Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Novel Escherichia coli Ribosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques

ABSTRACT Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16°C and 37°C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.
Complement Activation Mediated by Mannan‐Binding Lectin in Plasma from Healthy Individuals and from Patients with SLE, Crohn's Disease and Colorectal Cancer. Suppressed Activation by SLE Plasma

We have developed a method for quantitating mannan‐binding lectin (MBL)‐induced activation of the complement system (MBL‐C4‐AC) in human plasma. This method and an assay for MBL concentration were applied to plasma samples from healthy individuals and patients with systemic lupus erythematosus (SLE), Crohn's disease (CD) and colorectal cancer (CRC). The MBL concentration was measured by an enzyme‐linked immunosorbent assay (ELISA) using monoclonal anti‐MBL‐antibodies and MBL‐C4‐AC by an ELISA using solid‐phase mannan, incubating with plasma samples and quantitating the complement (C) activation by the use of antibodies against the C split‐products C4b/C4c. The MBL concentration was nonsignificantly elevated in plasma from SLE‐patients, whereas MBL‐C4‐AC was suppressed ( P < 0.04). There was no correlation between MBL concentration and MBL‐C4‐AC in plasma from SLE‐patients. In contrast, a significant correlation was found between the MBL concentration and MBL‐C4‐AC in plasma from healthy individuals. The C4 concentration was significantly reduced ( P < 0.002) in plasma from the SLE patients and showed a significant correlation to MBL‐C4‐AC. The MBL‐C4‐AC assay was highly effective in discriminating the SLE patients from the other patient groups and healthy individuals.
A growth factor delivery system for chondrogenic induction of infrapatellar fat pad‐derived stem cells in fibrin hydrogels

Articular cartilage has a limited capacity for self‐renewal and repair. Tissue engineering of cartilage in vitro has been proposed as a solution to this problem; however, this approach is costly and requires a significant amount of time to grow the graft. An alternative approach is to implant chondroprogenitor cells seeded within a growth factor delivery scaffold directly into the defect site to promote tissue regeneration. The objective of this study was to develop a biocompatible growth factor delivery system capable of promoting chondrogenesis of infrapatellar fat pad (IFP)‐derived stem cells. Transforming growth factor beta‐1 (TGF‐β1) was loaded into gelatin microspheres and incorporated into fibrin hydrogels containing IFP‐derived stem cells. The release of TGF‐β1 was quantified using an enzyme‐linked immunosorbent assay, whereas chondrogenesis was demonstrated histologically and by quantifying sulfated glycosaminoglycan production after 21 days of in vitro culture. TGF‐β1 loaded into gelatin microspheres appeared to be as effective in promoting chondrogenesis of IFP‐derived stem cells as adding TGF‐β1 directly to the medium. The influence of different microsphere fabrication parameters and TGF‐β1 loading concentrations was also investigated but appeared to only have a small effect on subsequent chondrogenesis. The development of such growth factor delivery systems in combination with IFP‐derived stem cells represents a potential new strategy for cartilage defect repair.
Impact of renin angiotensin system blockade on night to day blood pressure ratio in diabetic nephropathy.

Sir, Elevated systemic blood pressure is a risk factor for progression of diabetic nephropathy. Ambulatory blood pressure measurements offer additional risk stratification compared to office blood pressure in patients with hypertension [1]. In addition, an abnormal diurnal blood pressure pattern characterized by an elevated night to day ratio is found more commonly in diabetic patients and, as reviewed by Miller et al. [2], is associated with poor renal outcome. The renin angiotensin system (RAS) is involved in both initiation and progression of diabetic nephropathy and blocking this system with ACE-inhibitors (ACE-I) and/or angiotensin II receptor blockers (ARBs) improves kidney survival and prognosis. Miller et al. [2] reported that treatment with enalapril (0.1 mg/kg BID) corrects the abnormally high night to day blood pressure ratio found in 10 uncomplicated adolescents, and this could contribute to the beneficial renoprotective effects of RAS blockade. In this letter, we further investigate whether RAS blockade corrects an abnormal 24 h blood pressure pattern by presenting data on the short-term effects of single and dual blockade of the RAS on a 24 h blood pressure profile and a night to day blood pressure ratio in type 1 diabetic patients with diabetic nephropathy. Our data are a post-hoc analysis of three earlier studies [3–5]. As described previously [3], we performed a randomized, double blind, cross-over trial, in which 18 patients received 8 weeks of placebo, benazepril 20 mg once daily, valsartan 80 mg once daily and a combination of benazepril 20 mg and valsartan 80 mg once daily in random order [3]. The main findings were: (1) mono-therapy with ACE-I or ARBs treatment was equally effective with regard to antialbuminuric and antihypertensive effects; (2) dual blockade of the RAS caused a further reduction in albuminuria of 43% and 7/6 mmHg in 24 h blood pressure compared with both mono-therapies; (3) night to day ratio of 24 h blood pressure on each treatment is shown in Table 1. A post-hoc power calculation estimated a power in each study of � 0.80 to detect a difference of 0.05 in night to day ratio with a significance level of 0.05. In agreement, when looking at the fraction of patients with night to day blood pressure ratio above the median on placebo treatment (>0.91), we found no changes in the night to day ratio on RAS blockade. Furthermore, in two other studies demonstrating that dual blockade of the RAS
Developmental expression of mouse Krüppel-like transcription factor KLF7 suggests a potential role in neurogenesis.

To identify potential functions for the Krüppel-like transcription factor KLF7, we have determined the spatiotemporal pattern of gene expression during embryogenesis and in the adult organism. We show that the profile of Klf7 expression predominantly involves the central and peripheral nervous systems and is broadly identified by three separate phases. The first phase occurs early in embryogenesis with increasingly strong expression in the spinal cord, notably in motor neurons of the ventral horn, in dorsal root ganglia, and in sympathetic ganglia. The second robust phase of Klf7 expression is confined to the early postnatal cerebral cortex and is downregulated thereafter. The third phase is characterized by high and sustained expression in the adult cerebellum and dorsal root ganglia. Functionally, these three phases coincide with establishment of neuronal phenotype in embryonic spinal cord, with synaptogenesis and development of mature synaptic circuitry in the postnatal cerebral cortex, and with survival and/or maintenance of function of adult sensory neurons and cerebellar granule cells. Consistent with Klf7 expression in newly formed neuroblasts, overexpression of the gene in cultured fibroblasts and neuroblastoma cells repressed cyclin D1, activated p21, and led to G1 growth arrest. Based on these data, we argue for multiple potential functions for KLF7 in the developing and adult nervous system; they include participating in differentiation and maturation of several neuronal subtypes and in phenotypic maintenance of mature cerebellar granule cells and dorsal root ganglia.
Inducible Expression of Stat4 in Dendritic Cells and Macrophages and Its Critical Role in Innate and Adaptive Immune Responses1

Autocrine activation of APC by IL-12 has recently been revealed; we demonstrate here that inducible expression of Stat4 in APC is central to this process. Stat4 is induced in dendritic cells (DC) in a maturation-dependent manner and in macrophages in an activation-dependent manner. Stat4 levels directly correlate with IL-12-dependent IFN-γ production by APC as well as IFN-γ production by DC during Ag presentation. The Th2 cytokines IL-4 and IL-10 suppress Stat4 induction in DC and macrophages when present during maturation and activation, respectively, diminishing IFN-γ production. In contrast, IL-4 has no effect on Stat4 levels in mature DC and actually augments IFN-γ production by DC during Ag presentation, indicating that IL-4 acts differently in a spatiotemporal manner. The functional importance of Stat4 is evident in Stat4−/− DC and macrophages, which fail to produce IFN-γ. Furthermore, Stat4−/− macrophages are defective in NO production in response to IL-12 and are susceptible to Toxoplasma. Autocrine IL-12 signaling is required for high-level IFN-γ production by APC at critical stages in both innate and adaptive immunity, and the control of Stat4 expression is likely an important regulator of this process.
Pathologic correlates of survival in 378 lymph node‐negative infiltrating ductal breast carcinomas. Mitotic count is the best single predictor

Pathologic features of 378 breast carcinomas without axillary lymph node metastases were correlated with long‐term prognosis. Mitotic count, the feature best predicting prognosis, was most useful at lower mitotic count levels than usually studied. Cases with less than 4.5 mitotic figures per ten high‐power fields had a 20‐year tumor‐related survival of 73% versus 48% for those with higher mitotic counts. Low and high mitotic count groups had significantly different prognoses for T1c, T2, and T3 tumors. Multivariate analysis showed that the best combination of features predicting tumor‐related death were high mitotic count (relative risk, ×2.8), large tumor size (relative risk, ×1.7), lymphatic invasion (relative risk, ×1.7), and skin or subjacent muscle or chest wall invasion (relative risk, ×2.5). Nuclear grade, Bloom‐Richardson grade, modified Scarff‐Bloom‐Richardson grade, Fisher's grade, and necrosis correlated well with survival but had no significant additional predictive value when adjusted for the mitotic count.
Minimizing Concentration Effects in Water-Based, Laminar-Flow Condensation Particle Counters

Concentration effects in water condensation systems, such as used in the water-based condensation particle counter, are explored through numeric modeling and direct measurements. Modeling shows that the condensation heat release and vapor depletion associated with particle activation and growth lowers the peak supersaturation. At higher number concentrations, the diameter of the droplets formed is smaller, and the threshold particle size for activation is higher. This occurs in both cylindrical and parallel plate geometries. For water-based systems, we find that condensational heat release is more important than vapor depletion. We also find that concentration effects can be minimized through use of smaller tube diameters, or more closely spaced parallel plates. Experimental measurements of droplet diameter confirm modeling results. © 2013 American Association for Aerosol Research
Endoscopic sclerotherapy for esophageal hemangioma.

Esophageal hemangioma is extremely rare among the benign tumors, and surgical1-3 or endoscopic resections4,5 have mainly been reported, with surgical resection being generally accepted as the standard treatment. More recently, endoscopic resection has been successful, but it has been limited to small or pedunculated tumors that have an associated risk of hemorrhage. Sclerotherapy has commonly been applied to varices for both hemostasis of active bleeding and subsequent obliterative treatment. We therefore applied this technique as a unique and alternative means of successful, uncomplicated treatment for an esophageal hemangioma.
Identification and characterization of a novel, shorter isoform of the small conductance Ca2+‐activated K+ channel SK2

Throughout the CNS, small conductance Ca2+‐activated potassium (SK) channels modulate firing frequency and neuronal excitability. We have identified a novel, shorter isoform of standard SK2 (SK2‐std) in mouse brain which we named SK2‐sh. SK2‐sh is alternatively spliced at exon 3 and therefore lacks 140 amino acids, which include transmembrane domains S3, S4 and S5, compared with SK2‐std. Western blot analysis of mouse hippocampal tissue revealed a 47 kDa protein product as predicted for SK2‐sh along with a 64 kDa band representing the standard SK2 isoform. Electrophysiological recordings from transiently expressed SK2‐sh revealed no functional channel activity or interaction with SK2‐std. With the help of real‐time PCR, we found significantly higher expression levels of SK2‐sh mRNA in cortical tissue from AD cases when compared with age‐matched controls. A similar increase in SK2‐sh expression was induced in cortical neurons from mice by cytokine exposure. Substantial clinical evidence suggests that excess cytokines are centrally involved in the pathogenesis of Alzheimer’s disease. Thus, SK2‐sh as a downstream target of cytokines, provide a promising target for additional investigation regarding potential therapeutic intervention.
EFFECT OF FOCUSED FLUSHING AT THE END OF THE ANTICIPATED NORMAL LUTEAL PHASE ON SYNCHRONIZATION OF OESTRUS BY INTRODUCTION OF RAM IN THE FLOCK

NEDELKOV, K. , N. TODOROV and М. SIMEONOV, 2013. Effect of focused flushing at the end of the anticipated normal luteal phase on synchronization of oestrus by introduction of ram in the flock. Bulg. J. Agric. Sci., 19: 1085-1092 The purpose of this study was: 1) to determine the influence of short-time high nutrient intake focused in second part of luteal phase over the response of ewes to the synchronizing oestrus effect of the ram; 2) to determine the effect of a complex of factors known that could influence on the “ram effect”. The experiment has been carried out with 344 Pleven Blackhead ewes, divided into two groups. The first group of 168 ewes with average BCS 3.5 and mean live body weight of 66.7 kg, served as a control. The second group of 176 ewes with average BCS 3.2 and mean live body weight of 63.2 kg was put on an intensive short time feeding. Ewes from both groups received 300 g barley per day while the experimental group received an additional 400 g of soybean screenings. In this way, it was investigated whether the lower BCS could be compensated by short-time abundant feeding. The experiment was conducted in the beginning of the natural breeding season of ewes. The artificial insemi nation started at 06.08. 2011. It was observed a delay in the onset of oestrus with two days at the focused (acute) flushed ewes compared with the control group. Perhaps the difference could be associated with the different body condition of groups and with the applied intensive feeding to the experimental group, which may have influenced the lifespan of the last non-ovulatory and ovulatory follicles. Within 11 days, which coincided with the two peaks induced by the “ram effect”, ewes in oestrus were 72.0% of all sheep in the control group or 80.1% of all lambed ewes. In addition, at the experimental group the respective indexes are 76.1% and 83.8%. Therefore, with a proper implication of the oestrus synchronization by the “ram effect” it could be achieved 80.1% to 83.8% of inseminated ewes within 11 days. Despite some differences in BCS and live weight between the two groups, it was not found differences in the biological fecundity of ewes.
Significance of oral health in persons with Down syndrome: a literature review

Down syndrome (DS) is an autosomal chromosomal anomaly resulting from trisomy of all or a critical part of chromosome 21. It affects approximately 1 in 700 to 800 live births. Despite the development of prenatal diagnosis, the incidence of DS births is predicted to remain static or even to increase over the next decade, partly due to increased maternal age in Western societies. Many of the medical and physiological characteristics of DS have direct consequences for the oral health of subjects affected and indirect consequences for the quality of life of persons with DS and their carers. This article aims to give an overview of the current literature concerning the orofacial problems confronting patients with DS, and to explain the different treatment modalities available.
Interannual long equatorial waves in the tropical Atlantic from a high-resolution ocean general circulation model experiment in 1981-2000

We investigate the tropical Atlantic vertical structure variability (1981-2000) based on the CLIPPER ocean general circulation model (OGCM). We aim at determining to what extent the observed interannual variability can be explained by the low-frequency wave dynamics. The linear vertical modes of the OGCM climatological stratification are estimated along the equator. The baroclinic mode contributions to surface zonal current and sea level anomalies are calculated and analyzed at interannual timescales. The second baroclinic mode is the most energetic. The first (third) mode exhibits a variability peak in the west (east). The summed-up contribution of the high-order baroclinic modes (4-6) is as energetic as the gravest modes and is largest in the east. Wave components are then derived by projection onto the associated meridional structures. The effect of longitudinal boundaries near the equator is taken into consideration. Equatorial Kelvin and Rossby waves propagations, with phases speed close to the theory, are identified for the first three baroclinic modes. The comparison with a multimode linear simulation corroborates the propagating properties of the OGCM waves coefficients. An estimation of the meridional boundary reflection efficiency indicates that wave reflections take place at both boundaries. A 65% reflection efficiency is found at the eastern boundary. Our study suggests that low-frequency wave dynamics is to a large extent at work in the tropical Atlantic. On the basis of what is known on the Pacific El Nino-Southern Oscillation mode this may provide a guidance for investigating ocean-atmosphere mechanisms that can lead to the Atlantic zonal equatorial mode.
Mineral content of some medicinal herbs.

This paper is a study on the distribution of trace minerals in different native plants used in the preparation of medicinal teas: Cynara scolymus, Achillea millefolium, Calendula officinalis, Mentha piperita, Hypericum perforatum and Matricaria chamomilla. Were determined by flame atomic absorption spectrometry (FAAS), the following microelements: Fe, Mn, Zn, Cu, Ni, Co, Cr, Pb and Cd. The experimental results show appreciable content of bio-micro-elements, especially Fe, Mn, Cu, Zn and very low concentrations, insignificants, of toxic elements: Pb and Cd. We can conclude that the analysed herbal teas are of interest not only for their pharmaco-dynamic properties, but also for their micro-elements content, which makes herbal teas both foods and medicines. It is nutritionists who should recommend the type of herbal tea depending on the micro-elements contents.
Operation of Randle's Cycle in Patients With NIDDM

It has been suggested that the insulin resistance of non-insulin-dependent diabetes mellitus (NIDDM) may be caused by substrate competition between glucose and free fatty acids (FFAs) (Randle's cycle). We measured substrate oxidation and energy metabolism in 10 nonobese untreated NIDDM patients with fasting glucose levels of 7–8 mM with indirect calorimetry in the basal state and during an isoglycemic-hyperinsulinemic (∼100 mU/L) clamp without (control) and with a concomitant infusion (∼0.35 mmol/min) of Intralipid, a triglyceride emulsion. In the control study, fasting rates of total glucose turnover ([3−3H]glucose) and glucose and lipid oxidation (9.4 ± 1.4, 7.3 ± 1.3, and 3.0 ± 0.4 μmol · kg−1 · min−1, respectively) were comparable with those of nondiabetic individuals. After insulin administration, lipid oxidation was normally suppressed (to 1.3 ± 0.3 μ · kg−1 · min−1 P < 0.01), as were the circulating levels of FFA, glycerol, and β-hydroxybutyrate, whereas glucose oxidation doubled (14.1 ± 1.8 μmol; · kg−1 · min−1 P <0.01). Because glycemia was clamped at 7.5 mM, endogenous glucose production (EGP) was completely suppressed, and total glucose disposal was stimulated (to 25.7 ± 5.2 μmol · kg−1 · min−1 P < 0.01 vs. baseline), but glucose clearance (3.6 ± 0.8 ml · kg−1 · min−1) was 30% reduced compared with normal. With concomitant lipid infusion, FFA, glycerol, and β-hydroxybutyrate all rose during the clamp; correspondingly, lipid oxidation was maintained at fasting rates (3.6 ± 0.2 μmol · kg−1 · min−1 P < 0.01 vs. control). As a consequence, the insulin-induced increase in glucose oxidation was abolished (7.9 ±1.3 μmol · kg−1 · min−1 P < 0.01 vs. control), and total glucose disposal was inhibited (21.8 ± 4.6 μmol · kg−1 · min−1 P < 0.05 vs. control) by an amount almost equal to the decrement in glucose oxidation. Lipid infusion did not detectably interfere with insulin-induced suppression of EGP. Energy expenditure failed to increase during the control insulin clamp but was significantly stimulated (∼10%, P < 0.01) by concomitant lipid administration (diet-induced thermogenesis). We conclude that in mildly hyperglycemic, nonobese NIDDM patients, excessive fatty substrate oxidation is unlikely to be responsible for the insulin resistance; increased lipid provision, however, enhances lipid oxidation and energy expenditure and inhibits glucose oxidation and total disposal. Thus, in this type of diabetes, Randle's cycle does not appear to be spontaneously overactive but can be induced acutely, with metabolic and energetic consequences similar to those observed in nondiabetic subjects.
Modeling of the Cure Fraction in Survival Studies

Cure models are a special type of survival analysis model where it is assumed that there are a proportion of subjects who will never experience the event and thus the survival curve will eventually reach a plateau. In population-based cancer studies, cure is said to occur when the mortality (hazard) rate in the diseased group of individuals returns to the same level as that expected in the general population. The cure fraction is of interest to patients and a useful measure to monitor trends and differences in survival of curable disease. I will describe the strsmix and strsnmix commands, which fit the two main types of cure fraction model, namely, the mixture and nonmixture cure fraction models. These models allow incorporation of the expected background mortality rate and thus enable the modeling of relative survival when cure is a possibility. I give an example to illustrate the commands.