Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered alanine plasma levels despite normalized hepatic alanine extraction in the long-term course after liver transplantation

Background. The amino acid (AA) metabolism in cirrhosis is deranged, reflected by an altered plasma AA profile. Alanine is a unique AA with predominant production by muscle and the highest hepatic extraction rate. Methods. We studied circulating levels and hepatic alanine extraction in 52 patients with advanced cirrhosis, 16 stable patients more than 6 months after orthotopic liver transplant (OLT), and 50 controls. In addition, hepatic hemodynamics (portal pressure, hepatic blood flow, and splanchnic percent indocyanine green extraction) and parameters of hepatic metabolism (splanchnic oxygen uptake and splanchnic glucose production) were assessed. Results. Circulating alanine levels decreased independently of the clinical stage in cirrhosis (262±15 &mgr;mol/L vs. 330±14 &mgr;mol/L in controls, P <0.001) and decreased even further after OLT (209±10 &mgr;mol/L, P <0.001). Hepatic alanine extraction decreased dependently on the clinical stage in cirrhosis (59±7 &mgr;mol/min) and was normalized after OLT (100±10 &mgr;mol/min, P <0.001), indicating that decreased plasma alanine levels in OLT patients are the result of changes in extrahepatic metabolism. Hepatic alanine extraction correlated with splanchnic oxygen uptake (r =0.64, P <0.001) and hepatic glucose production (r =0.65, P <0.001). Conclusions. These results demonstrate that significant alterations in muscular AA metabolism persist even in the clinically stable long-term course after OLT when the hepatic AA metabolism is normalized.
Multiuser OFDM with adaptive subcarrier, bit, and power allocation

Multiuser orthogonal frequency division multiplexing (OFDM) with adaptive multiuser subcarrier allocation and adaptive modulation is considered. Assuming knowledge of the instantaneous channel gains for all users, we propose a multiuser OFDM subcarrier, bit, and power allocation algorithm to minimize the total transmit power. This is done by assigning each user a set of subcarriers and by determining the number of bits and the transmit power level for each subcarrier. We obtain the performance of our proposed algorithm in a multiuser frequency selective fading environment for various time delay spread values and various numbers of users. The results show that our proposed algorithm outperforms multiuser OFDM systems with static time-division multiple access (TDMA) or frequency-division multiple access (FDMA) techniques which employ fixed and predetermined time-slot or subcarrier allocation schemes. We have also quantified the improvement in terms of the overall required transmit power, the bit-error rate (BER), or the area of coverage for a given outage probability.
Bioequivalence study of two formulations of candesartan cilexetil tablet in healthy subjects under fasting conditions

Introduction The present study was conducted to compare the bioavailability of two candesartan cilexetil 16 mg tablet formulations (test and reference formulations). Materials and methods This study was a randomized, single- blind, two-period, cross-over study which included 24 healthy adult male and female subjects under fasting conditions. The pharmacokinetic parameters were determined based on the concentrations of candesartan (CAS 139481-59-7), using ultra-pressure high-performance liquid chromatography with a tandem mass spectrometer detector. In each of the two study periods (separated by a washout period of 1 week), a single dose of test or reference product was administered. The pharmacokinetic parameters assessed were area under the plasma concentration time curve (AUC) from time 0 hours to 24 hours, AUC from time zero to infinity, the peak plasma concentration of the drug (Cmax), time to achieve the Cmax, and the elimination half-life. Results The geometric mean ratios (90% confidence interval) of the test drug/reference drug for candesartan were 100.92% (92.15%–110.52%) for the AUC from 0 hours to 24 hours, 100.24% (92.24%–108.95%) for the AUC from time zero to infinity, and 106.71% (93.20%–122.18%) for the Cmax. The differences between the test and reference product in the time to achieve Cmax values and elimination half-life values were not statistically significant (P > 0.05). The 90% confidence intervals of the test/reference AUC ratio and Cmax ratio of candesartan were within the acceptance range for bioequivalence. There was no adverse event encountered during this bioequivalence study. Conclusion It was concluded that the two candesartan tablet formulations (the test and reference product) were bioequivalent.
Mining sequence annotation databanks for association patterns

MOTIVATION Millions of protein sequences currently being deposited to sequence databanks will never be annotated manually. Similarity-based annotation generated by automatic software pipelines unavoidably contains spurious assignments due to the imperfection of bioinformatics methods. Examples of such annotation errors include over- and underpredictions caused by the use of fixed recognition thresholds and incorrect annotations caused by transitivity based information transfer to unrelated proteins or transfer of errors already accumulated in databases. One of the most difficult and timely challenges in bioinformatics is the development of intelligent systems aimed at improving the quality of automatically generated annotation. A possible approach to this problem is to detect anomalies in annotation items based on association rule mining. RESULTS We present the first large-scale analysis of association rules derived from two large protein annotation databases-Swiss-Prot and PEDANT-and reveal novel, previously unknown tendencies of rule strength distributions. Most of the rules are either very strong or very weak, with rules in the medium strength range being relatively infrequent. Based on dynamics of error correction in subsequent Swiss-Prot releases and on our own manual analysis we demonstrate that exceptions from strong rules are, indeed, significantly enriched in annotation errors and can be used to automatically flag them. We identify different strength dependencies of rules derived from different fields in Swiss-Prot. A compositional breakdown of association rules generated from PEDANT in terms of their constituent items indicates that most of the errors that can be corrected are related to gene functional roles. Swiss-Prot errors are usually caused by under-annotation owing to its conservative approach, whereas automatically generated PEDANT annotation suffers from over-annotation. AVAILABILITY All data generated in this study are available for download and browsing at http://pedant.gsf. de/ARIA/index.htm.
Biomarkers of subclinical inflammation and increases in glycaemia, insulin resistance and beta-cell function in non-diabetic individuals: the Whitehall II study.

OBJECTIVE Higher systemic levels of pro-inflammatory biomarkers and low adiponectin are associated with increased risk of type 2 diabetes, but their associations with changes in glycaemic deterioration before onset of diabetes are poorly understood. We aimed to study whether inflammation-related biomarkers are associated with 5-year changes in glucose and insulin, HbA1c, insulin sensitivity and beta-cell function before the diagnosis of type 2 diabetes and whether these associations may be bidirectional. DESIGN AND METHODS We used multiple repeat measures (17 891 person-examinations from 7683 non-diabetic participants) from the Whitehall II study to assess whether circulating high-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL6), IL1 receptor antagonist (IL1Ra) and adiponectin are associated with subsequent changes in glycaemia, insulin, insulin resistance and beta-cell function (based on oral glucose tolerance tests). We examined bidirectionality by testing if parameters of glucose metabolism at baseline are associated with changes in inflammation-related biomarkers. RESULTS Higher hsCRP and IL6 were associated with increases in fasting insulin, insulin resistance and, for IL6, with beta-cell function after adjustment for confounders. Higher adiponectin was associated with decreases in fasting glucose, HbA1c, fasting insulin, insulin resistance and beta-cell function. The reverse approach showed that 2-h glucose and insulin sensitivity were associated with changes in IL1Ra. Fasting insulin and insulin resistance showed inverse associations with changes in adiponectin. CONCLUSIONS Subclinical inflammation is associated with development of increased glycaemia, insulin resistance and beta-cell function in non-diabetic individuals. These findings are consistent with the hypothesis that inflammation-related processes may increase insulin resistance and lead to a compensatory upregulation of beta-cell function.
Exponential Stabilization of the Wave Equation by Dirichlet Integral Feedback

We consider the problem of boundary feedback stabilization of a vibrating string that is fixed at one end and with control action at the other end. In contrast to previous studies that have required $L^2$-regularity for the initial position and $H^{-1}$-regularity for the initial velocity, in this paper we allow for initial positions with $L^1$-regularity and initial velocities in $W^{-1,1}$ on the space interval. It is well known that for a certain feedback parameter, for sufficiently regular initial states the classical energy of the closed-loop system with Neumann velocity feedback is controlled to zero after a finite time that is equal to the minimal time where exact controllability holds. In this paper, we present a Dirichlet boundary feedback that yields a well-defined closed-loop system in the ($L^1$, $W^{-1,1}$) framework and also has this property. Moreover, for all positive feedback parameters our feedback law leads to exponential decay of a suitably defined $L^1$-energy. For more regular initia.
Spatial Distribution of Protein Damage by Singlet Oxygen in Keratinocytes

Singlet oxygen may be generated in cells by either endogenous or exogenous photosensitizers as a result of exposure to UV or visible irradiation. We have used immuno‐spin trapping (Free Radic. Biol. Med. 36: 1214, 2004) to identify the subcellular targets of singlet oxygen generated by rose bengal (RB). Confocal fluorescence microscopy of HaCaT keratinocytes incubated with RB clearly showed that the dye entered the cells and was located mainly in the perinuclear region, probably associated with the Golgi apparatus and endoplasmic reticulum. Previous studies by Wright et al. (Free Radic. Biol. Med.34: 637, 2003) have shown that long‐lived protein hydroperoxides (POOH) are present in cells exposed to singlet oxygen‐generating dyes. The addition of reducing metal ions such as Cu+ to POOH results in the generation of protein‐derived radicals, POO• and PO•, which react with the spin trap 5,5‐dimethyl‐1‐pyrroline N‐oxide (DMPO) to give relatively stable spin adducts. In order to determine the subcellular localization of the protein‐DMPO adducts, we exposed keratinocytes to RB/light exposure and then incubated the cells with Cu+ and DMPO. After staining with antibody against DMPO followed by a secondary Alexa Fluor 488 goat anti‐rabbit IgG, the intracellular distribution of protein‐DMPO adducts was determined by confocal microscopy. The subcellular localization of the protein DMPO adducts was coincident with that of RB. This approach may provide information on the spatial distribution of singlet oxygen generated in cells.
Differential effects of octreotide and pasireotide on somatostatin receptor internalization and trafficking in vitro.

OBJECTIVE The clinically used somatostatin analogs, octreotide and lanreotide, act primarily by binding to somatostatin receptor 2 (sst2). In contrast, the novel multireceptor ligand pasireotide (SOM230) binds with high affinity to somatostatin receptor subtypes sst1, sst2, sst3, and sst5. SOM230 is currently under clinical evaluation for treatment of acromegaly, Cushing's disease, and octreotide-resistant carcinoid tumors. However, the effects of SOM230 on internalization and postendosomal sorting of individual human somatostatin receptor subtypes have not been determined so far. RESULTS Here we show that SOM230 was less potent than octreotide in inducing internalization and signaling of sst2 receptors expressed in human embryonic kidney cells. In contrast, SOM230 was more potent than octreotide in inducing internalization and signaling of sst3 and sst5 receptors. Both SOM230 and octreotide stimulated a rapid down-regulation of sst3 but not of sst2 or sst5 receptors. SOM230 and octreotide profoundly differed in their patterns of sst2-stimulated beta-arrestin mobilization. Whereas octreotide-mediated receptor activation led to the formation of stable complexes facilitating the internalization of sst2 and beta-arrestin-2 into the same endocytic vesicles, SOM230-mediated receptor activation led to the formation of unstable complexes that dissociated at or near the plasma membrane. Consequently, sst2 receptors recycled rapidly to the plasma membrane after endocytosis in SOM230-treated cells, but not in octreotide-treated cells. CONCLUSION We show that SOM230 modulates somatostatin receptor trafficking in a manner clearly distinct from octreotide and somatostatin. These findings may provide an explanation for the differential regulation of somatostatin receptor responsiveness during long-term administration of stable somatostatin analogs.
Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure.

Copper has been intensively used in industry and agriculture since mid-18(th) century and is currently accumulating in soils. We investigated the diversity of potential active bacteria by 16S rRNA gene transcript amplicon sequencing in a temperate grassland soil subjected to century-long exposure to normal (∼15 mg kg(-1)), high (∼450 mg kg(-1)) or extremely high (∼4500 mg kg(-1)) copper levels. Results showed that bioavailable copper had pronounced impacts on the structure of the transcriptionally active bacterial community, overruling other environmental factors (e.g. season and pH). As copper concentration increased, bacterial richness and evenness were negatively impacted, while distinct communities with an enhanced relative abundance of Nitrospira and Acidobacteria members and a lower representation of Verrucomicrobia, Proteobacteria and Actinobacteria were selected. Our analysis showed the presence of six functional response groups (FRGs), each consisting of bacterial taxa with similar tolerance response to copper. Furthermore, the use of FRGs revealed that specific taxa like the genus Nitrospira and several Acidobacteria groups could accurately predict the copper legacy burden in our system, suggesting a potential promising role as bioindicators of copper contamination in soils.
Efficient processing and expression of human nerve growth factor receptors in Xenopus laevis oocytes: effects on maturation

The nerve growth factor (NGF) receptor is an integral membrane protein that is phosphorylated and heavily glycosylated. Determination of the amino acid sequence by molecular cloning indicates that the receptor is a cysteine-rich protein which contains a signal peptide sequence and spans the lipid bilayer with a single transmembrane sequence. A single mRNA of 3.8 kilobases was observed for the receptor, of which 1.5 kilobases is coding sequence. We have used microinjection of receptor RNA in Xenopus laevis oocytes to obtain cell surface expression of the receptor. The presence of NGF receptors in oocytes was verified by radioimmunoassay, specific binding of [125I]NGF, and metabolic labeling followed by immunoprecipitation. The NGF receptor protein was rapidly processed in oocytes and displayed extensive glycosylation. Furthermore, the presence of NGF receptors in oocytes potentiates the ability of progesterone to induce maturation.
Intravitreal delivery of oligonucleotides by sterically stabilized liposomes.

PURPOSE The efficacy of sterically stabilized liposomes for delivering a model phosphodiester oligonucleotide intravitreally was investigated in the rabbit. METHODS Ocular distribution and clearance from the vitreous humor of a model 16-mer oligothymidylate (pdT16) were evaluated in the rabbit by radioactivity measurements after intravitreal injection of either a solution or liposomes containing the [33P]pdT16 oligonucleotide. The integrity of pdT16 was investigated using a competitive hybridization assay. RESULTS The residual concentration of the [33P]pdT16 oligonucleotide within the ocular tissues was significantly increased after intravitreal administration of the liposomal suspension compared with a simple solution. Administration of liposome-encapsulated pdT16 oligonucleotide resulted in sustained release into the vitreous and the retina-choroid compared with release from the solution and in a reduced distribution to nontarget tissues (sclera, lens). In addition, liposomes protected the phosphodiester oligonucleotide against degradation. This was not observed after administration of the free oligonucleotide. CONCLUSIONS The intravitreal injection of a phosphodiester oligonucleotide encapsulated within liposomes is a new way of delivering intact oligonucleotide to the eye in a controlled manner. This offers interesting prospects for the treatment of retinal diseases.
Differentiating Behavioral Ratings of Inattention, Impulsivity, and Hyperactivity in Children

Objective: The purpose of the study is to differentiate between behaviors of ADHD: inattention, hyperactivity, and impulsivity and how each domain contributes to reading achievement in elementary school-aged children. Method: Data from 131 children were collected, which include performance from reading fluency and comprehension measures as well as parent and teacher ratings of ADHD behaviors based on the Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) criteria. Results: Correlation and regression analyses revealed that inattentive behaviors were strongly linked to reading fluency and comprehension. Hyperactivity and impulsive behaviors did not predict reading achievement. A significant two-way interaction was found only for gender and inattention with reading comprehension as the outcome. Conclusion: Many of the behaviors related to inattention strongly predicted reading fluency, reading comprehension, and overall reading ability. Boys who exhibited inattentive behaviors performed more poorly on reading comprehension measures than girls with inattentive behaviors.
Relay Selection for Cooperative MAC Considering Retransmission Overhead

Relay node (RN) plays a key role in cooperative communications and RN selection may substantially affects the performance gain. In this paper we address the issue of RN selection while taking into account Medium Access Control (MAC) overhead, which is incurred by not only handshake signaling but also frame retransmissions due to transmission error. We use a theoretical model to analyze the cooperation performance gains of cooperative MAC mechanism, and are thus able to select the optimal relay node. We derive the network saturation throughput of the designed MAC with our RN selection algorithm. Numerical results validate the effectiveness of our analytical model and show that our designed MAC significantly outperforms existing cooperative MAC mechanisms which do not consider retransmission MAC overhead.
Efficacy of Deer Stopper™ Repellent for Reducing White-Tailed Deer Damage to Ornamental Plantings

A 2-year study was undertaken to assess the efficacy of Deer Stopper repellent for reducing white-tailed deer damage to ornamental plantings. Efficacy testing was conducted on a captive deer herd at Auburn University’s White-tailed Deer Research Facility and the Stimpson Wildlife Sanctuary, Jackson, AL. Japanese Holly (Ilex crenata), a highly preferred browse species in this area, was used as the test plant at all study sites. Plants were arranged randomly between treatment and control. Treatment plants were sprayed with prescribed applications of Deer Stopper and percent defoliation and browsing estimated for each plant. Repeated measures analysis of variance was used to compare effectiveness of treatments. During the first 3 months of the study, deer became acclimated to the plants with little browsing pressure to either treatment or control plants. Once deer began to browse on the shrubs consistently, the mean number of leaves on treatment plants was significantly higher (df=26,1; F=22.11; P=0.000) than the mean number of leaves on control plants. Preliminary analyses of these data suggest that Deer Stopper was effective in reducing browsing damage to Japanese Holly.
GEAR: A Good Enough Architectural Requirements Process

The GEAR process integrates three approaches to architectural requirements engineering: model-driven requirements engineeering, quality attribute scenarios, and global analysis, within an iterative, incremental analysis process. In so doing, it shows where these methods overlap and where they complement each other. It also adds insight into the differences between product requirements and architecture requirements. GEAR incorporates experience from over a dozen diverse industrial software architecture projects.
Role and potentials of low-flow CO2 removal system in mechanical ventilation

Purpose of reviewAn analysis of the technological implementation of extracorporeal CO2 removal (ECCO2R) techniques and of its clinical application. A new classification of ECCO2R, based on technological aspects, clinical properties and physiological performance, is proposed. Recent findingsThe use of a ventilation with lower tidal volumes has been proved successful in acute respiratory distress syndrome (ARDS) patients but can be extremely problematic, especially when dealing with respiratory acidosis. The implementation of ECCO2R devices can represent the missing link between the prevention of ventilator-induced lung injury and pH control. ECCO2R has attracted increasing interest because of new less-invasive approaches allowing an easier management of ARDS patients. Recent studies have also shown that ECCO2R can also be used in patients with exacerbation of chronic obstructive pulmonary disease (COPD) and as a bridge to lung transplantation. SummaryThe future ventilatory management of patients with acute respiratory failure may include a minimally invasive extracorporeal carbon dioxide removal circuit associated with the least amount of ventilatory support (noninvasive in COPD and/or invasive in ARDS) to minimize sedation, prevent ventilator-induced acute lung injury and nosocomial infections. Randomized clinical trials in the pipeline will confirm this fascinating hypothesis.
Summarization Techniques : A Brief Survey

In recent years, there has been a explosion in the amount of text data from a variety of sources. This volume of text is an invaluable source of information and knowledgewhich needs to be e ectively summarized to be useful. In this review, the main approaches to automatic text summarization are described. We review the di erent processes for summarization and describe the e ectiveness and shortcomings of the di erent methods.
Achieving fully proportional representation is easy in practice

We provide experimental evaluation of a number of known and new algorithms for approximate computation of Monroe's and Chamberlin-Courant's rules. Our experiments, conducted both on real-life preference-aggregation data and on synthetic data, show that even very simple and fast algorithms can in many cases find near-perfect solutions. Our results confirm and complement very recent theoretical analysis of Skowron et al., who have shown good lower bounds on the quality of (some of) the algorithms that we study.