Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Predicted Epimerases and Reductases of the Campylobacter jejuni d-altro- and l-gluco-Heptose Synthesis Pathways*

Background: Modified heptoses are important for bacterial virulence. Results: We characterized novel l-gluco-heptose synthesis enzymes from Campylobacter jejuni and compared their specificity with d-altro-heptose synthesis enzymes. Conclusion: Significant differences of activities and specificities were observed despite high sequence similarities. Significance: The versatility of the enzymes can be exploited to synthesize novel carbohydrates for technological applications and to develop therapeutic inhibitors. Uniquely modified heptoses found in surface carbohydrates of bacterial pathogens are potential therapeutic targets against such pathogens. Our recent biochemical characterization of the GDP-6-deoxy-d-manno- and GDP-6-deoxy-d-altro-heptose biosynthesis pathways has provided the foundation for elucidation of the more complex l-gluco-heptose synthesis pathway of Campylobacter jejuni strain NCTC 11168. In this work we use GDP-4-keto,6-deoxy-d-lyxo-heptose as a surrogate substrate to characterize three enzymes predicted to be involved in this pathway: WcaGNCTC (also known as Cj1427), MlghB (Cj1430), and MlghC (Cj1428). We compare them with homologues involved in d-altro-heptose production: WcaG81176 (formerly WcaG), DdahB (Cjj1430), and DdahC (Cjj1427). We show that despite high levels of similarity, the enzymes have pathway-specific catalytic activities and substrate specificities. MlghB forms three products via C3 and C5 epimerization activities, whereas its DdahB homologue only had C3 epimerase activity along its cognate pathway. MlghC is specific for the double C3/C5 epimer generated by MlghB and produces l-gluco-heptose via stereospecific C4 reductase activity. In contrast, its homologue DdahC only uses the C3 epimer to yield d-altro-heptose via C4 reduction. Finally, we show that WcaGNCTC is not necessary for l-gluco-heptose synthesis and does not affect its production by MlghB and MlghC, in contrast to its homologue WcaG81176, that has regulatory activity on d-altro-heptose synthesis. These studies expand our fundamental understanding of heptose modification, provide new glycobiology tools to synthesize novel heptose derivatives with biomedical applications, and provide a foundation for the structure function analysis of these enzymes.
Differentiating Homonymy and Polysemy in Information Retrieval

Recent studies into Web retrieval have shown that word sense disambiguation can increase retrieval effectiveness. However, it remains unclear as to the minimum disambiguation accuracy required and the granularity with which one must define word sense in order to maximize these benefits. This study answers these questions using a simulation of the effects of ambiguity on information retrieval. It goes beyond previous studies by differentiating between homonymy and polysemy. Results show that retrieval is more sensitive to polysemy than homonymy and that, when resolving polysemy, accuracy as low as 55% can potentially lead to increased performance.
REMOTE MEASUREMENT AND PREDICTION OF BREAKING WAVE PARAMETERS

The analysis of wave breaking in shallow water has been on-going for almost 150 years. Numerous research papers have been published that investigate methods to predict breaking conditions and the geometric characteristics of breaking waves. This study presents a novel, safe, and low cost method to extract breaking wave properties from irregular waves in the surf zone, using optical and in-situ measurement systems. Sensitivities studies on methods of measuring the breaking water depth are compared and the water depth at the wave trough depth, corrected for optical offsets using a still water correction of 1/3 wave height, is found to be exhibit the least variability. A new effective seafloor slope definition, based on individual breaking wavelength to depth ratios, was found to increase predictive ability over previously variable seafloor slope extraction methods. Collected field data is compared against established breaking wave height formulas with general exponential form consistently finding best correlation. An optimized breaking wave height predictor featured a root mean square relative error of only 1.672% against the measured dataset. Finally, the study of the geometric shape of the plunging wave vortex as a possible indicator for the breaking intensity of ocean waves has been ongoing for almost 50 years with limited success. The validity of using the vortex ratio and vortex angle as a method of predicting breaking intensity is examined. Through the first complete analysis of field collected irregular wave breaking vortex parameters it is illustrated that the vortex ratio and vortex angle cannot be accurately predicted using standard breaking wave characteristics and hence are not suggested as a possible indicator for breaking intensity
Colonization of the developing murine enteric nervous system and subsequent phenotypic expression by the precursors of peptidergic neurons

The development of peptidergic neurons was analyzed in the murine bowel. Neurons, detected immunocytochemically with antisera to substance P (SP) and vasoactive intestinal polypeptide (VIP), respectively, were selected for study. Explantation of the primordial bowel with subsequent growth in organotypic tissue culture served as an assay for the presence of neuronal precursor cells within the developing gut. One objective of the study was to determine whether the neural crest population that initially colonizes the mammalian bowel contains the precursors of peptidergic neurons as well as those of neurons that contain small molecule neurotransmitters, or whether peptidergic neurons are derived from a later migration of émigrés to the gut. A second objective was to compare the timing of peptidergic phenotypic expression with that of the small molecule neurotransmitters, acetylcholine (ACh) and serotonin (5‐HT). The precursors of peptidergic neurons were found to have colonized the bowel prior to the appearance of recognizable neurons of any type. The immunocytochemical detection of SP and VIP in vivo lagged behind the appearance of cholinergic and serotonergic markers by at least 2 days in the foregut and by greater than 3 days in the hindgut. Peptidergic neurons showed a proximodistal pattern of phenotypic expression. These observations support the hypothesis that the murine bowel is colonized by a single wave of precursor cells that contains the primordia of peptidergic neurons as well as neurons that use small molecule neurotransmitters. Data are consistent with the earlier expression of the small molecule phenotype. The proximodistal sequence of phenotypic expression in the absence of a similar sequence in precursor colonization supports an interaction between the precursors of enteric neurons and the microenvironment of the gut that modulates neuronal phenotypic expression.
Drugs and Platelet Activation in Migraine and Transient Ischemic Attacks

In order to study the role of platelets in migraine and cerebrovascular disease, beta-thromboglobulin (β-TG) and platelet factor 4 (PF4) plasma levels, indices of in vivo platelet activation, were assayed in two groups of patients suffering from migraine (common/classic and classic/complicated migraine, respectively) and in one group suffering from transitory ischemic attacks (TIAs). Plasma determinations were carried out in the absence of treatment and during the administration of aspirin (50 mg/daily) and flunarizine (10 mg/daily). Platelet activation was found in patients suffering from TIA; patients affected by classic and complicated migraine showed a high incidence of activation, in comparison with common migraine sufferers, also in headache-free periods. Administration of aspirin (ASA) was more effective than flunarizine in inducing a decrease in β-TG and PF4 plasma levels in migraineurs. Aspirin, however, did not affect platelet activation in subjects suffering from ischemic attack even though we did not observe any relapse after one year of treatment. The different effect of ASA in TIAs and migraine indicates that the platelet activation in TIA patients is due not only to cyclo-oxygenase pathway but also to other in vivo pathways.
Design of Axial Flux PM Synchronous Machines Through 3-D Coupled Electromagnetic Thermal and Fluid-Dynamical Finite-Element Analysis

This paper investigates the thermal behavior of axial flux synchronous permanent-magnet machines (AFSPMMs) through a 3-D thermal-magnetic finite-element analysis (FEA). This paper offers a systematic approach to magnetothermal FEA. The considered axial flux machine is wound on a soft magnetic compound core. The computation of thermal field is performed via a coupled thermal and fluid-dynamical model based on FEA, where the thermal sources are obtained from a DC current flow model and a magnetostatic model. This paper includes an overview of the finite-element method (FEM) model implementation. Simulation results are presented, and, to validate the model, the simulated surface temperature rise of the motor parts is compared by experimental data.
Kidney Transplantation in the Diabetic Patient

Diabetes mellitus is one of the most important causes of chronic kidney disease (CKD). In patients with advanced diabetic kidney disease, kidney transplantation (KT) with or without a pancreas transplant is the treatment of choice. We aimed to review current data regarding kidney and pancreas transplant options in patients with both type 1 and 2 diabetes and the outcomes of different treatment modalities. In general, pancreas transplantation is associated with long-term survival advantages despite an increased short-term morbidity and mortality risk. This applies to simultaneous pancreas kidney transplantation or pancreas after KT compared to KT alone (either living donor or deceased). Other factors as living donor availability, comorbidities, and expected waiting time have to be considered whens electing one transplant modality, rather than a clear benefit in survival of one strategy vs. others. In selected type 2 diabetic patients, data support cautious utilization of simultaneous pancreas kidney transplantation when a living kidney donor is not an option. Pancreas and kidney transplantation seems to be the treatment of choice for most type 1 diabetic and selected type 2 diabetic patients.
Efficient Competitive Equilibria with Adverse Selection

Do Walrasian markets function orderly in the presence of adverse selection? In particular, is their outcome efficient when exclusive contracts are enforceable? This paper addresses these questions in the context of a Rothschild‐Stiglitz insurance economy. We identify an externality associated with the presence of adverse selection as a special form of consumption externality. Consequently, we show that competitive equilibria always exist but are not typically incentive efficient. However, as markets for pollution rights can internalize environmental externalities, markets for consumption rights can be designed to internalize the consumption externality due to adverse selection. With such markets competitive equilibria exist and incentive‐constrained versions of the first and second welfare theorems hold.
Non-Linear Aspects of Outer Hair Cell Transduction and the Temporary Threshold Shifts after Acoustic Trauma

The 200-Hz cochlear microphonic potential (CM) and the compound action potential (CAP) of the auditory nerve evoked by tone-bursts were recorded in the basal turn of the cochlea of anaesthetised guinea pigs, before and after exposure to traumatic high-frequency tones that produce a temporary threshold shift (TTS) in this cochlear region. The drop in CM and the TTS were highly correlated, suggesting that it is the disruption of the outer hair cells generating the CM that causes the TTS. The previously measured rise in endocochlear potential and drop in organ of Corti K+ levels suggest that the TTS is due to a temporary closure of outer hair cell mechanoelectrical transduction (MET) channels, which produces a drop in the mechanical sensitivity of the organ of Corti, due to disruption of the active process provided by outer hair cells. The time course of the onset and recovery of TTS is consistent with a kinetic folding and refolding of MET channels over a time course of hours and days. Mathematical modelling of this putative channel folding suggests that TTS recovery may be accelerated by the presentation of additional sounds during the recovery period. We present electrophysiological data (CM and CAP measurements) showing that this accelerated recovery occurs. Using two-tone complexes (phase-locked 5- and 10-kHz traumatic tones, and 10-kHz traumatic tones with 25-Hz bias tones), we also show that the mechanisms producing TTS are non-linear and asymmetric, and that the greatest ‘trauma’ occurs when the hair bundles of outer hair cells are deflected away from the basal body of these cells (i.e. in the direction normally causing hyperpolarisation of the cell membrane potential).
Developmental Cognitive Neuroscience Neural Mechanisms of Inhibitory Control Continue to Mature in Adolescence

Keywords: Go/No-go task Adolescence Magnetoencephalography (MEG) Inhibitory control Inferior frontal gyri a b s t r a c t Inhibition is a fundamental executive function necessary for self-management of behaviour. The ability to withhold prepotent responses shows protracted development, extending through childhood and into adulthood. Using magnetoencephalography (MEG) with co-registered MRI, the spatiotemporal neural processes involved in inhibitory control were examined in 15 adolescents and 15 adults during a Go/No-go task. Two tasks were run that contained inverse ratios of Go to No-go trials for the experimental (2:1) and control conditions (1:2). Using vector beamforming, images of neural activation between No-go and Go trials were compared for both age-groups and revealed recruitment of the right inferior frontal gyrus in adults (BA 45; 200–250 ms), but delayed recruitment of the left inferior frontal gyri in adolescents (BA 45; 250–300 ms). Left anticipatory-related activity near the hand motor region (BA 6) was present in both adolescents and adults, but for a longer duration in adults. Adolescents additionally recruited the right middle and superior temporal gyri (BA21, BA22), while adults engaged the right temporal gyrus (BA41) but for a much briefer duration. These findings of delayed recruitment of canonical inhibitory control areas with supplementary and prolonged involvement of temporal areas in adolescents compared to adults indicate an immature inhibitory network even in adolescence.
Social brains, simple minds: does social complexity really require cognitive complexity?

The social brain hypothesis is a well-accepted and well-supported evolutionary theory of enlarged brain size in the non-human primates. Nevertheless, it tends to emphasize an anthropocentric view of social life and cognition. This often leads to confusion between ultimate and proximate mechanisms, and an over-reliance on a Cartesian, narratively structured view of the mind and social life, which in turn lead to views of social complexity that are congenial to our views of ourselves, rather than necessarily representative of primate social worlds. In this paper, we argue for greater attention to embodied and distributed theories of cognition, which get us away from current fixations on ‘theory of mind’ and other high-level anthropocentric constructions, and allow for the generation of testable hypotheses that combine neurobiology, psychology and behaviour in a mutually reinforcing manner.
Experimental Behavior of FRP Strengthened Masonry Arches

This paper deals with the experimental behavior of solid clay brick masonry arches strengthened with glass fiber-reinforced polymer composites. Twelve half-scaled segmental masonry arches subjected to a load applied at the quarter span were tested under displacement control up to failure. The arches were built using handmade low strength bricks and a commercial lime-based mortar, trying to mimic ancient structures. Besides reference unreinforced arches, five different strengthening arrangements, including the use of spike anchors, were studied. The experimental results provide significant information for validation of advanced numerical models and analytical tools and for code drafting. The experimental results also show that (1) only continuous strengthening strategies are able to prevent typical local failure mechanisms of unreinforced arches; (2) strengthening at the intrados is the most effective option to increase strength; and (3) strengthening applied at the extrados provides the higher deformation.
Specific expression and promoter analysis of the albumin gene promoter of the duck (Anas platyrhynchos domesticus)

ABSTRACT 1. Albumin (ALB) is a serum protein most highly expressed in liver and regarded as an effective indicator for liver pathologies. The objectives of this study were to determine the expression of duck ALB gene (duALB) in various non-hepatic tissues and identify the potential cis-regulatory elements in the promoter. 2. A model was established to assess duALB promoter activity in different cell lines by construction of a duALB promoter-driven GFP (Green Fluorescent Protein)-expressing vector, which exhibited high expression activity in liver-derived cells and lower expression in other cells. Through the firefly luciferase reporter gene driven by a series of constructs carrying progressive deletions, the core transcriptional regulatory region within the duALB promoter was identified. Mutations in candidate-binding sites were made by site-directed mutagenesis. 3. The core transcriptional regulatory region was located in the −190/−51 bp region. This region contains three potential transcription factor-binding sites, one each for hepatocyte nuclear factor (HNF-3β) (−158/−149), CCAAT/Enhancer-binding protein element (C/EBPα) (−119/−107) and nuclear factor-1 (HNF-1) (−67/−57). Site-directed mutagenesis of HNF-1 and C/EBPα-binding sites resulted in a significant reduction in duALB promoter activity. Two potential cis-regulatory elements (C/EBPα and HNF-1) were responsible for its transcriptional activity in liver-derived cells. 4. These findings contribute to the further understanding of the fundamental mechanisms of ALB gene regulation and the use of tissue-specific gene promoters to regulate tissue-specific expression of exogenous genes in vivo.
Semi-Supervised travel mode detection from smartphone data

With the advent of the incorporation of GPS receivers and then GPS-enabled smartphones in transportation data collection, many studies have looked at how to infer meaningful information from this data. Research in this field has concentrated on the use of heuristics and supervised machine learning methods to detect: trip ends, trip itineraries, travel mode and trip purpose. All the methods used until now have depended on methods relying uniquely on fully-validated data. However, respondent burden associated with validation lowers participation rates and results in less reliable data. In this paper, we propose the use of semi-supervised methods that use both validated and un-validated data. We compare the accuracy for two popular supervised methods (i.e. decision tree and random forest) with a simple semi-supervised method (i.e. label propagation with KNN kernel). We use speed, duration and length of trip, as well as proximity of trip start and end points to the transit network to detect mode of transport. The results show that the semi-supervised method slightly outperforms the supervised methods in the presence of high portions of unvalidated data, while run-times of the more efficient of the two supervised methods was on average almost 16 times longer than the average run-times of the semi-supervised method.
Durability and ageing of sealants

General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal
Cadmium concentration in muscle, liver and kidney of sheep slaughtered in Falavarjan abattoir, Iran

The aim of the present study was to investigate the levels of cadmium in sheep’s muscle, liver and kidney from Isfahan and also to compare them with the levels reported in several other countries and with the maximum tolerance levels for the human consumption. The samples of muscle, liver and kidney of 60 animals around 1 to 6 years old were collected from the carcasses slaughtered in Flavarjan abattoir, Isfahan. Samples (acid digested and cadmium concentrations) were determined by graphite furnace atomic absorption spectrophotometry (GFAAS). The mean fresh weight concentrations in muscle, liver and kidney were about 0.0017 mg/kg, 0.0743 mg/kg and 0.02290 mg/kg, respectively. The mean concentration of cadmium in tissue samples was generally lower than the maximum acceptable concentration in European Commission (EC). Statistical analysis revealed a significant difference in cadmium concentration of liver and kidney between various age groups (p < 0.05).
Classification and Representation of Conflict in Multi-Agent Systems

This paper explores the nature of conflict in agent-based systems. A conflict classification scheme based on a differentiation between goal, plan, and belief conflicts is presented. A formal definition of these three conflict classes is provided. A three layered representation of conflict is employed. Each layer is assigned to its respective conflict type (i.e. goal, plan, belief). The representation serves to trace the source(s) of conflict, provides a map to potential resolutions, and assists in resolving or avoiding conflicts.
Quantitative evaluation of urinalysis test strips.

BACKGROUND Urine test strip results are generally reported in categories (i.e., ordinal scaled), but automated strip readers are now available that can report quantitative data. We investigated the possible use of these meters to complement flow cytometry of urine and compared reflectance readings with quantitative determinations of urinary glucose and microalbumin. METHODS We compared URISYS 2400 (Roche) quantitative reflectance data with data from the UF-100 (Sysmex) and biochemical data for 436 nonpathologic and pathologic urine samples. RESULTS Reproducibility of the reflectance signal was good for high- and low-concentration urine pools for protein (0.8% and 0.9% and 1.5% and 2.2% within and between runs, respectively), leukocyte esterase (1.1% and 1.0%; 5.1% and 1.2%), hemoglobin (1.7% and 1.1%; 8.9% and 1.1%) and glucose (2.1% and 0.5%; 6.5% and 2.3%). Fair agreement was obtained between UF-100 and test strip reflectance data for erythrocytes and hemoglobin (r = -0.680) and leukocytes and leukocyte esterase (r = -0.688). Higher correlations were observed for biochemical and test strip data comparing protein and albumin (r = -0.825) and glucose data (r = -0.851). The lower limits of detection for erythrocytes and leukocytes were 8 x 10(6)/L and 19 x 10(6)/L, respectively. The protein test (n = 220) detected 86% (95% confidence interval, 78-92%) of samples with <30 mg/L albumin with a specificity of 84% (95% confidence interval, 76-91%). CONCLUSIONS In urine test strip analysis, quantitative hemoglobin and leukocyte esterase reflectance data are complementary with flow cytometric results and glucose and albumin results.