Miracle-dz/UniFAR-FTUs huggingface dataset:
The dependence of lipid asymmetry upon phosphatidylcholine acyl chain structure[S]

Lipid asymmetry, the difference in inner and outer leaflet lipid composition, is an important feature of biomembranes. By utilizing our recently developed MβCD-catalyzed exchange method, the effect of lipid acyl chain structure upon the ability to form asymmetric membranes was investigated. Using this approach, SM was efficiently introduced into the outer leaflet of vesicles containing various phosphatidylcholines (PC), but whether the resulting vesicles were asymmetric (SM outside/PC inside) depended upon PC acyl chain structure. Vesicles exhibited asymmetry using PC with two monounsaturated chains of >14 carbons; PC with one saturated and one unsaturated chain; and PC with phytanoyl chains. Vesicles were most weakly asymmetric using PC with two 14 carbon monounsaturated chains or with two polyunsaturated chains. To define the origin of this behavior, transverse diffusion (flip-flop) of lipids in vesicles containing various PCs was compared. A correlation between asymmetry and transverse diffusion was observed, with slower transverse diffusion in vesicles containing PCs that supported lipid asymmetry. Thus, asymmetric vesicles can be prepared using a wide range of acyl chain structures, but fast transverse diffusion destroys lipid asymmetry. These properties may constrain acyl chain structure in asymmetric natural membranes to avoid short or overly polyunsaturated acyl chains.
Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in the wild. Here we describe spatial and temporal resource partitioning among Vibrionaceae strains coexisting in coastal bacterioplankton. A quantitative model (AdaptML) establishes the evolutionary history of ecological differentiation, thus revealing populations specific for seasons and life-styles (combinations of free-living, particle, or zooplankton associations). These ecological population boundaries frequently occur at deep phylogenetic levels (consistent with named species); however, recent and perhaps ongoing adaptive radiation is evident in Vibrio splendidus, which comprises numerous ecologically distinct populations at different levels of phylogenetic differentiation. Thus, environmental specialization may be an important correlate or even trigger of speciation among sympatric microbes.
Penetration of Experimental Infiltrants with Different Penetration Coefficients and Ethanol Addition into Natural Caries Lesions in Primary Molars

This study evaluated the influence of the penetration coefficient (PC) and ethanol addition on the penetration depth (PD) of experimental infiltrants into proximal caries lesions in primary molars. Caries lesions (n = 45) were randomly treated with 1 of 4 experimental infiltrants (PC63; PC185; PC204; PC391) for 5 min. Lesion depths and PDs were analysed using dual fluorescence confocal microscopy. Lesions were almost completely infiltrated in all groups. Median PDs and percentage penetrations were not significantly different between groups (p > 0.05). When applied for 5 min, all tested infiltrants were able to infiltrate proximal caries in primary molars nearly completely.
Unsupervised Discovery of Morphemes

We present two methods for unsupervised segmentation of words into morpheme-like units. The model utilized is especially suited for languages with a rich morphology, such as Finnish. The first method is based on the Minimum Description Length (MDL) principle and works online. In the second method, Maximum Likelihood (ML) optimization is used. The quality of the segmentations is measured using an evaluation method that compares the segmentations produced to an existing morphological analysis. Experiments on both Finnish and English corpora show that the presented methods perform well compared to a current state-of-the-art system.
The effect of self-healing process on the strength increase in clay

Abstract In this study, the effect of an additive with nano-montmorillonite brand on the process of self-healing on clay soil was considered. Laboratory tests include Atterberg limits and unpressurized compressive strength on the natural soil and soil samples contain different weight percentages of the additive. The results reveal that the addition of the additive up to 5% of the soil dry weight led to significant changes in the physical and mechanical properties of improved soil such as increasing plasticity index, increasing compressive strength and consequently, increasing the self-healing on clay soil. These changes are functions of the weight percent of the additive and the age of the samples. Moreover, laboratory results were investigated by SEM and FESEM images. Data was collected from uniaxial test and Scanning Electron Microscope images indicate that the maximum amount of self-healing occurred in the samples with 5% nano-clay on the sixtieth day after the initial failure.
Corrosion Margins for Redundant Ship Structures

The work presented here analyses the structural corrosion degradation of two sets of corrosion depth measurements collected with a one-decade difference. The corrosion degradation process is associated to a first order system, subjected to a sudden disturbance, where a step function is used as an input to define the solution of the differential equation of this system leads to the exponential corrosion degradation model as developed earlier. Corrosion margins of redundant ship structures with serious consequences of failure are derived and several conclusions related to the new trend in the ageing structures are presented and discussed. Partial safety factors with respect to the corrosion environment and corrosion margins are developed that can be used in the design, avoiding a complex probabilistic analysis.
Current concepts in genetics of nonsyndromic clefts

Nonsyndromic cleft lip and palate is a complex genetic disorder with variable phenotype, largely attributed to the interactions of the environment and multiple genes, each potentially having certain effects. Numerous genes have been reported in studies demonstrating associations and/or linkage of the cleft lip and palate phenotypes to alleles of microsatellite markers and single nucleotide polymorphisms within specific genes that regulate transcription factors, growth factors, cell signalling and detoxification metabolisms. Although the studies reporting these observations are compelling, most of them lack statistical power. This review compiles the evidence that supports linkage and associations to the various genetic loci and candidate genes. Whereas significant progress has been made in the field of cleft lip and palate genetics in the past decade, the role of the genes and genetic variations within the numerous candidate genes that have been found to associate with the expression of the orofacial cleft phenotype remain to be determined.
Elimination of Nondeterminacy for Testing and Debugging Parallel Programs

Nondeterminacy implies two unpleasant properties for testing and debugging parallel programs: successive executions of the same program with the same input values often do not show identical behaviour and watching the program influences the execution. It is therefore not always possible to test and debug parallel programs like sequential ones. This article presents an approach how to make test, regression test and cyclic debugging as easy as in the sequential case. To meet this goal we provide the user with the ability to specify not only input data for tests, but also the sequence of interprocess communications. This also guarantees reproducibility for debugging and regression testing.
Joining of metal matrix composites using friction stir welding: a review

ABSTRACT The application of fusion welding process is restricted to certain grades of alloys and materials. Solid-state joining process offers greater advantages over fusion welding process such as fumeless and effective joining, minimum or no preparation time, environment friendly, etc. One such solid-state joining process is friction stir welding (FSW), which uses a non-consumable rotating tool. This rotating tool joins the two faying surfaces of the workpiece by forging them. This joining technique successfully joins metals, alloys and metal matrix composite (MMC), which are considered as difficult to join using conventional processes. The present study is an endeavor to review a specific domain of FSW, i.e. joining of MMCs. The initial part of the study provides a detailed introduction about the FSW process, and along with it, an overview of the published literature related to FSW of alloys has been presented. The later part of the study pays specific attention to macrostructure, microstructure, joint properties and residual stresses in welded joints along with wearing of tool during welding of MMC. The observations of this study provide a basis for future research in the specified domain.
Importance of autophosphorylation at Ser186 in the A‐loop of salt inducible kinase 1 for its sustained kinase activity

Autophosphorylation is an important mechanism by which protein kinases regulate their own biological activities. Salt inducible kinase 1 (SIK1) is a regulator in the feedback cascades of cAMP‐mediated gene expression, while its kinase domain also features autophosphorylation activity. We provide evidence that Ser186 in the activation loop is the site of autophosphorylation and essential for the kinase activity. Ser186 is located at the +4 position of the critical Thr residue Thr182, which is phosphorylated by upstream kinases such as LKB1. The relationship between phosphorylation at Ser186 and at Thr182 in COS‐7 cells indicates that the former is a prerequisite for the latter. Glycogen synthase kinase‐3β (GSK‐3β) phosphorylates Ser/Thr residues located at the fourth position ahead of the pre‐phosphorylated Ser/Thr residues, and inhibitors of GSK‐3β reduce the phosphorylation at Thr182. The results of an in vitro reconstitution assay also indicate that GSK‐3β could be the SIK1 kinase. However, overexpression and knockdown of GSK‐3β in LKB1‐defective HeLa cells suggests that GSK‐3β alone may not be able to phosphorylate or activate SIK1, indicating that LKB1 may play a crucial role by phosphorylating SIK1 at Thr182, possibly as an initiator of the autophosphorylation cascade, and GSK‐3β may phosphorylate SIK1 at Thr182 by recognizing the priming‐autophosphorylation at Ser186 in cultured cells. This may also be the case for the other isoform SIK2, but not for SIK3. J. Cell. Biochem. 104: 1724–1739, 2008. © 2008 Wiley‐Liss, Inc.
Thymic cyst: A fourth branchial cleft anomaly

We report a unique case of a fourth branchial cleft cyst found within the thymus of an adult patient. In the literature to date, there have been no reports of such a finding in the adult population. These anomalies can often cause recurrent acute suppurative thyroiditis or recurrent deep neck abscesses. Delay in recognizing the underlying etiology can lead to significant complications. Laryngoscope, 2010
Human bocavirus infections in hospitalized Greek children

Introduction The epidemiology of human bocavirus (HBoV) infections has not been described in Greece, a south-eastern European country. To define the epidemiological profile and the clinical characteristics associated with HBoV infection in a population of children hospitalized with respiratory tract infection. Material and methods During a one-year period throat swab samples were collected from 370 previously healthy children, aged 14 days to 13 years, admitted to two different paediatric wards because of respiratory tract infection. Samples were tested for HBoV by PCR amplifying a part of the NS1 gene. Results Human bocavirus was detected in 12 children (3.2%). Four of the 12 cases were co-infections, 3 of them with influenza A and 1 with coronavirus OC43. Cases were observed only during the cold months. The mean age of children was 1.8 years (range 2 months to 4 years). The most common symptoms were fever, cough and various degrees of respiratory distress. All children were clinically diagnosed as having lower respiratory tract infections, mainly pneumonia and acute laryngotracheobronchitis, and recovered uneventfully. Conclusions HBoV infections occur in Greece mostly among very young children. They accounted for 3.2% of children hospitalized with acute respiratory disease. Cases were observed only in late autumn to early spring.
A study of aerobic bacterial pathogens associated with vaginitis in reproductive age group women (15-45 years) and their sensitivity pattern

Background: Aerobic vaginitis (AV) is caused by a displacement of the healthy vaginal Lactobacillus species with aerobic pathogens such as Enterococcus faecalis, Escherichia coli and Staphylococcus aureus that triggers a localized vaginal inflammatory immune response. AV if it is not diagnosed and treated early, especially during pregnancy can place the health of both the mother and the foetus at risk as it is associated with preterm birth, premature rupture of membranes (PROM) and chorioamnionitis. Hence the present study aims at analysing the prevalence of aerobic vaginitis in females in the reproductive age group (15-45 years) with special reference to pregnancy, pathogens involved and their antibiogram. Methods: Over one year period, high vaginal swabs were collected from 125 women with clinical suspicion of vaginitis. They were then subjected to Gram’ staining and culture was made onto blood agar, chocolate agar and MacConkey agar and incubated aerobically at 37 0c for 24 hours. The AV score was determined and the organisms were then identified and antibiotic sensitivity test of isolates were performed. Results: The prevalence of Aerobic vaginitis in this study was 20.8% (26/125) and the most common age group affected was between 26-30 years. Out of the 26 positive cases, 21 samples yielded monobacterial growth and 5 cases polybacterial growth. The most common organism isolated was Enterococcus faecalis (32.26%), followed by Escherichia coli (25.8%), Staphylococcus aureus (19.35%) and β-hemolytic streptococci (9.68%). Antibiotics like β–lactams/ β–lactamase inhibitor combinations, vancomycin and linezolid were found to be more effective against all Gram positive isolates whereas the Gram negative isolates were more sensitive towards β–lactams/ β–lactamase inhibitor combination, aminoglycosides and meropenem. Conclusions: This study emphasized on the need to identify the aerobic vaginal pathogens associated with vaginitis especially in reproductive age group women which can go a long way in preventing the adverse outcomes associated with pregnancy and also ensures the necessity to determine the antibiotic sensitivity pattern of the pathogens which can aid in making a suitable therapeutic choice for 'aerobic vaginitis' by considering an antibiotic that is characterized by an intrinsic activity against the majority of bacteria of faecal origin, bactericidal effect and without any interference with the vaginal microbiota.
Lithium but not carbamazepine augments antidepressant efficacy of mirtazapine in unipolar depression: An open-label study

Background. The purpose of the present open-label study was to investigate the antidepressant efficacy of lithium and carbamazepine as augmentation strategies in unipolar depressed inpatients. Method. Forty-six patients suffering from unipolar depression (major depressive episode according to DSM-IV criteria) were pre-treated with mirtazapine for 2 weeks initially (week −2 to week 0). Thereafter, the patients received either continuation of mirtazapine monotherapy (n = 23), combination treatment with mirtazapine and lithium (n = 13), or combination therapy with mirtazapine and carbamazepine (n = 10) for further 3 weeks (week 0 to week 3). Severity of depression was estimated weekly using the 21-item version of the Hamilton Depression Rating Scale (21-HAMD). Response was defined by a reduction of at least 50% in the 21-HAMD sum score after 3 weeks of pharmacotherapy (week 0–3). Results. Additional administration of lithium, but not adjunctive carbamazepine significantly augmented the antidepressant efficacy of mirtazapine in the unipolar depressed patients. Moreover, carbamazepine but not lithium significantly lowered the serum concentrations of mirtazapine. Conclusion. Whereas the clinical importance of anticonvulsants in the treatment of bipolar disorder is not in doubt, the therapeutic efficacy of antiepileptic drugs such as carbamazepine is obviously limited in the pharmacotherapy of unipolar depression.
Micro-CT evaluation of residual material in canals filled with Activ GP or GuttaFlow following removal with NiTi instruments.

AIM To assess the efficacy of removing Activ GP or GuttaFlow from canals using NiTi instruments. METHODOLOGY Root canals in 55 extracted pre-molars were prepared to apical size 40, 0.04 taper. The teeth were imaged with micro-CT, and 30 teeth selected that had consistent apical size and taper of the shaped canals. They were randomly assigned to root filling with either the glass-ionomer-based ActivGP system (n = 15) or the polyvinylsiloxane-based GuttaFlow system (n = 15). After 2 weeks, canals were retreated stepwise with size 40-50 EndoSequence 0.04 taper instruments. Micro-CT scans (8 mum) were taken after use of each instrument to detect root filling residue in the coronal, middle and apical segment, and the retreatment time recorded. Residue, expressed as percentage of canal surface area, was compared between groups with t-tests, and within groups with repeated measures anova and Bonferroni-adjusted pairwise comparisons. Retreatment time was analysed with one-way anova. RESULTS The percentage of sealer residue-coated canal surface was consistently highest (P < 0.001) in the apical third of canals, and it did not differ significantly between the two root filling groups. Stepwise enlargement from size 40 to 50 significantly decreased the amount of sealer residue in both groups (P < 0.001). Retreatment time did not differ significantly between groups. CONCLUSIONS Both root fillings with ActivGP and GuttaFlow were removed with nickel-titanium rotary instruments. Enlargement of canals up to two sizes beyond the pre-retreatment size was necessary to minimize the amount of sealer remaining.
An Information Theoretic Approach to Text Sentiment Analysis

Most approaches to text sentiment analysis rely on human generated lexicon-based feature selection methods, supervised vector-based learning methods, and other solutions that seek to capture sentiment information. Most of these methods, in order to yield acceptable accuracy, require a complex preprocessing stage and careful feature engineering. This paper introduces a coding-theoretic-based sentiment analysis method that dispenses with any text preprocessing or explicit feature engineering, but still achieves state-of-the-art accuracy. By applying theZiv-Merhav methodto estimate the relative entropy (Kullback-Leibler divergence) and the cross parsing length from pairs of sequences of text symbols, we get information theoretic measures that make very few assumptions about the models which are assumed to have generated the sequences. Using these measures, we follow a dissimilarity space approach, on which we apply a standard support vector machine classifier. Experimental evaluation of the proposed approach on a text sentiment analysis problem (more specifically, movie reviews sentiment polarity classification) reveals that it outperforms the previous state-of-the-art, despite being much simpler than the competing methods.
The distribution of exoplanet masses

The present study derives the distribution of secondary masses M2 for the 67 exoplanets and very low-mass brown-dwarf companions of solar-type stars, known as of April 4, 2001. This distribution is related to the distribution of M2 sini through an integral equation of Abel's type. Although a formal solution exists for this equation, it is known to be ill-conditioned, and is thus very sensitive to the statistical noise present in the input M2 sini distribution. To overcome this diculty, we present two robust, independent approaches: (i) the formal solution of the integral equation is numerically computed after performing an optimal smoothing of the input distribution and (ii) the Lucy-Richardson algorithm is used to invert the integral equation. Both approaches give consistent results. The resulting statistical distribution of exoplanet true masses reveals that there is no reason to ascribe the transition between giant planets and brown dwarfs to the threshold mass for deuterium ignition (about 13.6 MJ). The M2 distribution shows instead that most of the objects have M2 10 MJ, but there is a small tail with a few heavier candidates around 15 MJ.
RhlA Converts β-Hydroxyacyl-Acyl Carrier Protein Intermediates in Fatty Acid Synthesis to the β-Hydroxydecanoyl-β-Hydroxydecanoate Component of Rhamnolipids in Pseudomonas aeruginosa

ABSTRACT Pseudomonas aeruginosa secretes a rhamnolipid (RL) surfactant that functions in hydrophobic nutrient uptake, swarming motility, and pathogenesis. We show that RhlA supplies the acyl moieties for RL biosynthesis by competing with the enzymes of the type II fatty acid synthase (FASII) cycle for the β-hydroxyacyl-acyl carrier protein (ACP) pathway intermediates. Purified RhlA forms one molecule of β-hydroxydecanoyl-β-hydroxydecanoate from two molecules of β-hydroxydecanoyl-ACP and is the only enzyme required to generate the lipid component of RL. The acyl groups in RL are primarily β-hydroxydecanoyl, and in vitro, RhlA has a greater affinity for 10-carbon substrates, illustrating that RhlA functions as a molecular ruler that selectively extracts 10-carbon intermediates from FASII. Eliminating either FabA or FabI activity in P. aeruginosa increases RL production, illustrating that slowing down FASII allows RhlA to more-effectively compete for β-hydroxydecanoyl-ACP. In Escherichia coli, the rate of fatty acid synthesis increases 1.3-fold when RhlA is expressed, to ensure the continued formation of fatty acids destined for membrane phospholipid even though 24% of the carbon entering FASII is diverted to RL synthesis. Previous studies have placed a ketoreductase, called RhlG, before RhlA in the RL biosynthetic pathway; however, our experiments show that RhlG has no role in RL biosynthesis. We conclude that RhlA is necessary and sufficient to form the acyl moiety of RL and that the flux of carbon through FASII accelerates to support RL production and maintain a supply of acyl chains for phospholipid synthesis.