Miracle-dz/UniFAR-FTUs huggingface dataset:
FtsZ ring formation without subsequent cell division after replication runout in Escherichia coli

In this report, we have investigated cell division after inhibition of initiation of chromosome replication in Escherichia coli. In a culture grown to the stationary phase, cells containing more than one chromosome were able to divide some time after restart of growth, under conditions not allowing initiation of chromosome replication. This shows that there is no requirement for cell division to take place within a certain time after initiation of chromosome replication. Continued growth without initiation of replication resulted in filamented cells that generally did not have any constrictions. Interestingly, FtsZ rings were formed in a majority of these cells as they reached a certain cell length. These rings appeared and were maintained for some time at the cell quarter positions on both sides of the centrally localized nucleoid. These results confirm previous findings that cell division sites are formed independently of chromosome replication and indicate that FtsZ ring assembly is dependent on cell size rather than on the capacity of the cell to divide. Disruption of the mukB gene caused a significant increase in the region occupied by DNA after the replication runout, consistent with a role of MukB in chromosome condensation. The aberrant nucleoid structure was accompanied by a shift in FtsZ ring positioning, indicating an effect of the nucleoid on the positioning of the FtsZ ring. A narrow cell length interval was found, under and over which primarily central and non‐central FtsZ rings, respectively, were observed. This finding correlates well with the previously observed oscillatory movement of MinC and MinD in short and long cells.
An Investigation of the Discriminatory Ability of the Clustering Effect of the Frailty Survival Model

A strategy is proposed to examine the importance of the clustering effect of the frailty model by means of the concordance probability. To this end, the methodology proposed in earlier work is extended to general frailty models and a new definition of the concordance probability is developed. The resulting measures allow to separate the discriminatory ability of the covariate effects and the clustering effect on a within- and between-cluster level. Using a Bayesian and a likelihood approach, point estimates and 95% credible/ confidence intervals are computed for the measures. Estimation properties and sensitivity against misspecification are checked in an extensive simulation study. As such, the likelihood estimation procedure showed difficulties in estimating unbiasedly the predictive ability of the clustering effect, while the Bayesian estimation procedure resulted in good estimation properties for all three measures. Other features are developed to complement the earlier methodology, such as an internal validation strategy as well as a procedure to calculate internally validated interval estimates in the presence of clustered data. The ensemble of the developments is illustrated on a dental data set.
Optimizing the crystal size and habit of β-sitosterol in suspension

The aim of this work was to survey how processing parameters affect the crystal growth of β-sitosterol in suspension. The process variables studied were the cooling temperature, stirring time and stirring rate during recrystallization. In addition, we investigated the effect a commonly used surfactant, polysorbate 80, has on crystal size distribution and the polymorphic form. This study describes the optimization of the crystallization process, with the object of preparing crystals as small as possible. Particle size distribution and habit were analyzed using optical microscopy, and the crystal structure was analyzed using X-ray diffractometry. The cooling temperature had a remarkable influence on the crystal size. Crystals with a median crystal length of ≈23 μm were achieved with a low cooling temperature (<10°C); however, a fairly large number of crystals over 50 μm appeared. Higher cooling temperatures (>30°C) caused notable crystal growth both in length and width. Rapid (250 rpm), continuous stirring until the suspensions had cooled to room temperature created small, less than 50 μm long (median <20 μm), needle-shaped crystals. The addition of surfactant slightly reduced the size of the initially large crystals. Both hemihydrate and monohydrate crystal forms occurred throughout, regardless of the processing parameters. By using an optimized process, it was possible to obtain a microcrystalline suspension, with a smooth texture.
Differential gene expression during capillary morphogenesis in a microcarrier-based three-dimensional in vitro model of angiogenesis with focus on chemokines and chemokine receptors.

AIM To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogenesis system with affymetrix oligonucleotide array. METHODS A microcarrier-based in vitro angiogenesis system was developed, in which ECs migrated into the matrix, proliferated, and formed capillary sprouts. The sprouts elongated, branched and formed networks. The total RNA samples from the HMVECs at the selected time points (0.5, 24, and 72 h) during the capillary morphogenesis were used for microarray analyses, and the data were processed with the softwares provided by the manufacturers. The expression patterns of some genes were validated and confirmed by semi-quantitative RT-PCR. The regulated genes were grouped based on their molecular functions and expression patterns, and among them the expression of chemokines and chemokine receptors was specially examined and their functional implications were analyzed. RESULTS A total of 1 961 genes were up- or down-regulated two-folds or above, and among them, 468 genes were up- or down-regulated three-folds or above. The regulated genes could be grouped into categories based on their molecular functions, and were also clustered into six groups based on their patterns of expression. As for chemokines and chemokine receptors, CXCL1/GRO-alpha, CXCL2/GRO-beta, CXCL5/ENA-78, CXCL6/GCP2, IL-8/CXCL8, CXCL12/SDF-1, CXCL9/Mig, CXC11/ITAC, CX3CL1/fractalkine, CCL2/MCP-1, CCL3, CCL5/RANTES, CCL7, CCL15, CCL21, CCL23, CCL28, and CCR1, CCR9, CXCR4 were identified. Moreover, these genes demonstrated different changing patterns during the capillary morphogenesis, which implied that they might have different roles in the sequential process. Among the chemokines identified, CCL2/MCP-1, CCL5/RANTES and CX3CL1 were specially up-regulated at the 24-h time point when the sprouting characterized the morphological change. It was thus suggested that they might exert crucial roles at the early stage of angiogenesis. CONCLUSION The present study demonstrates a global profile of gene expression during endothelial capillary morphogenesis, and the results provide us much information about the molecular mechanisms of angiogenesis, with which further evaluation of individual genes can be conducted.
Single-Tube Real-Time Nested Polymerase Chain Reaction for Detecting Human Papillomavirus DNA

A single-tube real-time nested polymerase chain reaction (PCR) was developed to detect human Papillomavirus (HPV) DNA in a closed tube system. The oligonucleotide primers MY09/MY11 and GP5+/GP6+ were included in contiguous reactions, thus eliminating the need to transfer first round PCR product into a second tube. The sensitivity and specificity of the optimized single-tube nested PCR were comparable with that achieved by two separate reactions on a conventional thermal block system using serial dilutions derived from plasmids containing DNA of 20 HPV types. A minimum of 10 copies of HPV types 11 and 16 DNA could be detected by both systems. In clinical samples, HPV types 1A, 2, 3, 5, 6–8, 10, 11, 14, 16, 17, 18, 20, 31, 33, 35, 39, 45, 49, 50, 52–54, 57, 62, 66, 70, CP8304 and LVX82/MM7 could be detected by both PCR methods. A total of 145 samples collected from patients were tested for the presence of HPV DNA with the two PCR systems: 124 (86.1%) of 144 samples gave concordant results in both assays. The HPV DNA positive PCR amplicons were typed and concordant results were obtained in 47 of 67 positive samples tested in both amplicons. In samples containing multiple HPV types at least one type was common to both amplicons.
Race differences in the relationship between role experiences and well-being

Theory and research generally support the notion that social roles benefit subjective well-being. These conclusions, however, are largely based on studies examining Whites. Studies that have included Blacks have found race differences in the influence of social roles on well-being, yet most of these studies focus on role occupancy. With few exceptions, little attention has been paid to whether there are race differences in how individuals experience their roles, and the extent to which race differences in role experiences relate to differences in well-being. In this article we examine racial variation in the experience of work and family roles. We find that Blacks and Whites are similar in their experiences of role conflict and perceptions of role success and balance, but the association between these experiences and well-being varies, to some extent, by race and gender. The implications of these findings as well as suggestions for future research are discussed.
Human liver fibronectin complementary DNAs: identification of two different messenger RNAs possibly encoding the alpha and beta subunits of plasma fibronectin.

Human fibronectin polymorphism arises from variation in the C-terminal region [e.g., Sekiguchi, K. , Siri, A. , Zardi, L. , & Hakomori, S. (1985) J. Biol. Chem. 260, 5105-5114]. In order to verify the chemical basis of the fibronectin polymorphism, cDNAs encoding the C-terminal region of human liver fibronectin have been isolated, sequenced, and compared with cDNAs encoding so-called "cellular fibronectin" (i.e., fibronectin produced by cultured cells in vitro). Among the five independent cDNAs thus isolated, two cDNAs, named pLF2 and pLF4, differed in the nucleotide sequence at the "type III connecting segment" (IIIcs) region. pLF4 contained 192 bases in this region whereas pLF2 completely lacked these bases. S1 mapping analysis indicated that both cDNAs with and without the 192 bases are faithful copies of two fibronectin mRNA species abundantly present in human liver. Comparison of the liver cDNAs with those coding for cellular fibronectin indicates that the latter cDNAs contain the 75-base and/or 93-base extra segments at the 5' and 3' boundaries of the 192-base IIIcs region. These extra segments have the consensus sequences for the 3' splice sites at their 3' ends, suggesting that fibronectin mRNAs with partial or complete deletion of the IIIcs sequence result from alternative splicing of a primary RNA transcript. Liver fibronectin cDNAs also lacked the 270-based "extra domain" (ED) segment present in some, but not all, cDNAs encoding cellular fibronectin. Thus, cellular fibronectin appears to have three extra peptide segments, encoded by the 75-base and 93-base segments in the IIIcs region and by the 270-base ED region, that are mostly absent in the liver fibronectin. (ABSTRACT TRUNCATED AT 250 WORDS)
Clinical characteristics and management of hospitalized and ambulatory patients with heart failure–results from ESC heart failure long‐term registry–Egyptian cohort

Our aim is to describe the clinical characteristics and management of patients hospitalized with acute heart failure (HHF) and ambulatory patients with chronic heart failure (CHF) in Egypt and compare them with heart failure (HF) patients from other countries in the European Society of Cardiology‐Heart Failure (ESC‐HF) registry.
The use of a proteinaceous “cushion” with a polystyrene‐binding peptide tag to control the orientation and function of a target peptide adsorbed to a hydrophilic polystyrene surface

In immobilizing target biomolecules on a solid surface, it is essential (i) to orient the target moiety in a preferred direction and (ii) to avoid unwanted interactions of the target moiety including with the solid surface. The preferred orientation of the target moiety can be achieved by genetic conjugation of an affinity peptide tag specific to the immobilization surface. Herein, we report on a strategy for reducing the extent of direct interaction between the target moiety and surface in the immobilization of hexahistidine peptide (6His) and green fluorescent protein (GFP) on a hydrophilic polystyrene (PS) surface: Ribonuclease HII from Thermococcus kodakaraensis (cHII) was genetically inserted as a “cushion” between the PS‐affinity peptide tag and target moiety. The insertion of a cushion protein resulted in a considerably stronger immobilization of target biomolecules compared to conjugation with only a PS affinity peptide tag, resulting in a substantially enhanced accessibility of the detection antibody to the target 6His peptide. The fluorescent intensity of the GFP moiety was decreased by approximately 30% as the result of fusion with cHII and the PS‐affinity peptide tag but was fully retained in the immobilization on the PS surface irrespective of the increased binding force. Furthermore, the fusion of cHII did not impair the stability of the target GFP moiety. Accordingly, the use of a proteinaceous cushion appears to be promising for the immobilization of functional biomolecules on a solid surface. © 2016 American Institute of Chemical Engineers Biotechnol. Prog. , 32:527–534, 2016
Trade Liberalization, Market Share Reallocation, and Aggregate Productivity: The Case of the Indonesian Manufacturing Industry

We investigate how trade liberalization affects aggregate productivity growth, focusing on market reallocation as well as within-firm productivity improvement. To this end, using Indonesian plant-level data from 1993 to 2005, we estimate the plant-level impact of trade liberalization focusing on productivity, output, and the probability to exit. Then, using the simple dynamic simulation method, we calculate the likely impact if tariff rates remain constant in the initial period. Comparing the actual and counterfactual scenarios, our results show that although within-plant productivity improvement through tariff reduction has a sizable impact on aggregate productivity growth, the contribution of market share reallocation is less significant.
Leisure and social participation in patients 4–10 years after aneurysmal subarachnoid haemorrhage

Abstract Objective: To investigate the long-term resumption of leisure and social activities in patients with aneurysmal subarachnoid haemorrhage (aSAH) and to determine the role of executive dysfunction and aneurysms in anterior brain regions in particular. Method: Leisure and social functioning of 200 patients with aSAH having anterior or posterior aneurysms was determined using the Role Resumption List (RRL). Executive functioning was investigated using the Dysexecutive Questionnaire (DEX) and sub-scales Social Convention (SC) and Executive Cognition (EC). Mood, fatigue and cognitive problems were investigated with the Hospital Anxiety and Depression Scale (HADS) and Brain Injury Symptom Checklist (BISC). Results: Of all patients, 46.5% reported complete return to previous leisure activities and 61.5% reported no changes in social interactions. HADS depression score, fatigue, DEX-EC sub-scale score and work status post-aSAH were predictors of leisure resumption. For social re-integration, HADS depression score, cognitive problems and fatigue were predictors. Aneurysm location did not influence leisure and social re-integration. Conclusions: A substantial number of the patients still experience problems in resuming previous activities in the chronic phase post-aSAH, influenced by cognitive, executive and depressive problems, as well as current work status and fatigue. Aneurysm location does not seem to influence this resumption.
Prevalence of restless legs syndrome in a rural community in Japan

To assess the prevalence and clinical significance of restless legs syndrome (RLS) in a Japanese population, we carried out a community‐based survey in a rural area of Japan. We sent questionnaires requesting information on demographics, the Center for Epidemiological Studies Depression scale, the Short Form‐8, the Pittsburgh Sleep Quality Index, the National Institutes of Health/International RLS Study Group (IRLSSG) consensus questionnaire, and the IRLSSG severity scale for RLS (IRLS) to 5,528 eligible adult residents in the town of Daisen in the Tottori prefecture of Japan. Next, we performed telephone interviews to identify subjects with probable RLS. Of the 2,812 subjects (51.1%) who gave complete answers on the IRLSSG questionnaire, 50 (1.8%) were judged as RLS positive. The prevalence of RLS was significantly higher in women than in men, and significantly lower in individuals 60 years of age or older. Multiple logistic regression analysis revealed that the existence of RLS was significantly associated with depression, lowered mental quality of life, and sleep disturbances. The prevalence of RLS in adult Japanese populations may be lower than that reported in Caucasian populations. However, in a group of Japanese subjects, RLS had a significant impact on daytime functioning as well as subjective sleep quality. © 2008 Movement Disorder Society
Anti-inflammatory Activity of Berry Fruits in Mice Model of Inflammation is Based on Oxidative Stress Modulation

Background: Many fruits have been used as nutraceuticals because the presence of bioactive molecules that play biological activities. Objective: The present study was designed to compare the anti-inflammatory and antioxidant effects of methanolic extracts of Lycium barbarum (GOJI), Vaccinium macrocarpon (CRAN) and Vaccinium myrtillus (BLUE). Materials and Methods: Mices were treated with extracts (50 and 200 mg/kg, p.o.), twice a day through 10 days. Phytochemical analysis was performed by high-performance liquid chromatography. Antioxidant activity was determine by 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, reducing power, lipid peroxidation thiobarbituric acid reactive substances (TBARS), reduced glutathione (GSH) and catalase (CAT) activity. Anti-inflammatory activity was evaluated by paw edema followed by determination of myeloperoxidase (MPO) and TBARS. Results: High amount of phenolic compounds, including rutin, were identified in all berries extracts. However, quercetin was observed only in BLUE and CRAN. GOJI presents higher scavenging activity of DPPH radical and reducing power than BLUE and CRAN. The extracts improved antioxidant status in liver; BLUE showed the largest reduction (75.3%) in TBARS when compared to CRAN (70.7%) and GOJI (65.3%). Nonetheless, CAT activity was lower in BLUE group. However, hepatic concentrations of GSH were higher in animals treated with GOJI rather than CRAN and BLUE. Despite all fruits caused a remarkable reduction in paw edema and TBARS, only BLUE and CRAN were able to reduce MPO. Conclusion: These results suggest that quercetin, rutin, or other phenolic compound found in these berry fruits extracts could produce an anti-inflammatory response based on modulation of oxidative stress in paw edema model.
Early colonizers of unoccupied habitats represent a minority of the soil bacterial community.

In order to understand (re-)colonization of microhabitats and bacterial succession in soil, it is important to understand which members of soil bacterial communities are most motile in the porous soil matrix. To address this issue, we carried out a series of experiments in sterilized soil microcosms. Using two different model strains, Pseudomonas fluorescens strain Pf0-1 and Collimonas fungivorans strain Ter331, we first determined the influence of nutrient availability on bacterial expansion rates. Based on these results, we then conducted similar microcosm experiments to examine microbial mobility within natural soil bacterial communities under a single nutrient regime. The expansion of bacterial populations within the community was assayed by quantitative PCR and pyrosequencing of 16S rRNA gene fragments. We observed that only a relatively small subset of the total community was able to expand to an appreciable distance (more than 2 cm) within 48 h, with the genera Undibacterium, Pseudomonas and Massilia and especially the family Enterobacteriaceae dominating the communities more distant from the point of inoculation. These results suggest that (re-)colonization of open habitats in soil may be dominated by a few rapidly moving species, which may have important consequences for microbial succession.
Kinetic studies with transglutaminases. The human blood enzymes (activated coagulation factor 13 and the guinea pig hair follicle enzyme.

Abstract The transfer reaction of [14C]methylamine into the acetylated B chain of oxidized insulin as catalyzed by several transglutaminases has been studied at pH 7.5 in the presence of calcium ion. The only radioactive product of the transfer reaction with each transglutaminase was identified as peptide-bound γ-glutamic acid methylamide. Initial velocity and product inhibition patterns for the human plasma and guinea pig hair follicle transglutaminases are consistent with a ping-pong mechanism, previously proposed for guinea pig liver transglutaminase (Folk, J. E. (1969) J. Biol. Chem. 244, 3707) in which acyl enzyme formed from peptide-bound glutamine may react with water (hydrolysis) or with a primary amine (transfer). Hydrolysis and isotope exchange in the presence of one substrate and one product add substantial support for this mechanism. The pattern of calcium activation of plasma transglutaminase in the transfer reaction is in accord with an equilibrium-ordered activation mechanism in which the first substrate, acetylated B chain of oxidized insulin, adds only to enzyme-metal complex. The similarity in the kinetic constants obtained for human plasma and platelet transglutaminases adds support to recent evidence that the catalytic subunits of the plasma and platelet zymogens and enzymes are closely related (Schwartz, M. L., Pizzo, S. V., Hill, R. L., and McKee, P. A. (1971) J. Biol. Chem. 246, 5851). Improved purification procedures for plasma and platelet protransglutaminases are presented.
System-level design of low-cost FPGA hardware for real-time ICA-based blind source separation

Blind source separation (BSS) of independent sources from their convolutive mixtures is a common problem in many real world multi-sensor applications. We present a low-cost real-time FPGA (field programmable gate array) implementation of an improved BSS algorithm for audio signals based on ICA (independent component analysis) technique. The separation is performed by implementing noncausal filters instead of causal filters within the feedback network. This reduces the required length of the unmixing filters as well as provides better separation and faster convergence. The result of testing the designed FPGA in real-time is reported.