Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico deletion of PtsG gene in Escherichia coli genome-scale model predicts increased succinate production from glycerol

Systems metabolic engineering and in silico analyses are necessary to study gene knockout candidate for enhanced succinic acid production by Escherichia coli. Metabolically engineered E. coli has been reported to produce succinate from glucose and glycerol. However, investigation on in silico deletion of ptsG/b1101 gene in E. coli from glycerol using minimization of metabolic adjustment algorithm with the OptFlux software platform has not yet been elucidated. Herein we report what is to our knowledge the first direct predicted increase in succinate production following in silico deletion of the ptsG gene in E. coli GEM from glycerol with the OptFlux software platform. The result indicates that the deletion of this gene in E. coli GEM predicts increased succinate production that is 20% higher than the wild-type control model. Hence, the mutant model maintained a growth rate that is 77% of the wild-type parent model. It was established that knocking out of the ptsG/b1101 gene in E. coli using glucose as substrate enhanced succinate production, but the exact mechanism of this effect is still obscure. This study informs other studies that the deletion of ptsG/b1101 gene in E. coli GEM predicted increased succinate production, enabling a model-driven experimental inquiry and/or novel biological discovery on the underground metabolic role of this gene in E. coli central metabolism in relation to increasing succinate production when glycerol is the substrate.
Comparison of Compositions and Metabolic Activities of Fecal Microbiotas in Young Adults and in Antibiotic-Treated and Non-Antibiotic-Treated Elderly Subjects

ABSTRACT The colonic microbiota mediates many cellular and molecular events in the host that are important to health. These processes can be affected in the elderly, because in some individuals, the composition and metabolic activities of the microbiota change with age. Detailed characterizations of the major groups of fecal bacteria in healthy young adults, in healthy elderly people, and in hospitalized elderly patients receiving antibiotics were made in this study, together with measurements of their metabolic activities, by analysis of fecal organic acid and ammonia concentrations. The results showed that total anaerobe numbers remained relatively constant in old people; however, individual bacterial genera changed markedly with age. Reductions in numbers of bacteroides and bifidobacteria in both elderly groups were accompanied by reduced species diversity. Bifidobacterial populations in particular showed marked variations in the dominant species, with Bifidobacterium angulatum and Bifidobacterium adolescentis being frequently isolated from the elderly and Bifidobacterium longum, Bifidobacterium catenulatum, Bifidobacterium boum, and Bifidobacterium infantis being detected only from the healthy young volunteers. Reductions in amylolytic activities of bacterial isolates in healthy elderly subjects and reduced short-chain fatty acid concentrations supported these findings, since bifidobacteria and bacteroides are important saccharolytic groups in the colon. Conversely, higher numbers of proteolytic bacteria were observed with feces samples from the antibiotic-treated elderly group, which were also associated with increased proteolytic species diversity (fusobacteria, clostridia, and propionibacteria). Other differences in the intestinal ecosystem in elderly subjects were observed, with alterations in the dominant clostridial species in combination with greater numbers of facultative anaerobes.
Time spent outdoors and seasonal variation in serum concentrations of 25-hydroxyvitamin D in Korean women.

The vitamin D status of 179 Korean women between the ages of 20 and 75 were measured by the use of high performance liquid chromatography (HPLC). Related biochemical indices such as iPTH, alkaline, phosphatase, creatinine, albumin, Ca, Mg, and P were also measured. Factors such as demographic characteristics, intake of foods containing vitamin D, and proxy measure of sunlight exposure (time spent outdoors) were assessed to determine their effect on vitamin D status and used in the analysis. The purpose of this study was twofold. The first was to define reference data for the distribution of vitamin D status and to explore the relationship between vitamin D and the variables that affect the vitamin D status in Korean women. The second was to analyze the risk factors of the vitamin D status and the relation between the factors. The results of this study will provide valuable information regarding the role of vitamin D in Korean women. The mean serum 25-hydroxyvitamin D (25-OHD) level was 25.8 ng/ml. Of the total subjects, 16.5% showed vitamin D deficiency (i.e. s-25-OHD < 10 ng/ml). Serum 25-OHD was inversely related to iPTH and alkaline phosphatase. There were significant changes in serum 25-OHD level from the pre- to the post-menopausal women with a positive correlation between vitamin D intake and serum at the 25-OHD level. Significant seasonal variation of serum 25-OHD and PTH were noted in 26 of the subjects and the serum 25-OHD level also correlated with sunlight exposure especially at 12.00 p.m. to 2.00 p.m. as assessed by the time spent outdoors. The relative importance of the two sources of vitamin D such as dietary intake (33.6% explained) and endogenous production of the time spent outdoors (19.7% explained) in serum 25-OHD were also evaluated. Multiple regression analysis revealed that the effects of aging on serum 25-OHD could largely be accounted for. Both the decline in dietary vitamin D intake and the time spent outdoors were closely related to the decreasing serum 25-OHD level. Among the determinants of low serum 25-OHD were age, dietary vitamin D intake, serum calcium level and dietary calcium intake, and serum alkaline phosphatase.
Yeast Pre-mRNA Splicing Requires a Pair of U1 snRNP-Associated Tetratricopeptide Repeat Proteins

ABSTRACT The U1 snRNP functions to nucleate spliceosome assembly on newly transcribed pre-mRNA. Saccharomyces cerevisiae is unusual among eukaryotes in the greatly extended length of its U1 snRNA and the apparent increased polypeptide complexity of the corresponding U1 snRNP. In this paper, we report the identification of a novel U1 snRNP protein, Prp42p, with unexpected properties. Prp42p was identified by its surprising structural similarity to the essential U1 snRNP protein, Prp39p. Both Prp39p and Prp42p possess multiple copies of a variant tetratricopeptide repeat, an element implicated in a wide range of protein assembly events. Yeast strains depleted of Prp42p by transcriptional repression of a GAL1::PRP42fusion gene arrest for splicing prior to pre-mRNA 5′ splice site cleavage. Prp42p was not observed in a recent biochemical analysis of purified U1 snRNPs from S. cerevisiae (28). Nevertheless, antibodies directed against an epitope-tagged version of Prp42p specifically precipitate U1 snRNA from yeast extracts. Furthermore, Prp42p is required for U1 snRNP biogenesis, because yeast strains depleted of Prp42p formed incomplete U1 snRNPs that failed to produce stable complexes with pre-mRNA in vitro. The evidence shows that Prp39p and Prp42p are both required to configure the atypical yeast U1 snRNP into a structure compatible with its evolutionarily conserved role in pre-mRNA splicing.
Binding of fluoresceinated epidermal growth factor to A431 cell sub‐populations studied using a model‐independent analysis of flow cytometric fluorescence data.

A method is developed for determining ligand‐cell association parameters from a model‐free analysis of data obtained with a flow cytometer. The method requires measurement of the average fluorescence per cell as a function of ligand and cell concentration. The analysis is applied to data obtained for the binding of fluoresceinated epidermal growth factor to a human epidermoid carcinoma cell line, A431. The results indicate that the growth factor binds to two classes of sites on A431 cells: 4 X 10(4) sites with a dissociation constant (KD) of less than or equal to 20 pM, and 1.5 X 10(6) sites with a KD of 3.7 nM. A derived plot of the average fluorescence per cell versus the average number of bound ligands per cell is used to construct binding isotherms for four sub‐populations of A431 cells fractionated on the basis of low‐angle light scatter. The four sub‐populations bind the ligand with equal affinity but differ substantially in terms of the number of binding sites per cell. We also use this new analysis to critically evaluate the use of ‘Fluorotrol’ as a calibration standard in flow cytometry.
A long-term comparison of tacrolimus (FK506) and cyclosporine in kidney transplantation: evidence for improved allograft survival at five years.

BACKGROUND The 1-year results of the Phase III U.S. Multicenter Trial comparing tacrolimus (FK506)- and cyclosporine (CsA)-based immunosuppressive therapy in kidney transplantation revealed a significant reduction in the incidence and severity of acute rejection episodes among patients maintained on tacrolimus. The present report at 5 years of follow-up focuses on the long-term impact of tacrolimus treatment on kidney allograft outcome. METHODS The study protocol permitted crossover of patients to the alternate treatment arm under stringent conditions. The effect of crossover on graft survival was analyzed. Cardiovascular risk factors and serious adverse events were also monitored over 5 years. RESULTS Intent-to-treat analysis revealed equivalent patient and graft survival between treatment arms at 5 years of follow-up (79.1% vs. 81.4%; P=0.472 and 64.3% vs. 61.6%; P=0.558 among tacrolimus and CsA-treated patients, respectively). However, the rate of crossover was significantly higher among patients randomized to receive CsA-based therapy (27.5% vs. 9.3%; P<0.001). The incidence of treatment failure (43.8% vs. 56.3%; P=0.008) was significantly lower among tacrolimus-treated patients. Graft survival was significantly improved in the tacrolimus treatment arm when crossover due to rejection was counted as graft failure (63.8% vs. 53.8%; P=0.014). Tacrolimus therapy was also associated with a significantly reduced requirement for medications to control hypertension and hyperlipidemia. There was a substantial rate of reversal of tacrolimus-associated insulin dependence. CONCLUSION Tacrolimus-based therapy resulted in significantly reduced risk of graft failure, without an increase in the incidence of adverse events associated with long-term immunosuppression.
ON THE OCCURRENCE IN THE RETINA OF CONDITIONS CORRESPONDING TO THE «BLOOD‐BRAIN BARRIER»

In a previous communication the present author has discussed the conditions under which substances pass from the blood into the central nervous system (CNS) and into the eye (Palm 1946). An account will be given here of some vital-staining experiments made with the aim of comparing the retina with the brain. It is generally known that in the CNS peculiar conditions prevail with respect to the passage of substances from blood to tissue. These conditions are included under the term >>bloodbrain barriercc. A very large part of the work carried out in this sphere has consisted of experiments with dyestuffs. References to the literature are to be found in S p a f z (1934) and the various papers by Broman (1938-45). The results of these staining experiments may be roughly summarized as follows: If certain dyestuffs, not too finely dispersed, are injected into test animals, the dye penetrates into all the tissues of the body, which are hence stained more or less distinctly. The CNS constitutes an exception. The brain and the spinal cord remain completely unstained, although some small parts of the brain take the colour, such as the pineal body and the pituitary body with its immediate environment. Pia mater is unstained, while dura mater is strongly coloured. In contrast to the CNS, howe-
Impact of medication therapy discontinuation on mortality after myocardial infarction.

BACKGROUND Nonadherence to medications is common, but the determinants and consequences are poorly defined. The objectives of this study were to identify patient and myocardial infarction (MI) treatment factors associated with medication therapy discontinuation and to assess the impact of medication discontinuation 1 month after MI on 12-month mortality. METHODS This was a multicenter prospective cohort of patients with MI enrolled in the Prospective Registry Evaluating Myocardial Infarction: Event and Recovery study. The outcomes were use of aspirin, beta-blockers, and statins at 1 month after MI hospitalization among patients discharged with all 3 medications as well as 12-month mortality. RESULTS Of 1521 patients discharged with all 3 medications, 184 discontinued use of all 3 medications, 56 discontinued use of 2 medications, 272 discontinued use of 1 medication, and 1009 continued taking all 3 medications at 1 month. In multivariable analyses, patients not graduating from high school (odds ratio [OR], 1.76; 95% confidence interval [CI], 1.20-2.60) were more likely to discontinue use of all medications. The effect of increasing age on medication therapy discontinuation was greater for females (OR, 1.77; 95% CI, 1.34-2.34) than males (OR, 1.23; 95% CI, 1.02-1.47). Patients who discontinued use of all medications at 1 month had lower 1-year survival (88.5% vs 97.7%; log-rank P<.001) compared with patients who continued to take 1 or more medication(s). In multivariable survival analysis, medication therapy discontinuation was independently associated with higher mortality (hazards ratio, 3.81; 95% CI, 1.88-7.72). Results were consistent when evaluating discontinuation of use of aspirin, beta-blockers, and statins separately. CONCLUSIONS Medication therapy discontinuation after MI is common and occurs early after discharge. Patients who discontinue taking evidence-based medications are at increased mortality risk. These findings suggest the need to improve the transition of care from the hospital to outpatient setting to ensure that patients continue to take medications that have mortality benefit.
Ocean Color products from Visible Infared Imager Radiometer Suite (VIIRS)

The Ocean Color CAL/VAL team is evaluating the VIIRS bio-optical products for real-time operations. VIIRS ocean data are being processed using standard government algorithms, and channel calibration and product validation evaluation activities are ongoing. A network of 27 global “Golden Regions” has been established to evaluate and validate bio-optical products. Satellite inter-comparison for data consistency with current ocean color products, and real time vicarious adjustment calculation are performed using in situ water leaving radiance propagated to Top of Atmosphere in coastal and open ocean regions. In addition, routine matchups with VIIRS and MODIS-Aqua are done with in situ data collection from ships and real time coastal AERONET-OC sites. The above activities, product evaluation and tracking of channel stability, are being contributed to the JPSS Team to evaluate the overall mission, including calibration and inter-satellite product consistency. Initial NPP VIIRS ocean bio-optical products are demonstrated with other ocean color satellites.
Multiple-coupled microstrip hairpin-resonator filter

This letter presents the design of six-resonator multiple-coupled microstrip filter. A low-pass prototype of six-resonator multiple-coupled filter is developed first based on the conventional Chebyshev filter. The characteristics of attenuation poles located on both sides of the frequency response are described. According to the low-pass prototype, the design of a six-resonator multiple-coupled microstrip hairpin filter at 6 GHz is completed with the aid of EM simulation. The experimental results are demonstrated and discussed.
Perceived impaired physical and cognitive functions after stroke in men and women between 18 and 55 years of age – a national survey

Purpose. We describe self-reported consequences for physical and cognitive functions, detect possible gender differences, and find factors that were associated with deteriorated physical function in younger stroke patients, independent in their personal activities of daily life. Methods. This study involved all first ever stroke patients, aged 18–55 years, registered in the Swedish national quality register for stroke. A questionnaire was answered by 1068 patients 8–36 months after the stroke. Changes were sought in physical and cognitive functions as compared with the pre-stroke condition. Results. Eight hundred and sixty-seven patients (83%) were independent in personal activities of daily life. Significant differences between men and women were found: deteriorated physical ability was reported by 56–71% of the men and 65–79% of the women; deteriorated cognitive function was reported by 48–57% of the men and 57–68% of the women. Many patients (70% men, 77% women) reported that they had received insufficient information about physical exertion. Significant associations were found between deteriorated physical function and deteriorated cognitive function as well as fear of physical exertion. Conclusions. Deterioration was found in physical and cognitive functions greater in women then in men. Insecurity regarding physical exertion existed indicating that younger stroke patients might need information directly aimed at physical functioning and more gender specific than today. This study has raised the awareness that there also might be gender differences in other fields, which needs further studies.
Labor Costs and Foreign Direct Investment: A Panel VAR Approach

This paper examines the endogenous interaction between labor costs and Foreign Direct Investment (FDI) in the OECD countries via the Panel VAR approach under system GMM estimates for the period 1995–2009. The available data allows identifying the relevance of the components of labor costs, and allows a detailed analysis across different sectors. Empirical findings have revealed that sectoral composition of FDI and the decomposition of labor costs play a significant role in investigating the dynamic association between labor costs and FDI. Further, results suggest that labor market policies should focus on productivity-enhancing tools in addition to price hindering tools.
Lamotrigine-induced toxic epidermal necrolysis in a young epileptic

A 20-year-old young female presented with extensive skin rashes with bullae and extensive epidermal necrolysis about 20 days after the addition of lamotrigine (LTG) to her anticonvulsant medication. The patient was managed by stopping LTG and supportive treatment. The seizures were controlled with increase in the doses of carbamazepine. The report emphasises exercising of caution once LTG is added to a regimen containing valproic acid.
Iron metabolism and hemochromatosis.

&5252gE5225ZHIS review will be divided into four parts. In the first U J|part we will enumerate and classify the iron compounds of the body. In the second part we will describe the properties of some of these iron compounds. In the third part, the properties and the hypotheses concerned with the regulation of iron absorption by the gastro-intestinal mucosa will be discussed, and in the last part we will consider certain of the aspects of iron metabolism as they might be related to hemochromatosis.
The presence of Merkel cells and CD10- and CD34-positive stromal cells compared in benign and malignant oral tumors.

BACKGROUND To describe sequential changes in Merkel cells (MC), and CD10(+) and CD34(+) stromal cells (SC) during the transition from benign to malignant oral lesions and correlate with clinicopathologic parameters. MATERIALS AND METHODS Changes in cytokeratin 20-positive (CK20(+)) Merkel cells, CD10(+) and CD34(+) SC were immunohistochemically examined in specimens of 28 oral verrucous carcinomas (VC), 32 squamous cell carcinomas (SCC) and 36 benign squamous lesions (BSL). Immunoreactivity and localized inflammation were measured quantitatively and/or semiquantitatively, and between-group results were statistically compared. RESULTS The mean number of CD34(+) SC was significantly lower in VC (57.36) and SCC (33.81) than BSL (351.56, P < 0.001). However, the three tumor types had similar staining level and number of CD10(+) SC. We found a significant difference in the density of MC between BSL and VC (P < 0.001) or SCC (P < 0.001). The number of CK20(+) MC was significantly lower in highly inflamed specimens than mildly inflamed specimens (P = 0.001). CONCLUSION CD34(+) SC and to a lesser extent MC, but not CD10(+) SC, reveal statistically different density during the transition from benign to malignant oral lesions. The correlations between the CD34(+) SC expression and squamous lesions may be associated with epithelial dysplasia and/or tumor invasion.
Transmyocardial laser revascularization.

To perform transmyocardial laser revascularization, the surgeon exposes the beating heart through a lateral thoracotomy, places a laser (carbon dioxide or holmium) on the epicardial surface of the left ventricle, and applies sufficient energy to create small channels from the epicardial to the endocardial surfaces. During a typical procedure, 10 to 50 such channels are created. Initially, these small, laser-created transmyocardial channels were thought to improve the perfusion of ischemic myocardium by providing it with direct access to oxygen-rich left ventricular blood, but it was subsequently found that the channels quickly occlude after the procedure.1 Nonetheless, initial observational studies of .
The myofibroblast and its tumours

Tumours and tumour-like lesions of myofibroblasts may present diagnostic difficulty because of their rarity and because of uncertainties in identifying the myofibroblast. The objectives of this review are to provide a definition of the myofibroblast and an account of its biology for facilitating an understanding of the cell and of myofibroblastic lesions; and to describe, in the context of common diagnostic problems, the features of benign and malignant myofibroblastic lesions. The main characteristics of the myofibroblast include a spindled or stellate morphology; immunostaining for α-smooth muscle actin and the extra domain A variant of cellular fibronectin; and an ultrastructure of rough endoplasmic reticulum, peripheral contractile filaments and the cell-to-matrix junction known as the fibronexus. On this basis, lesions traditionally regarded as myofibroblastic are shown to vary in their level of differentiation, and some appear to be smooth muscle rather than myofibroblastic. Immunohistochemistry and electron microscopy, used together, are emphasised as being important for maximum diagnostic confidence in some myofibroblastic lesions.