Miracle-dz/UniFAR-FTUs huggingface dataset:
Inability of Refined CT to Assess Local Extent of Prostatic Cancer

A refined procedure for CT was evaluated as a staging procedure in 19 patients with localized prostatic carcinoma. The CT images were compared to histopathologic whole-mount step sections of the surgical specimens. Fourteen of the patients had pathologic stage T3 (pT3) and 5 had stage pT2 giving a prevalence of extracapsular growth of 0.74. The CT images were read by 2 radiologists independently with a diagnostic accuracy of 0.37 for both observers. This is no better than in previous studies using a routine CT procedure. We conclude that CT is of little value in the staging protocol for the local extent of prostatic carcinoma before radical prostatectomy.
Performance of chronic kidney disease epidemiology collaboration creatinine‐cystatin C equation for estimating kidney function in cirrhosis

Conventional creatinine‐based glomerular filtration rate (GFR) equations are insufficiently accurate for estimating GFR in cirrhosis. The Chronic Kidney Disease Epidemiology Collaboration (CKD‐EPI) recently proposed an equation to estimate GFR in subjects without cirrhosis using both serum creatinine and cystatin C levels. Performance of the new CKD‐EPI creatinine‐cystatin C equation (2012) was superior to previous creatinine‐ or cystatin C‐based GFR equations. To evaluate the performance of the CKD‐EPI creatinine‐cystatin C equation in subjects with cirrhosis, we compared it to GFR measured by nonradiolabeled iothalamate plasma clearance (mGFR) in 72 subjects with cirrhosis. We compared the “bias,” “precision,” and “accuracy” of the new CKD‐EPI creatinine‐cystatin C equation to that of 24‐hour urinary creatinine clearance (CrCl), Cockcroft‐Gault (CG), and previously reported creatinine‐ and/or cystatin C‐based GFR‐estimating equations. Accuracy of CKD‐EPI creatinine‐cystatin C equation as quantified by root mean squared error of difference scores (differences between mGFR and estimated GFR [eGFR] or between mGFR and CrCl, or between mGFR and CG equation for each subject) (RMSE = 23.56) was significantly better than that of CrCl (37.69, P = 0.001), CG (RMSE = 36.12, P = 0.002), and GFR‐estimating equations based on cystatin C only. Its accuracy as quantified by percentage of eGFRs that differed by greater than 30% with respect to mGFR was significantly better compared to CrCl (P = 0.024), CG (P = 0.0001), 4‐variable MDRD (P = 0.027), and CKD‐EPI creatinine 2009 (P = 0.012) equations. However, for 23.61% of the subjects, GFR estimated by CKD‐EPI creatinine‐cystatin C equation differed from the mGFR by more than 30%. Conclusion: The diagnostic performance of CKD‐EPI creatinine‐cystatin C equation (2012) in patients with cirrhosis was superior to conventional equations in clinical practice for estimating GFR. However, its diagnostic performance was substantially worse than reported in subjects without cirrhosis. (Hepatology 2014;59:1532‐1542)
PERSISTENCE, VALUE RELEVANCE, AND ACCRUALS QUALITY IN EXTREME EARNINGS AND CASH FLOW SITUATIONS

Purpose: To analyze the impact of extreme earnings and cash flows on the persistence, value relevance, and accruals quality of Brazilian public firms. Originality/gap/relevance/implications: The present study contributes to the literature by analyzing extreme earnings and cash flows. Because they change the results of the period in which they occur in an unusual manner, this study suggests that studying their behaviors and impacts on the quality of the information disclosed by companies tends to contribute to optimal decision making in the capital market. Key methodological aspects: The analyzed sample comprised non-financial public companies traded on the BM&FBovespa stock exchange from 2005 to 2014, with estimates made using quantile regression. Summary of key results: The main results indicate that cash flows are more persistent than earnings because the accruals component of the latter makes them less persistent. Extreme values of both earnings and cash flows affect the persistence of these variables, with a strong and negative effect on cash flows. Finally, extreme values of accruals negatively affect accruals quality because, compared to moderate quantiles, they significantly alter the standard deviation of extreme quantiles. Key considerations/conclusions: The presence of extreme values in this study’s focus variables negatively influenced market information quality, reducing its predictive power and, consequently, its relevance. Furthermore, controlling for extreme values, it was possible to observe the incremental information content of these two metrics.
Voltage sag independent operation of induction motor based on Z-source inverter

This paper describes an adjustable speed drive system for driving an induction motor beyond its nominal speed, even in the presence of input voltage sags. The system is based on the Z-source inverter, which offers several advantages over traditional current or voltage source inverters as it can operate in both buck or boost mode. The boost operation is achieved with controlled short-circuiting of the inverter phase legs that is otherwise forbidden in traditional inverters. These shoot through states are accomplished with the modification of the space vector modulation which is thoroughly explained. In order to assure the required output voltage and ride-through ability during voltage sags, the method for selecting the proper inverter voltage is introduced. The control of the induction motor is carried out with the field oriented control coupled with the field weakening regime of the induction motor. The experimental setup is based on a prototype with a DSP control system to verify the operation of the proposed system.
Localization of enzymes in Ureaplasma urealyticum (T-strain mycoplasma)

Ureaplasma urealyticum cells were lysed by osmotic shock or by digitonin. The membrane fraction contained four to ten times as much protein as the cytoplasmic fraction. These values are in large excess of those reported for classical mycoplasmas, suggesting that the Ureaplasma membrane fraction was heavily contaminated with proteins derived from the growth medium. The U. urealyticum urease activity was localized in the cytoplasmic fraction, whereas the adenosine triphosphatase activity was localized in the membrane fraction. Significant urease activity could be detected also in nonviable cells. Urea, at concentrations above 0.25 M, was mycoplasmastatic to Acholeplasma laidlawii, Mycoplasma hominis, and U. urealyticum, so that the Ureaplasma urease did not afford preferential protection against urea toxicity. The intracellular localization of the urease would be expected to release ammonia from urea in the cytoplasm. The ammonia will take up protons to become ammonium ions. It can be hypothesized that the intracellular NH4+ plays a role in proton elimination or acid-base balance, which might be coupled to an energy producing ion gradient and/or transport mechanisms.
Robotic Micromanipulation and Microassembly Using Monoview and Multiscale Visual Servoing

This paper investigates sequential robotic micromanipulation and microassembly in order to build 3-D microsystems and devices. A monoview and multiple scale 2-D visual control scheme is implemented for this purpose. The imaging system used is a photon video microscope endowed with an active zoom enabling to work at multiple scales. It is modeled by a nonlinear projective method, where the relation between the focal length and the zoom factor is explicitly established. A distributed robotic system (xyθ system and φz system) with a two-fingers gripping system is used in conjunction with the imaging system. The results of experiments demonstrate the relevance of the proposed approaches. The tasks were performed with the following accuracy: 1.4 μm for the positioning error and 0.5° for the orientation error.
Characterization of Two Thermostable Cyanobacterial Phytochromes Reveals Global Movements in the Chromophore-binding Domain during Photoconversion*

Photointerconversion between the red light-absorbing (Pr) form and the far-red light-absorbing (Pfr) form is the central feature that allows members of the phytochrome (Phy) superfamily to act as reversible switches in light perception. Whereas the chromophore structure and surrounding binding pocket of Pr have been described, those for Pfr have remained enigmatic for various technical reasons. Here we describe a novel pair of Phys from two thermophilic cyanobacteria, Synechococcus sp. OS-A and OS-B′, that overcome several of these limitations. Like other cyanobacterial Phys, SyA-Cph1 and SyB-Cph1 covalently bind the bilin phycocyanobilin via their cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) domains and then assume the photointerconvertible Pr and Pfr states with absorption maxima at 630 and 704 nm, respectively. However, they are naturally missing the N-terminal Per/Arndt/Sim domain common to others in the Phy superfamily. Importantly, truncations containing only the GAF domain are monomeric, photochromic, and remarkably thermostable. Resonance Raman and NMR spectroscopy show that all four pyrrole ring nitrogens of phycocyanobilin are protonated both as Pr and following red light irradiation, indicating that the GAF domain by itself can complete the Pr to Pfr photocycle. 1H-15N two-dimensional NMR spectra of isotopically labeled preparations of the SyB-Cph1 GAF domain revealed that a number of amino acids change their environment during photoconversion of Pr to Pfr, which can be reversed by subsequent photoconversion back to Pr. Through three-dimensional NMR spectroscopy before and after light photoexcitation, it should now be possible to define the movements of the chromophore and binding pocket during photoconversion. We also generated a series of strongly red fluorescent derivatives of SyB-Cph1, which based on their small size and thermostability may be useful as cell biological reporters.
Structural basis for acceptor‐substrate recognition of UDP‐glucose: anthocyanidin 3‐O‐glucosyltransferase from Clitoria ternatea

UDP‐glucose: anthocyanidin 3‐O‐glucosyltransferase (UGT78K6) from Clitoria ternatea catalyzes the transfer of glucose from UDP‐glucose to anthocyanidins such as delphinidin. After the acylation of the 3‐O‐glucosyl residue, the 3′‐ and 5′‐hydroxyl groups of the product are further glucosylated by a glucosyltransferase in the biosynthesis of ternatins, which are anthocyanin pigments. To understand the acceptor‐recognition scheme of UGT78K6, the crystal structure of UGT78K6 and its complex forms with anthocyanidin delphinidin and petunidin, and flavonol kaempferol were determined to resolutions of 1.85 Å, 2.55 Å, 2.70 Å, and 1.75 Å, respectively. The enzyme recognition of unstable anthocyanidin aglycones was initially observed in this structural determination. The anthocyanidin‐ and flavonol‐acceptor binding details are almost identical in each complex structure, although the glucosylation activities against each acceptor were significantly different. The 3‐hydroxyl groups of the acceptor substrates were located at hydrogen‐bonding distances to the Nε2 atom of the His17 catalytic residue, supporting a role for glucosyl transfer to the 3‐hydroxyl groups of anthocyanidins and flavonols. However, the molecular orientations of these three acceptors are different from those of the known flavonoid glycosyltransferases, VvGT1 and UGT78G1. The acceptor substrates in UGT78K6 are reversely bound to its binding site by a 180° rotation about the O1–O3 axis of the flavonoid backbones observed in VvGT1 and UGT78G1; consequently, the 5‐ and 7‐hydroxyl groups are protected from glucosylation. These substrate recognition schemes are useful to understand the unique reaction mechanism of UGT78K6 for the ternatin biosynthesis, and suggest the potential for controlled synthesis of natural pigments.
Lesion bypass in yeast cells: Pol η participates in a multi‐DNA polymerase process

Replication through (6–4)TT and G‐AAF lesions was compared in Saccharomyces cerevisiae strains proficient and deficient for the RAD30‐encoded DNA polymerase η (Pol η). In the RAD30 strain, the (6–4)TT lesion is replicated both inaccurately and accurately 60 and 40% of the time, respectively. Surprisingly, in a rad30Δ strain, the level of mutagenic bypass is essentially suppressed, while error‐free bypass remains unchanged. Therefore, Pol η is responsible for mutagenic replication through the (6–4)TT photoproduct, while another polymerase mediates its error‐free bypass. Deletion of the RAD30 gene also reduces the levels of both accurate and inaccurate bypass of AAF lesions within two different sequence contexts up to 8‐fold. These data show that, in contrast to the accurate bypass by Pol η of TT cyclobutane dimers, it is responsible for the mutagenic bypass of other lesions. In conclusion, this paper shows that, in yeast, translesion synthesis involves the combined action of several polymerases.
Evaluation of Data Transformations and Validation of a Model for the Effect of Temperature on Bacterial Growth

The temperature of chilled foods is an important variable for controlling microbial growth in a production and distribution chain. Therefore, it is essential to model growth as a function of temperature in order to predict the number of organisms as a function of temperature and time. This article deals with the correct variance-stabilizing transformation of the growth parameters A (asymptotic level), μ (specific growth rate), and λ (lag time). This is of importance for the regression analysis of the data. A previously gathered data set and model for the effect of temperature on the growth of Lactobacillus plantarum (M. H. Zwietering, J. T. de Koos, B. E. Hasenack, J. C. de Wit, and K. van 't Riet, Appl. Environ. Microbiol. 57:1094-1101, 1991) is extended with new data. With the total data set (original and new data), a variance-stabilizing transformation is selected in order to determine which transformation should precede fitting. No transformation for the asymptote data, a square root for the growth rate, and a logarithmic transformation for the lag time were found to be appropriate. After these transformations, no significant correlation was found between the variance and the magnitude of the variable. Model corrections were made and model parameters were estimated by using the original data. With the new data, the models were validated by comparing the lack of fit of the models with the measurement error, using an F test. The predictions of the models for μ and λ were adequate. The model for A showed a systematic deviation, and therefore a new model for A is proposed.
Transitory evoked otoacoustic emission (TEOAE) and distortion product otoacoustic emission (DPOAE) outcomes from a three-stage newborn hearing screening protocol.

OBJECTIVE Comparison of the efficacy of Transitory Evoked Otoacoustic Emissions (TEOAEs) and Distortion Product Otoacoustic Emissions (DPOAEs) in a neonatal hearing screening protocol, based on a three-stage strategy. METHODS In the first stage, a hearing screening using both evoked emissions was conducted in 3,480 neonates from March 2006 through January 2012. Both TEOAEs and DPOAEs were recorded. Neonates, who did not undergo the test before being discharged, were examined within 30 days at a scheduled appointment. Follow-up of the referred newborns (second-stage screening) was performed as an outpatient re-screening, within a month. The third-stage evaluation, i.e., the diagnostic testing, included a clinical otolaryngological examination, high-frequency tympanometry at 1,000 Hz and Auditory Brainstem Response (ABR) measurements. RESULTS A total of 3,480 (97%) newborns (n =1,765 males) out of 3,595 infants were enrolled in the study. In the first-stage evaluation, 8.9 % of the infants were referred according to TEOAEs, while the percentage of the referred infants for DPΟΑΕs was 25.7 %. At this initial assessment stage, the specificity of TEOAES and DPOAEs were determined as 92% and 75%, while positive predictive values (PPV) were 3.8 % and 1.3 %, respectively. In the second stage of evaluation, the specificity of TEOAES and DPOAEs were 86 % and 76 %, while the PPV increased to 18 % and 15 %, respectively. CONCLUSIONS With a lower follow-up rate, TEOAEs testing was significantly easier to perform and more reliable compared to the DPOAEs test. Hippokratia 2016, 20(2): 104-109.
Variability of a closed, rebreathing setup for multiple breath wash‐out testing in children

The multiple breath wash‐out technique (MBW) that measures lung clearance index (LCI) and functional residual capacity (FRC) may be more sensitive than spirometry for identification of early obstructive airways disease. The open MBW setup using mass spectrometry referenced in previous publications is not readily available in the U.S. Our objective was to assess validity and sensitivity of a commercially available device that uses a closed (rebreathing) setup with photoacoustic spectroscopy for MBW testing.
Uraemic serum induces dysfunction of vascular endothelial cells: role of ubiquitin–proteasome pathway

The ubiquitin–proteasome pathway (UPP) has been indicated to contribute to dysfunction of endothelial cells (ECs). Nevertheless, the relationship between UPP and vascular complications of uraemia remains unknown. We aimed to determine whether the UPP is activated in vascular ECs when cultured with uraemic serum, and to examine the role of the UPP on dysfunction of ECs in uraemia. Rabbit aortic endothelial cells (RAECs) were cultured with normal serum or different concentrations of uraemic serum. The expression of the ubiquitin‐activating enzyme (E1), an indicator of the UPP, was detected by real‐time RT‐PCR and Western blot; proteasome activity was determined by fluorescence spectrophotometry; and nuclear factor‐κB (NF‐κB) activity and expression, as well as tumour necrosis factor‐α (TNF‐α) expression, were also detected. We found that the expression of E1 and the activities of three kinds of proteasomes were increased significantly in RAECs after incubation with uraemic serum. Proliferation of RAECs was increased significantly by incubation with 3–15% uraemic serum but decreased markedly when incubated with uraemic serum above 15% (increased apoptosis). Incubation of RAECs with uraemic serum induced increased NF‐κB DNA‐binding activity and nuclear translocation of NF‐κB, decreased nitric oxide production and increased expression of TNF‐α, which is the final effector of inflammatory activation of cells. All of these responses in RAECs were suppressed by the specific proteasome inhibitor, MG132. The inhibition of inflammatory responses by MG132 was further supported by a parallel experiment with pyrrolidine dithiocarbamate, a specific inhibitor of NF‐κB. These findings suggest that the UPP was activated in RAECs by administration of uraemic serum, and played a pivotal role in the dysfunction of vascular ECs, such as inflammatory activation.
RESIDUAL FEED INTAKE AND THE RELATIONSHIP WITH PERFORMANCE, TEMPERAMENT AND CARCASS TRAITS IN GROWING AND FINISHING STEERS

i ACKNOWLEDGEMENTS. ii TABLE OF CONTENTS. iii LIST OF FIGURES. iv LIST OF TABLES. v INTRODUCTION. 1 LITERATURE REVIEW. 2 Measures of Feed Efficiency. 2 Feed Efficiency and Temperament. 9 Feed Efficiency and Body Composition. 10 Conclusion. 11 Objectives. 12 EXPERIMENT. 13 Materials and Methods. 13 Results. 23 Discussion. 42 Conclusion. 50 LITERATURE CITED. 51 APPENDIX. 56 VITA. 106
Child Maltreatment and Adult Living Standards at 50 Years

BACKGROUND AND OBJECTIVE: Child maltreatment (abuse and neglect) has established effects on mental health. Less is known about its influence on adult economic circumstances. We aimed to establish associations of child maltreatment with such outcomes and explore potential pathways. METHODS: We used 1958 British birth cohort data (N = 8076) to examine associations of child neglect and abuse with adult (50 years) long-term sickness absence, not in employment, education or training (NEET), lacking assets, income-related support, poor qualifications, financial insecurity, manual social class, and social mobility. We assessed mediation of associations by 16-year cognition and mental health. RESULTS: Abuse prevalence varied from 1% (sexual) to 10% (psychological); 16% were neglected. A total of 21% experienced 1 maltreatment type, 10% experienced ≥2 types. Sexual and nonsexual abuse were associated with several outcomes; eg, for sexual abuse, adjusted odds ratio (aOR) of income-related support was 1.75 (95% confidence interval [CI], 1.12–2.72). Associations were little affected by potential mediating factors. Neglect was associated with several adult outcomes (eg, aOR of NEET was 1.43 [95% CI, 1.10–1.85]) and associations were mediated by cognition and mental health (primarily by cognition): percent explained varied between 4% (NEET) to 70% (poor qualifications). In general, the risk of poor outcome increased by number of maltreatment types (eg, aOR for long-term sickness absence increased from 1.0 [reference] to 1.76 [95% CI, 1.32–2.35] to 2.69 [95% CI, 1.96–3.68], respectively, for 0, 1, and ≥2 types of maltreatment. CONCLUSIONS: Childhood maltreatment is associated with poor midadulthood socioeconomic outcomes, with accumulating risk for those experiencing multiple types of maltreatment. Cognitive ability and mental health are implicated in the pathway to outcome for neglect but not abuse.
NADPH Cytochrome P-450 Oxidoreductase and Susceptibility to Ketoconazole

ABSTRACT The phenotype of a strain of Saccharomyces cerevisiaecontaining a disruption of the gene encoding NADPH cytochrome P-450 oxidoreductase (CPR) was quantified biochemically and microbiologically, as were those of various transformants of this strain after expression of native CPR, cytochrome P-45051 (CYP51), and a fusion protein of CYP51-CPR (FUS). Only a 4-fold decrease in ergosterol biosynthesis was observed for the cpr strain, but ketoconazole sensitivity increased 200-fold, indicating hypersensitivity to the alternative electron donor system incpr strains. Both phenotypes could be reversed in transformants expressing the CPR and FUS, indicating the availability of the CPR in FUS as well as the expressed native CPR for monoxygenase-associated reactions. The complementation of function was observed both in vitro and in vivo for the monoxygenases squalene epoxidase, CYP51, and CYP61 in the ergosterol biosynthesis pathway with which CPR is coupled. Overexpression of CYP51 and FUS produced different levels of ketoconazole resistance in wild-type cells, indicating that the availability of CPR may limit the potential of overproduction of CYP51 as a mechanism of resistance to azole antifungal agents.
Tagging vs. Controlled Vocabulary: Which is More Helpful for Book Search?

The popularity of social tagging has sparked a great deal of debate on whether tags could replace or improve upon professionally assigned metadata as descriptors of books and other information objects. In this paper we present a large-scale empirical comparison of the contributions of individual metadata elements like core bibliographic data, controlled vocabulary terms, reviews, and tags to the retrieval performance. Our comparison is done using a test collection of over 2 million book records with metadata elements from Amazon, the British Library, the Library of Congress, and LibraryThing. We find that tags and controlled vocabulary terms do not actually outperform each other consistently, but seem to provide complementary contributions: some information needs are best addressed using controlled vocabulary terms whereas other are best addressed using tags.