-3 and 9.0 x 10-7-1.0 x 10-2 mol L-1, with detection limit of 5.0 x 10-7, 3.9 x 10-6 and 3.2 x 10-7 mol L-1 for electrode I, II and III, respectively. The pH range for the proposed electrodes was 4-7. The influence of possible interfering species such as common inorganic cations, many sugars, amino acids and a pharmacologically related drug ‘ezetimibe’ was studied. Statistical student’s t-test and F test showed insignificant systematic error between proposed and official methods.