Miracle-dz/UniFAR-FTUs huggingface dataset:
In-vivo perfusion quantification by contrast ultrasound: Validation of the use of linearized video data vs. raw RF data

Perfusion quantification software commonly analyzes log-compressed video images provided by ultrasound systems. Compared to analysis of raw RF signals, errors in perfusion parameter estimates may be introduced, even when proper linearization is applied to reverse the log-compression. In this work, the effects of log-compression, demodulation, scan conversion and 8-bit quantization have been investigated, in terms of the errors introduced on perfusion parameter estimates. An in-vivo contrast bolus sequence was processed using both raw RF data and linearized video data. The outcome is that linearizing log-compressed video sequences can provide estimates as accurate as processing RF data under two conditions: a) system gain should be such as to prevent both excessive truncation of pixel values to minimum level and saturation to maximum level; b) the dynamic range of log-compression should be 45 dB or higher.
Novel superimposed diamond search algorithm for medical image compression

A novel search algorithm called superimposed diamond search algorithm SDSA based on lifting wavelet transform LWT for medical image compression is proposed in this paper. Fuzzy C means clustering FCM is applied to extract the region of interest ROI from the medical image. MAXSHIFT method is used to scale the coefficients so that the bits associated with the ROI are placed in higher bit planes than the bits associated with the background without the requirement of the shape information and without the need for calculating the ROI mask. SDSA keeps track of significant pixels of wavelet sub-band in hexagonal search in the scan order of left to right and top to bottom. The experimental results show the good compression ratio over the other existing methods such as set partitioning in hierarchical trees SPIHT and embedded zerotree wavelet EZW.
Relating Tumor Score to Hematology in Green Turtles with Fibropapillomatosis in Hawaii

The relationship between hematologic status and severity of tumor affliction in green turtles (Chelonia mydas) with fibropapillomatosis (FP) was examined. During 1 wk periods in July 1997 and July 1998, we bled 108 free-ranging green turtles from Pala'au (Molokai, Hawaii, USA) where FP is endemic. Blood was analyzed for hematocrit, estimated total solids, total white blood cell (WBC) count and differential WBC count. Each turtle was assigned a subjective tumor score ranging from 0 (no visible external tumors) to 3 (heavily tumored) that indicated the severity of FP. There was a progressive increase in monocytes and a decrease in all other hematologic parameters except heterophils and total numbers of white blood cells as tumor score increased. These data indicate that tumor score can relate to physiologic status of green turtles afflicted with FP, and that tumor score is a useful field monitor of severity of FP in this species.
Population biology of the invasive freshwater snail Physa acuta approached through genetic markers, ecological characterization and demography

The respective role of factors acting on population functioning can be inferred from a variety of approaches, including population genetics and demography. We here investigated the role of four of these factors (mating systems, population size, bottlenecks and migration) in the hermaphroditic freshwater snail Physa acuta. Twenty‐four populations were sampled either around Montpellier (local scale), or at the scale of France (global scale). At local scale, eight populations were sampled twice, before and after summer drying out. The genetic structure of these populations was studied using microsatellite loci. Populations were classified according to openness (ponds vs. rivers) and water regime (permanent vs. temporary) allowing predictions on genetic patterns (e.g. diversity within populations and differentiation). At local scale, progeny‐arrays analysis of the selfing rate was conducted, and size distributions of individuals were followed over two years. Results with regard to the four factors mentioned above were: (i) Estimates of population selfing rates derived from inbreeding coefficients were only slightly higher than those from progeny‐arrays. (ii) More variation was detected in rivers than in ponds, but no influence of water regime was detected. One reason might be that permanent populations are not going less often through low densities than those from temporary habitats at the time scale studied. (iii) There was limited evidence for genetic bottlenecks which is compatible with the fact that even marked reduction in water availability was not necessarily associated with demographic bottlenecks. More generally, bottlenecks reducing genetic variation probably occur at population foundation. (iv) Lower genetic differentiation was detected among rivers than among ponds which might be related to limitations on gene flow. Demographic and temporal genetic data further indicates that flooding in rivers is unlikely to induce marked gene flow explaining the strong genetic differentiation at short geographical scale in such habitats. Finally, the demographic data suggest that some populations are transitory and subject to recurrent recolonization, a pattern that was also detected through genetic data.
Plasma amyloid beta-protein and C-reactive protein in relation to the rate of progression of Alzheimer disease.

OBJECTIVE To examine whether plasma markers of amyloid precursor protein metabolism (amyloid beta-protein ending in Val-40 [Abeta40] and Ala-42 [Abeta42]), inflammation (high-sensitivity C-reactive protein), and folic acid metabolism (folic acid, vitamin B(12), and total homocysteine levels) are associated with the rate of cognitive and functional decline in persons with Alzheimer disease. DESIGN Longitudinal study across a mean (SD) of 4.2 (2.6) years with assessments at approximately 6- to 12-month intervals. SETTING Outpatient care. PATIENTS A cohort of 122 patients having a clinical diagnosis of probable Alzheimer disease, each with at least 2 assessments across time. MAIN OUTCOME MEASURES Scores on the cognitive Information-Memory-Concentration subscale of the Blessed Dementia Scale and the functional Weintraub Activities of Daily Living Scale. RESULTS Low plasma levels of Abeta40, Abeta42, and high-sensitivity C-reactive protein were associated with a significantly more rapid cognitive decline, as indexed using the Blessed Dementia Scale, than were high levels. Low levels of Abeta42 and high-sensitivity C-reactive protein were significantly associated with more rapid functional decline on the Weintraub Activities of Daily Living Scale than were high levels. These plasma markers contributed about 5% to 12% of the variance accounted for on the Blessed Dementia Scale and the Activities of Daily Living Scale by fixed-effects predictors. Measures of folic acid metabolism were not associated with changes on either the Blessed Dementia Scale or the Activities of Daily Living Scale. CONCLUSIONS Plasma markers of amyloid precursor protein metabolism and C-reactive protein may be associated with the rate of cognitive and functional decline in patients with Alzheimer disease.
Application of Multilocus Sequence Typing To Study the Genetic Structure of Megaplasmids in Medicago-Nodulating Rhizobia

ABSTRACT A multilocus sequence typing (MLST) analysis was used to examine the genetic structure and diversity within the two large extrachromosomal replicons in Medicago-nodulating rhizobia (Sinorhizobium meliloti and Sinorhizobium medicae). The allelic diversity within these replicons was high compared to the reported diversity within the corresponding chromosomes of the same strains (P. van Berkum et al., J. Bacteriol. 188:5570-5577, 2006). Also, there was strong localized linkage disequilibrium (LD) between certain pSymA loci: e.g., nodC and nifD. Although both of these observations could be explained by positive (or diversifying) selection by plant hosts, results of tests for positive selection did not provide consistent support for this hypothesis. The strong LD observed between the nodC and nifD genes could also be explained by their close proximity on the pSymA replicon. Evidence was obtained that some nodC alleles had a history of intragenic recombination, while other alleles of this locus had a history of intergenic recombination. Both types of recombination were associated with a decline in symbiotic competence with Medicago sativa as the host plant. The combined observations of LD between the nodC and nifD genes and intragenic recombination within one of these loci indicate that the symbiotic gene region on the pSymA plasmid has evolved as a clonal segment, which has been laterally transferred within the natural populations.
Preproenkephalin mRNA is expressed by C1 and non‐C1 barosensitive bulbospinal neurons in the rostral ventrolateral medulla of the rat

The autonomic regions of the thoracolumbar spinal cord receive a dense enkephalinergic (ENK) innervation from supraspinal sources, including the rostral ventrolateral medulla (RVLM). In the present study, we sought to determine whether the barosensitive bulbospinal (BSBS) neurons of the RVLM express preproenkephalin (PPE) mRNA. After injection of Fluoro‐Gold (FG) into the upper thoracic spinal cord, neurons with PPE mRNA (PPE+ neurons) were retrogradely labeled throughout the ventrolateral medulla. At the most rostral RVLM level, 29% of bulbospinal PPE+ cells were tyrosine hydroxylase–immunoreactive (TH‐ir) and the latter constituted 19.4% of the bulbospinal TH‐ir cells. We determined whether the bulbospinal PPE+ RVLM neurons are barosensitive in two ways. First, we examined Fos production by FG‐labeled RVLM neurons after 2 hours of hydralazine‐induced hypotension (to 73 ± 2 mm Hg) in conscious rats. Hydralazine (10 mg/kg i.v.) increased the number of Fos‐ir neurons by two‐ to eightfold at all levels of the ventrolateral medulla examined. In the RVLM, 54% of bulbospinal PPE+ neurons were Fos‐ir, whereas such cells were more rarely found at caudal ventrolateral medullary levels. Second, we recorded individual BSBS RVLM units extracellularly in anesthetized rats and filled them juxtacellularly with biotinamide. Most biotinamide‐filled neurons were PPE+ (10 of 17), and the PPE+ BSBS cells had a faster axonal conduction velocity than those without PPE mRNA (4.2 vs. 0.67 m/sec). Four of the 10 PPE+ BSBS RVLM neurons were TH‐ir. In summary, PPE mRNA is predominantly expressed by RVLM BSBS neurons with lightly myelinated spinal axons. PPE mRNA is present in most noncatecholaminergic BSBS neurons and also in approximately 20% of the bulbospinal C1 neurons. BSBS RVLM neurons most likely provide a major ENK input to sympathetic preganglionic neurons and PPE mRNA is the first identified positive phenotype of the non‐C1 BSBS RVLM neurons. J. Comp. Neurol. 435:111–126, 2001. © 2001 Wiley‐Liss, Inc.
STRAND SELECTIVE TRANSCRIPTION OF T4 DNA IN VITRO.

Formation and detection of DNA-RNA hybrids: T4 DNA was denatured by heating for 15 min at 1000, then rapidly cooling to 00.18 DNA-RNA hybrids were formed by incubating solu-tions of denatured DNA and RNA in 2 X SSC for 5-7 hr at 590, except where noted. The solu-tions were then brought to 0.5 M NaCl and passed through nitrocellulose filters according to the DNA-RNA hybrid detection method of Nygaard and Hall. " The DNA-RNA complex remains on the filter while free RNA passes through. The radioactivity remaining on the filters was determined using a Nuclear-Chicago liquid scintillation spectrometer. It was unnecessary to employ RNAase in these experiments since the DNA concentration in the reaction mixtures was sufficiently low to avoid the formation of nonspecific DNA-RNA complexes. The percentage of input RNA hybridized was determined after subtraction of the background radioactivity found on filters in control reaction mixtures lacking DNA ('-0.5% of the total RNA input).
Explaining Bureaucratic Optimism: Theory and Evidence from U.S. Executive Agency Macroeconomic Forecasts

We offer a theory of intertemporal bureaucratic decision making which proposes that an agency's forecast optimism is related to the extent to which it discounts future reputation costs associated with bureaucratic incompetence. Agency forecasts of the distant future are more likely to be optimistic than short-term forecasts. We claim that unstable organizations will discount reputation costs at a steeper rate than stable organizations, and therefore will produce more optimistic forecasts. We test our theory using macroeconomic forecasts produced by the Office of Management and Budget (OMB) and the Social Security Administration (SSA) across six forecast horizons from 1979 to 2003. The statistical results are generally consistent with our theory: OMB generates more optimistic long-term forecasts than SSA. Further, differences in forecast optimism between these executive branch agencies widen as the forecast horizon increases. Our evidence suggests that more stable agencies place a premium on minimizing reputation costs. Conversely, less stable agencies are more likely to accommodate political pressures for forecast optimism. These findings underscore the importance of institutional design for understanding how executive agencies balance the conflicting goals of political responsiveness and bureaucratic competence within the administrative state.
Ontology Learning from Text Using Relational Concept Analysis

We propose an approach for semi-automated construction of ontologies from text whose core component is a relational concept analysis (RCA) framework which extends formal concept analysis (FCA), a lattice-theory paradigm for discovering abstractions within objects x attributes tables, to the processing of several sorts of individuals described both by own properties and inter-individual links. As a pre-processing, text analysis is used to transform a document collection into a set of data tables, or contexts, and inter-context relations. RCA then turns these into a set of concept lattices with inter-related concepts. A core ontology is derived from the lattices in a semi-automated manner, by translating relevant lattice elements into ontological concepts and relations, i.e., either taxonomic or transversal ones. The ontology is further refined by abstracting new transversal relations from the initially identified ones using RCA. We discuss as well the results of an application of the method to astronomy texts.
TCAD based segmented modelling of large RF power-transistors-die for finger level analysis and optimization

A modeling method for RF power transistor fingers and large discrete die is presented in order to evaluate, visualize, and optimize various performance parameters at the device finger level. The model is constructed using a combination of TCAD based active die model and passive interconnect models based on Wheeler's transmission line formulation. Active die model of a fraction of the total periphery are connected with the interconnect models to build arbitrarily sized RF power transistors. The advantage of such model is shown to be flexibility of probing different parameters (e.g. voltage, current) at distinct die locations. Additionally, interconnect of the power transistor can be optimized in the simulation space in order to realize improved performance.
GSK-3β Protein Phosphorylates and Stabilizes HLXB9 Protein in Insulinoma Cells to Form a Targetable Mechanism of Controlling Insulinoma Cell Proliferation*

Background: Germ line heterozygous loss of the MEN1 tumor suppressor gene causes tissue-specific tumors such as insulinomas. Results: GSK-3β and GSK-3β-mediated phosphorylation of HLXB9, a β-cell differentiation factor, is elevated in insulinomas, and GSK-3β inhibition blocks insulinoma cell proliferation. Conclusion: GSK-3β and phospho-HLXB9 form a targetable mechanism of insulinoma pathogenesis. Significance: Reactivation of a tissue-specific differentiation factor accounts for tumor tissue specificity. Insulinomas (pancreatic islet β cell tumors) are the most common type of functioning pancreatic neuroendocrine tumors that occur sporadically or as a part of the MEN1 syndrome that is caused by germ line mutations in MEN1. Tissue-specific tumor predisposition from germ line mutations in ubiquitously expressed genes such as MEN1 could occur because of functional consequences on tissue-specific factors. We previously reported the proapoptotic β cell differentiation factor HLXB9 as a downstream target of menin (encoded by MEN1). Here we show that GSK-3β inactivates the proapoptotic activity of HLXB9 by phosphorylating HLXB9 at Ser-78/Ser-80 (pHLXB9). Although HLXB9 is found in the nucleus and cytoplasm, pHLXB9 is predominantly nuclear. Both pHLXB9 and active GSK-3β are elevated in β cells with menin knockdown, in MEN1-associated β cell tumors (insulinomas), and also in human sporadic insulinomas. Pharmacologic inhibition of GSK-3β blocked cell proliferation in three different rodent insulinoma cell lines by arresting the cells in G2/M phase and caused apoptosis. Taken together, these data suggest that the combination of GSK-3β and pHLXB9 forms a therapeutically targetable mechanism of insulinoma pathogenesis. Our results reveal that GSK-3β and pHLXB9 can serve as novel targets for insulinoma treatment and have implications for understanding the pathways associated with β cell proliferation.
Comparing methods for handling missing values in food-frequency questionnaires and proposing k nearest neighbours imputation: effects on dietary intake in the Norwegian Women and Cancer study (NOWAC)

Abstract Objective To investigate item non-response in a postal food-frequency questionnaire (FFQ), and to assess the effect of substituting/imputing missing values on dietary intake levels in the Norwegian Women and Cancer study (NOWAC). We have adapted and probably for the first time applied k nearest neighbours (KNN) imputation to FFQ data. Design Data from a recent reproducibility study were used. The FFQ was mailed twice (test–retest) about 3 months apart to the same subjects. Missing responses in the test FFQ were imputed using the null value (frequencies = null, amount = smallest), the sample mode, the sample median, KNN, and retest values. Setting A methodological substudy of NOWAC, a national population-based cohort. Subjects A random sample of 2000 women aged 46–75 years was drawn from the cohort in 2002 (response 75%). The imputation methods were compared for 1430 women who completed at least 50% of the test FFQ. Results We imputed 16% missing values in the overall test data matrix. Compared to null value imputation, the largest differences in estimated dietary intake were seen for KNN, and for food items with a high proportion of missing. Imputation with retest values increased total energy intake, indicating that not all missing values are caused by respondents failing to specify no consumption, and that null value imputation may lead to underestimation and misclassification. Conclusion Missing values in FFQs present a methodological challenge. We encourage the application and evaluation of newer imputation methods, including KNN, which may reduce imputation errors and give more accurate intake estimates.
Increased Energy Metabolism and Suppressed Body Fat Accumulation in Mice by a Low Concentration of Conjugated Linoleic Acid

We investigated the dose-effect of the long-term intake of conjugated linoleic acid (CLA) on the energy metabolism and fat accumulation in mice. Five-week-old male Std ddY mice were fed on a diet containing none (control), 0.25%, 0.5% or 1.0% CLA for 4 or 8 weeks. The body weight was lower in the CLA groups than in the control group, and significant differences were detected between the 1.0% CLA group and the control group at both 4 and 8 weeks. The epididymal and perirenal adipose tissue weights were significantly lower in the CLA groups than in the control group. The liver weight and hepatic triglyceride values were higher in the 1.0% CLA group than in the other groups. The metabolic rate was measured after 8 weeks by using a gas analyzer. The oxygen consumption of the mice in the CLA groups was significantly higher than that of the control mice. Since there was a significant effect on the mice supplemented with 0.25% CLA, low concentration of CLA is suggested to suppress the body fat accumulation and increase the energy metabolism.
A randomized, controlled, parallel‐group clinical trial comparing multilayer bandaging followed by hosiery versus hosiery alone in the treatment of patients with lymphedema of the limb

Multilayered, low stretch bandages (MLB) combined with exercises, skin care, and manual lymphatic drainage therapy are recommended as an intensive phase of treatment for lymphedema patients. The relative efficacy of each of the components of this comprehensive treatment program have not been determined. This study aimed to compare the effect of multilayer bandaging as an initial phase of lymphedema treatment followed by elastic hosiery versus hosiery alone.
Characterization of Invasive Group B Streptococcus 1 from the Greater Toronto Area , Canada 2 3

# Author for correspondence: Nahuel Fittipaldi, Ph.D. Public Health Ontario, Toronto Laboratories, 81 17 Resources Rd, Toronto, Ontario M9P 3T1, Canada. Phone: (416) 235-5714. Fax: (416) 235-6063. E-mail: 18 nahuel.fittipaldi@oahpp.ca. 19 JCM Accepts, published online ahead of print on 19 February 2014 J. Clin. Microbiol. doi:10.1128/JCM.03554-13 Copyright © 2014, American Society for Microbiology. All Rights Reserved.
A reduced order model for the nonlinear analysis of coupled oscillator arrays with external injection locking

The dynamical properties of coupled oscillator arrays (COAs) have led to their application as phase shifters in phased array antennas [1,2]. Harmonic balance (HB) analysis, properly conditioned using auxiliary generator probes in order to guarantee convergence to the oscillating state has been used to accurately model free-running and externally injected coupled oscillator arrays in [3,4].
Scale Efficiency in the Banking Sector of Pakistan

The study employs data envelopment analysis to a panel of commercial banks operating in Pakistan for a period 2001 – 2008 in order to measure the technical efficiency of banks. Technical efficiency is then broken down into pure technical and scale components. We divide banks into three categories for analytical purposes: state owned banks, domestic private banks and foreign owned banks. We find foreign owned banks to be the most efficient, followed by state owned banks and domestic private banks are found least efficient. Further it is found that pure technical efficiency contributes more towards technical efficiency and banks are faced with serious scale problems. The scale inefficiency is found to be the main source of overall technical inefficiency. We observe an increasing trend in pure technical efficiency whereas an opposite trend is found in scale efficiency during the sample period.
Isolation and Characterization of DBR2 Gene Promoter from Iranian Artemisia annua

Artemisia annua is still the only commercial source of Artemisinin. To date, a number of biochemical and molecular studies about Artemisinin’s biosynthetic pathway have been carried out. In metabolic engineering approach, isolation and characterization of promoters leads to an understanding of which cis -acting elements are responsible for the regulation of gene expression. DBR2 is a key enzyme in Artemisinin biosynthetic pathway. In order to allow chromosome walking beyond the 5'-flanking region of DBR2 , two specific primers were used in combination with 6 arbitrary primers in TAIL-PCR method. A 696bp upstream of DBR2 start codon was isolated and cloned. The subsequent sequence analysis using bioinformatics softwares revealed that there were several cis acting elements such as TATA -box, CAAT -box, and MeJA-responsive element, and several W-box and light-responsive elements inside the DBR2 promoter. These results can be helpful in understanding of artemisinin biosynthesis regulation and will facilitate metabolic engineering of the compound.