Miracle-dz/UniFAR-FTUs huggingface dataset:
Establishing Standards for the Characterization of Human Embryonic Stem Cell Lines

As of August 2005, 22 human embryonic stem cell (hESC) lines listed on the National Institutes of Health (NIH) hESC Registry were being distributed to investigators. At a June 2005 meeting of NIH‐supported hESC researchers, we proposed that a set of shared standards should be available in order to characterize the cells unambiguously in multiple laboratories. Here, we elaborate such a plan to identify a set of standard methods and to initiate collaborative efforts to validate the standards. The standard assays we propose should be comprehensive enough to ensure that hESC banks can provide a consistent and reliable product for NIH researchers, and inexpensive enough that individual laboratories can afford to use at least some of the methods routinely in their laboratories. We expect that as data accumulate and standards evolve, a core set of tests will become the norm for routine assessment of hESC cultures and that these tests will lay the groundwork for clinical applications of these cells.
The energetics and dynamics of molecular recognition by calmodulin.

Amide hydrogen exchange has been used to examine the structural dynamics and energetics of the interaction of a peptide corresponding to the calmodulin binding domain of smooth muscle myosin light chain kinase with calcium-saturated calmodulin. Heteronuclear NMR 15N-1H correlation techniques were used to quantitate amide proton exchange rates of both 15N-labeled and unlabeled amide protons of the smMLCK peptide complexed to calmodulin. Hydrogen exchange slowing factors were determined for 18 of the 19 amide hydrogens and found to span 6 orders of magnitude. The first six residues of the bound peptide were found to have slowing factors near 1 and are considered not to be hydrogen bonded, consistent with the previously reported model for the structure of the peptide. The pattern of hydrogen exchange of hydrogen-bonded amide hydrogens is indicative of end-fraying behavior characteristic of helix-coil transitions. The effective statistical mechanical parameters revealed by the end fraying are consistent with exchange from a highly solvated state. However, the slowing factors of the first hydrogen-bonded amide hydrogens are large, indicating the requirement for a reorganization of the calmodulin-peptide complex before the helix-coil transitions leading to exchange can occur. Taken together, these observations suggest that the collapsed complex reorganizes with an associated free energy change of 5.5 kcal/mol to a more open state where the helical peptide is highly solvated and undergoes helix-coil transitions leading to exchange. The free energy difference between the most and least stable intrahelical amide hydrogen bonds of the bound peptide is estimated to be approximately 2.5 kcal/mol. (ABSTRACT TRUNCATED AT 250 WORDS)
[Proinflammatory markers serum concentrations in patients with adenomatous colon polyps].

BACKGROUND It has been shown that local chronic inflammation may lead to colorectal carcinogenesis via adenomatous polyps. Tumor necrosing factor-alpha (TNF-alpha), interleukin-6 (IL-6) and C-reactive protein (CRP) are biomarkers of inflammation and indicators of the immune response to tumors. Their elevated levels were observed in patients with colon adenomas, however their clinical significance is unclear. METHODS The study included sixty patients with the colorectal adenomatous polyps found on colonoscopy and confirmed pathologically. The control group consisted of 30 individuals with no positive findings on colonoscopy. The aim of our study was to determine the serum levels of TNF-alpha, IL-6 and CRP in colorectal adenomas patients and to assessed the relationships between them and colorectal adenoma location, dysplasia grading, histological type, and size. RESULTS One hundred nine adenomas (6-40 mm of size) were found in 60 study patients. The average age of patients with multiple polyps was significantly higher than of those with single pathologies (61.1 vs 56.7 years respectively (p < 0.05)). The prevalence of colon adenomas were observed in distal part of colon (83.3%), compared to the proximal part (16.7%; p < 0.01). The TNF-alpha concentration was similar in both group (24.51 +/- 13.50 pg/ml versus 29.61 +/- 14.94 pg/ml; p > 0.05) and not related to clinical data of patients. In contrast, CRP serum concentrations were higher in patients with adenomas located proximally (8.674 +/- 9.19 microg/ml) compared to control group (4.94 +/- 5.53 microg/ml; p < 0.05). There was also no differences between IL-6 serum level in patients with colon adenomas (19.80 +/- 7.44 pg/ml) and control group (20.46 +/-11.83 pg/ml; p > 0.05). Analyzed cytokines serum levels were not associated with size, number, degree of dysplasia and histological type of colon adenomas. CONCLUSION Our results indicate that CRP may be associated with development of tumors of proximal part of colon.
Engineering drought and salt tolerance in plants using SodERF3, a novel sugarcane ethylene responsive factor

The ability of plants to tolerate salt and drought conditions is crucial for agricultural production worldwide. The increased understanding of the regulatory networks controlling drought stress response has led to practical approaches for engineering salt and drought tolerance in plants. By a single-pass sequencing of randomly selected clones from a e ZAP-cDNA library generated from ethephon-treated young sugarcane leaves, we identified an expressed sequence tag encoding a putative protein with a DNA-binding domain that is typically found in EREBP/ AP2-type transcription factors. The full-length cDNA clone, named SodERF3 (EMBL accession number AM493723) was further isolated from the excised library. SodERF3 encodes a 240 amino acid DNA-binding protein that acts as a transcriptional regulator of the Ethylene Responsive Factor (ERF) superfamily, but also contains a C-terminal short hydrophobic region resembling an ERF-associated amphiphilic repression-like motif, typical for class II ERFs. This protein binds to the GGC box, and its deduced amino acid sequence contains an N-terminal putative nuclear localization signal. SodERF3 is induced in sugar cane leaves by ethylene, abscisic acid, salt stress and wounding as judged by Northern and Western blots assays. Greenhouse grown transgenic tobacco plants (Nicotiana tabacum L. cv. SR1) expressing SodERF3 were found to display increased tolerance to drought and osmotic stress without any visible phenotypic change in growth and development. According to our results SodERF3 will be a valuable tool to assist the manipulation of plants to improve their stress tolerance
Global Analysis of Antibody Repertoires. 1. An Immunoblot Method for the Quantitative Screening of a Large Number of Reactivities

This paper describes a procedure for analysing multiple antibody reactivities that explores a commercially available immunoblot system, and is based on a double staining of nitrocellulose membranes, revealing both antibody reactivities and the migration position of the blotted proteins in the membrane. Quantification of both stainings by densitometry allowed the accurate superposition of the immunoreactivity and total protein profiles of each Line. Moreover, the protein stainings ofthe different lanes could be adjusted with a simple‐scale transformation algorithm, correcting for possible distortions during electrophoretic migration, and allowing for the precise comparison ofthe immunoreactivity profiles in different lanes. The procedure is discriminatory enough to identify unique reactivity patterns in random pools of 104 activated B cells, and to define strain‐specific natural antibody repertoires. The utilily of this immunoblot method as an assay for simultaneously scoring multiple reactivities to hundreds of antigens in complex mixtures of antibodies, and thus defining antibody repertoires in a global manner, is discussed.
Preparing Stakeholders for the School Librarian’s Instructional Partnership Role: Whose Responsibility Is It?

Although the American Association of School Librarians and researchers in the field have identified the instructional partner role as critical to the future of school librarianship, many school librarians report that their colleagues and administrators are unaware of the importance of this role, and that they are reluctant to practice or support it. Other library stakeholders report that school librarians themselves are not adequately prepared to effectively practice this role. While many practitioners believe it is the university’s job to prepare preservice educators and administrators to participate in collaborative planning, teaching, and assessment, some university faculty believe that until classroom-library instructional partnerships are consistently practiced in the field, preservice education efforts to instill this model will fall flat. This chapter reports on an in-depth literature review of the research-based evidence for the value of successful instructional partnerships and the barriers that have been identified in enacting them. An analysis of the literature suggests a comprehensive effort on the part of all stakeholders—both in the field and the academy—is necessary to ensure that the work of school librarians is integrated into the classroom curriculum where it can make a measurable impact on student learning outcomes. Preparing Stakeholders for the School Librarian’s Instructional Partnership Role: Whose Responsibility Is It?
Analysis and design of three-state controlled transition mode for a buck-boost converter with efficiency and stability enhancement

This paper presents the analysis and design of three-state controlled transition mode for buck-boost converter. By introducing an additional state D2 to the transition mode, a significant efficiency improvement and output voltage ripple reduction are achieved due to the reduced average inductor current and inductor current ripple. Furthermore, the stability of the converter is enhanced according to the dynamic behavior analysis. A buck-boost converter operating in transition mode has been designed and implemented using AMS 0. 35μm CMOS technology. Simulation results demonstrate that over 10% efficiency improvement can be achieved at heavy loading and the converter can be stabilized with a smaller compensation capacitor.
Determinants of neonatal weight loss in term-infants: specific association with pre-pregnancy maternal body mass index and infant feeding mode

Objective We aimed to study the determinants of neonatal weight loss measured on the third day of life in term-infants. Design The EDEN mother–child cohort is a prospective study that recruited 2002 pregnant women before 24 weeks of gestation in two French university hospitals. Neonates were weighed every day until discharge that occurred on average 4.5 days after birth. Altogether, 1557 healthy term neonates with data on weight at day 3 and feeding mode available were included. The outcome variable was weight loss at day 3 (D3WL), expressed as a percentage of birth weight lost in the first 3 days of life. Our main explanatory variables were maternal pre-pregnancy body mass index (BMI), gestational weight gain, gestational diabetes, birth weight, gestational age and feeding mode. Results Factors associated with greater D3WL, whatever the feeding mode, were: higher birth weight, gestational diabetes and caesarean section; higher gestational age was associated with a reduced D3WL. The association between maternal pre-pregnancy BMI and D3WL differed by feeding mode (interaction p value=0.0002). In breastfed babies, mean D3WL ranged from 4.9% for neonates of underweight mothers to 5.8% for neonates of obese mothers (p trend=0.0005). In formula-fed babies, D3WL was highest for neonates of underweight mothers (4.1%) and lowest for those of obese mothers (2.6%) (p trend=0.01). Conclusions The lower D3WL in formula-fed neonates, especially in neonates of obese mothers, suggests a relative overfeeding in the early days compared with breastfed neonates, which may potentially have consequences on later health. Overweight and obese mothers may need extra support to prevent early breastfeeding discontinuation.
Reassessing the Role of Precious Metals as Safe Havens - What Colour is Your Haven and Why?

The role of gold as a safe haven asset has been extensively studied in recent years. This article extends previous literature and examines time varying safe haven properties versus equities and bonds of four precious metals (gold, silver, platinum and palladium) across eleven countries. Results suggest that the metals each play safe haven roles; there are times when one metal is not while another may be a safe haven against an asset. The second part of this article attempts to identify robust economic and political determinants of precious metals safe haven properties applying zero-inflated Poisson regression (ZIP) and extreme bound analysis (EBA). Economic Policy Uncertainty is found to be a positive and robust determinant of a precious metal being a safe haven. This holds across countries. Stock volatility, exchange rates, interest rate and credit spreads are also found to be significant, but results are quite mixed for different markets and are fragile of model specification.
Effect of phase separation on the kinetics of photocurrent relaxation in Sn–Sb–Se glassy films

The effects of phase separation on the structure and photoconductivity kinetics in SnxSb20Se80−x (x = 10,11,12.5) glassy films have been studied. Crystalline peaks for SnSe2, Sn2Sb4Se8 and Sn4Sb4Se10 phases are found in x = 12.5 films, while Sb2Se3 is the other major phase revealed from x-ray diffraction studies. The optical gap remains constant at 1.55 eV for x = 10,11 samples and then decreases to 1.50 eV for the x = 12.5 film, while a blueshift in reflectivity maxima (Rmax) has been observed with Sn content. An increase in room temperature conductivity and a decrease in dc activation energy with Sn content have been observed. Bimolecular recombination is the dominant recombination process under steady state illumination for all of the samples. Decay of photocurrent (after cessation of light) fits well to a stretched exponential function; the decay time constant and dispersion parameter have been discussed. The growth of network connectivity with an increase in compositional/configurational disorder induces states in the mobility gap and affects the structure of band tails. These results have been interpreted in the light of the barrier cluster model developed for chalcogenide glasses.
Epigenetic Changes Mediated by MicroRNA miR29 Activate Cyclooxygenase 2 and Lambda-1 Interferon Production during Viral Infection

ABSTRACT Lambda-1 interferon (IFN-λ1) and cyclooxygenase-2 (COX-2) were reported to play an important role in host antiviral defense. However, the mechanism by which IFN-λ1 and COX2 are activated and modulated during viral infection remains unclear. In this study, we found that expression of both circulating IFN-λ1 and COX2-derived prostaglandin E2 (PGE2) was coordinately elevated in a cohort of influenza patients compared to healthy individuals. Expression of IFN-λ1 was blocked by a selective COX2 inhibitor during influenza A virus infection in A549 human lung epithelial cells but enhanced by overexpression of COX2, indicating that the production of IFN-λ1 is COX2 dependent. COX2 was able to increase IFN-λ1 expression by promoting NF-κB binding to the enhancer in the IFN-λ1 promoter. We found that epigenetic changes activate COX2 expression and PGE2 accumulation during viral infection. The expression of DNA methyltransferase 3a (DNMT3a) and DNMT3b, but not that of DNMT1, was downregulated following influenza A virus infection in both A549 cells and peripheral blood mononuclear cells (PBMCs). We showed that microRNA miR29 suppresses DNMT activity and thus induces expression of COX2 and PGE2. Furthermore, miR29 expression was elevated 50-fold in virally infected A549 cells and 10-fold in PBMCs from influenza patients, compared to expression after mock infection of A549 cells or in healthy individuals, respectively. Activation of the protein kinase A signaling pathway and phosphorylation of CREB1 also contributed to COX2 expression. Collectively, our work defines a novel proinflammatory cascade in the control of influenza A virus infection.
Planetary transit candidates in the CoRoT LRa01 field

Context. The space mission CoRoT is devoted to the analysis of stellar variability and the photometric detection of extrasolar planets. Aims. We present the list of planetary transit candidates detected in the first short run observed by CoRoT that targeted SRc01, towards the Galactic center in the direction of Aquila, which lasted from April to May 2007. Methods. Among the acquired data, we analyzed those for 1269 sources in the chromatic bands and 5705 in the monochromatic band. Instrumental noise and the stellar variability were treated with several detrending tools, to which several transit-search algorithms were subsequently applied. Results. Fifty-one sources were classified as planetary transit candidates and 26 were followed up with ground-based observations. Until now, no planet has been detected in the CoRoT data from the SRc01 field.
Corridor System and Interest Rates: Volatility and Asymmetry

The corridor system in its current form is believed to reduce the volatility of overnight interest rates and to eliminate any chance of persistent upward or downward bias. The model presented here serves to highlight two main findings: one is that a central bank can further reduce the volatility of overnight interest rates by allowing banks some flexibility to meet their reserve targets within a small range, as observed in the UK data. The second is that a seemingly symmetric corridor may be asymmetric in practice due to several distortions, as the UK and euro area data suggest.
"Suboptimal" kidney donors: the experience with tacrolimus-based immunosuppression.

Female, pediatric, and older donors have been associated with inferior graft survival after renal transplantation. We analyzed these three subgroups in 397 patients receiving tacrolimus-based immunosuppression. There were no differences in recipient age, incidence of retransplantation, or percentage of sensitized patients. Female donors, compared with male donors, were associated with comparable 1- and 3-year patient survival rates (96% and 93% vs. 95% and 92%, respectively) and comparable 1- and 3-year graft survival rates (90% and 80% vs. 88% and 81%, respectively). Renal function was also similar. Recipients of pediatric en bloc kidneys, when compared with recipients of other cadaveric kidneys, also had comparable 1- and 3-year patient survival rates (94% and 94% vs. 95% and 91%, respectively) and comparable 1- and 3-year graft survival rates (84% and 84% vs. 89% and 79%, respectively). Renal function was better in recipients of en bloc kidneys, with a mean serum creatinine level of 1.4+/-1.8 mg/dl vs. 2.0+/-1.5 mg/dl (P=0.01). In contrast to the first two subgroups, donors over 60 years of age, when compared with donors under 60 years of age, were associated with worse 1- and 3-year patient survival rates (88% and 80% vs. 96% and 94%, respectively; P<0.03) and worse 1- and 3-year graft survival rates (74% and 62% vs. 91% and 83%, respectively; P<0.0001). Renal function was worse in the older donor group, with a serum creatinine level of 2.7+/-1.2 mg/ml vs. 1.9+/-1.5 mg/dl (P=0.01). We conclude that, under tacrolimus-based immunosuppression, kidneys from female or very young pediatric donors are not associated with adverse outcomes, whereas kidneys from donors over 60 years of age are associated with inferior outcomes.
Consequences of diagnostic delays in type 1 Gaucher disease: The need for greater awareness among Hematologists–Oncologists and an opportunity for early diagnosis and intervention

Gaucher disease (GD) is a progressive macrophage lipidosis capable of causing disabling and life‐threatening complications. Anecdotal experiences suggest that GD may go undiagnosed for many years, leading to severe complications that are preventable or reversible by enzyme replacement therapy (ERT) with imiglucerase. We conducted surveys of patients and Hematology–Oncology specialists to assess the frequency of diagnostic delays. Additionally, we report a series of patients who suffered diagnostic delays and as a result developed disabilities including potentially life‐threatening manifestations of GD. Of 136 patients surveyed, the average time from first appearance of GD symptoms to final diagnosis was 48.7 ± 123.6 months. More than two‐thirds were evaluated and managed by a Hematologist–Oncologist (Hem–Onc). A global survey of 406 Hem–Oncs found that only 20% considered GD in the differential diagnosis for all of its classic symptoms (cytopenia, hepatosplenomegaly, bone pain); the diagnosis considered most likely included leukemia, lymphoma, and multiple myeloma. To illustrate actual consequences of diagnostic delays, we describe 14 patients with GD who suffered from symptoms for up to 10 years before correct diagnosis. Diagnostic delays led to complications that are preventable or reversible with ERT (i.e., avascular necrosis, severe bleeding, chronic bone pain, life‐threatening sepsis, pathologic fractures, growth failure, liver pathology). Patients homozygous for N370S mutation in this series were vulnerable to diagnostic delays. In conclusion, prolonged diagnostic delays occur in GD and may result in severe disease manifestations. Our findings suggest that physician education will increase the likelihood of prompt detection of GD and improve its management with ERT with imiglucerase when indicated. Am. J. Hematol. , 2007. © 2007 Wiley‐Liss, Inc.
Pharmacokinetic drug interactions between triamterene and ranitidine in humans: alterations in renal and hepatic clearances and gastrointestinal absorption.

Ranitidine reduces the renal tubular secretion of the organic cations procainamide and N-acetylprocainamide in humans through competition for transport via the organic cation transport system. Ranitidine is thought to spare phase I hepatic metabolism mediated by cytochrome P-450, unlike its counterpart H2-receptor antagonist cimetidine. The aim of the present study was to determine, in eight human subjects, the effect of ranitidine on the disposition of the potassium-sparing diuretic triamterene, which undergoes renal tubular secretion, hepatic hydroxylation and subsequent sulphate conjugation to a pharmacologically active metabolite. Multiple blood and urine samples were collected throughout a dosing interval after chronic administration of triamterene alone, ranitidine alone or the two in combination. Ranitidine significantly (P less than .05) reduced the renal clearances of triamterene (51%) and p-hydroxytriamterene sulphate conjugate (47%), the clearance by hydroxylation of triamterene (30%) and the apparent absorption of triamterene (52%). In turn, triamterene reduced the renal clearance of ranitidine (14%). The interaction resulted in a small attenuation of the pharmacodynamic response to triamterene. These results necessitate consideration of the underlying mechanisms of the interactions and fall outside of our present understanding of the renal clearance of sulphate conjugates and the metabolic inhibitory effects of ranitidine. Competition for translocation across membranes is postulated as a common mechanism for the observed renal and hepatic interactions.