Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and Characterization of an Alternatively Processed Human Type II Interleukin-1 Receptor mRNA*

Two types of interleukin (IL)-1 receptors with three extracellular immunoglobulin-like domains, limited homology (28%), and different pharmacological characteristics termed type I and type II have been cloned from mouse and human cell lines. Both receptors exist in transmembrane and soluble forms; the soluble IL-1 receptor is thought to be post-translationally derived from cleavage of the extracellular portion of the membrane receptors. In preliminary cross-linking studies with radiolabeled IL-1, we found that monkey kidney COS1 cells express a soluble receptor with molecular mass of ∼55-60 kDa, which is different from previously reported soluble IL-1 receptors. This soluble IL-1 receptor protein from COS1 cells was purified to homogeneity by affinity chromatography using recombinant IL-1β as the ligand and shown to have an affinity for human 125I-IL-1β (KD ∼2-3 nM) comparable to the human type II IL-1 receptor (IL-1RII). The purified protein was microsequenced, and the sequence information was used to design primers to clone the COS1 IL-1RII using reverse transcription-coupled polymerase chain reaction; the DNA comparison with monkey COS1 and human IL-1RII indicate that they are 95% identical at the nucleic acid and amino acid levels. In addition, another cDNA, which represents an alternatively processed mRNA of the IL-1RII gene, was also cloned both from monkey COS1 and human Raji cells and was shown to have ∼95% sequence identity between these species. While the cDNA of the novel alternatively processed gene has a 5′ end identical to the IL-1RII, the 200 base pairs at the 3′ end are different and the sequence predicts a soluble IL-1 receptor protein of 296 amino acids. Radioligand binding studies of the alternatively processed IL-1RII mRNA demonstrated kinetic and pharmacological characteristics similar to the known type II IL-1 receptor. COS7 cells (which lack IL-1 receptor) transfected with the transmembrane form of the human IL-1RII cDNA showed 125I-IL-1β binding in both the membrane fractions and supernatant. In contrast, COS7 cells transfected with the alternatively processed human IL-1RII cDNA showed high affinity 125I-IL-1β binding (Ki ∼ 1.2 nM) predominantly in the supernatant; a very small amount of detectable membrane IL-1 binding activity was also observed presumably due to association of the soluble IL-1 receptor and membrane-integrated proteins. In cross-linking and ligand blot studies, the alternatively processed human IL-1RII cDNA-transfected COS7 cells expressed a soluble IL-1 receptor with molecular masses ranging from 60 to 160 kDa, further indicating the association between this soluble IL-1 receptor and other soluble proteins. In summary, we report the purification and characterization of a soluble IL-1 receptor expressed by COS1 cells and the cloning of an alternatively processed type II IL-1 receptor mRNA from both human and COS1 cells. The alternative splicing of a primary transcript leading to a secreted protein provides a potentially important mechanism by which soluble IL-1RII can be produced.
Differential behavior of E‐cadherin and occludin in their colocalization with ZO‐1 during the establishment of epithelial cell polarity

At the initial stage of cell‐cell contact of epithelial cells, primordial spot‐like junctions are formed at the tips of thin cellular protrusions radiating from adjacent cells, where E‐cadherin and ZO‐1 are precisely coconcentrated (Yonemura et al., 1995, J. Cell Sci. 108:127–142). In fully polarized epithelial cells, E‐cadherin and ZO‐1 are completely sorted into belt‐like adherens junctions (AJ) and tight junctions (TJ), respectively. Here we examined the behavior of occludin, an integral membrane protein consisting of TJ, during the establishment of epithelial cell polarity. Using confocal immunofluorescence microscopy, we quantitatively compared the spatial relationship of occludin/ZO‐1 with that of E‐cadherin/ZO‐1 during epithelial cellular polarization by replating or wounding cultured mouse epithelial cells (MTD1‐A). At the initial stage of cell‐cell contact, E‐cadherin and ZO‐1 appeared to be simultaneously recruited to the primordial form of spot‐like junctions at the tips of cellular processes which showed no concentration of occludin. Then, as cellular polarization proceeded, occludin was gradually accumulated at the ZO‐1–positive spot‐like junctions to form belt‐like TJ, and in a complementary manner E‐cadherin was sorted out from the ZO‐1–positive spot‐like junctions to form belt‐like AJ. The molecular mechanism of TJ/AJ formation during epithelial cellular polarization is discussed with special reference to the roles of ZO‐1. J. Cell. Physiol. 179:115–125, 1999. © 1999 Wiley‐Liss, Inc.
An Evaluation of the Polymerase Chain Reaction Amplicor Chlamydia trachomatis in Male Urine and Female Urogenital Specimens

Background and Objectives The new commercially available polymerase chain reaction (PCR)-based assay, Amplicor C. trachomatis, was compared with cell culture of C. trachomatis, for the detection of chlamydial urogenital infections. Goal of this Study To evaluate whether the Amplicor C. trachomatis PCR could improve the diagnosis of chlamydial urogenital infections, compared with cell culture of C. trachomatis considered as the reference method. Study Design A total of 466 men and 290 women attending a sexually transmitted disease (STD) clinic were tested by the Amplicor test in urine in men, and in the cervix and urethra in women, and by cell culture in the urethra of both men and women and in the cervix of the women. Results The prevalence of C. trachomatis was 13.7% by cell culture and 14.4% by the Amplicor test in men, and 3.5% by cell culture and 4.5% by the Amplicor test in women. After resolution of the discrepant results, the sensitivity of culture was 91.4% in male urethral specimens and 83.3% in endocervical and female urethral specimens. The resolved sensitivity of the PCR assay was 92.7% in male urine, 91.7% in endocervical samples, and reached 100% in testing both endocervical and female urethral specimens. Conclusion This rapid PCR-based assay showed an improvement in quality for diagnosing C. trachomatis infections.
Meiotic Competence in Horse Oocytes: Interactions Among Chromatin Configuration, Follicle Size, Cumulus Morphology, and Season1

Abstract Horse oocytes were collected from an abattoir over a 15-mo period. After classification of follicle size and cumulus morphology, oocytes were either fixed immediately (0 h) or matured in vitro (24 h). There was no effect of season on the number of antral follicles present on the ovaries, or on oocyte maturation rate for any class of oocyte. The proportion of oocytes having condensed chromatin at 0 h increased with increasing follicle size. The oocyte maturation rate also increased with follicle size, and for follicles ≤ 20-mm diameter, was higher for oocytes initially having expanded cumuli than for those having compact cumuli. The maturation rate was strongly correlated (r2 = 0.92) with the proportion of oocytes having condensed chromatin at 0 h. Oocytes with diffuse chromatin were found essentially only in follicles ≤ 20-mm diameter that yielded compact granulosa, indicating follicle viability. Presence of diffuse chromatin was inversely related to maturation rate. We conclude that the major signal for chromatin condensation, and thus acquisition of meiotic competence, occurs in viable follicles after 20-mm diameter in the horse. Condensation of chromatin in oocytes in smaller apparently viable follicles, while associated with acquisition of meiotic competence, may represent a pre-atretic change.
Incidence and Prevalence of Acinetobacter baumannii in King Fahd General Hospital , Saudi Arabia

The prevalence of multi-drug resistant (MDR) Acinetobacter that is causing patient infections at the King Fahad General Hospital, Jeddah, Saudi Arabia was studied. 104 bacterial isolates were collected in six month period, from April to December 2010 from 102 patients with various specimens including sputum, wound, urine; blood; cerebrospinal fluid and other locations (sites). Regardless of the specimen, there was a high rate of nosocomial MDR Acinetobacter spp. isolated from Intensive Care Unit (ICU). Of the 104 isolates of Acinetobacter spp. , 88.5% were identified as A. baumannii and 11.5% were other genospecies. The largest predominate antibiotype contained a total of 32 MDR isolates (resistant to quinolones, cephalosporins and carbapenems), including 29 A. baumannii (Ab) and 3 isolates were other genospecies. Respiratory tract specimens (sputum) represented nearly 72.2% of all the specimens collected in the ICU. Generally, Acinetobacter was isolated from various types of infection, specially respiratory tract infection (27.8%), followed by urinary tract infections (20.8%), Acinetobacter ventilator-associated pneumonia (11.1%), blood stream infections, burn wound infection and surgical site infection (9.7%), skin and soft tissues infection (6.9%), meningitis (1.4%) and other infection (6.2% . ) This study help taking effective measures for controlling Acinetobacter and data could be used in future as medical reference. [Al Masoudi SB, Aly MM, Al humidi NQ, Halwani M. Incidence and Prevalence of Acinetobacter baumannii in King Fahd General Hospital, Saudi Arabia. Life Sci J 2013;10(4):1702-1710] (ISSN:1097-8135). http://www.lifesciencesite. com. 225
CXCL12 Is a constitutive and inflammatory chemokine in the intestinal immune system

Background: Inflammatory bowel disease (IBD) is characterized by increased lymphocytic infiltrate to the lamina propria (LP) and upregulation of inflammatory chemokines and receptors. CXCL12 is a constitutive chemokine involved in lung, brain, and joint inflammation. We hypothesized that CXCL12 and its receptor, CXCR4, would have a constitutive and inflammatory role in the gut. Methods: Intestinal epithelial cells (IECs) and T lymphocytes were isolated from intestinal mucosa of IBD and control patients undergoing bowel resection. Autologous T cells were isolated from peripheral blood (PB). CXCL12 and CXCR4 expression by IECs was assessed by polymerase chain reaction and immunohistochemistry, lymphocyte phenotype by flow cytometry, and migration by Transwells. Results: IECs expressed CXCL12 and expression was increased and more diffuse in IBD compared to normal crypts (ulcerative colitis [UC] > Crohn's disease [CD], inflamed > noninflamed). CXCR4 was expressed by IECs, LP T cells (LPTs), and PB T cells (PBTs), and CXCR4+ cells were increased in IBD LP in situ. PBTs and LPTs from all patients had a high and comparable migration toward CXCL12 (P < 0.0001 and P < 0.05 vs. medium, respectively). Migration toward IBD‐IEC‐derived supernatant was significantly higher compared to normal. Antibodies against CXCR4 and CXCL12 blocked migration. Conclusions: CXCL12 is expressed by normal IECs and upregulated and differentially distributed in IBD IECs. CXCR4 is expressed by IECs and LPTs, and CXCR4+ cells are significantly increased in IBD LP. CXCL12 is chemotactic for both PBTs and LPTs. Thus, CXCL12 and CXCR4 have a constitutive and inflammatory role in the intestinal mucosa and their selective therapeutic manipulation may be considered in IBD management. (Inflamm Bowel Dis 2009;)
Long-lasting contribution of dopamine in the nucleus accumbens core, but not dorsal lateral striatum, to sign-tracking

The attribution of incentive salience to reward-paired cues is dependent on dopamine release in the nucleus accumbens core. These dopamine signals conform to traditional reward-prediction error signals and have been shown to diminish with time. Here we examined if the diminishing dopamine signal in the nucleus accumbens core has functional implications for the expression of sign-tracking, a Pavlovian conditioned response indicative of the attribution of incentive salience to reward-paired cues. Food-restricted male Sprague-Dawley rats were trained in a Pavlovian paradigm in which an insertable lever predicted delivery of food reward in a nearby food cup. After 7 or 14 training sessions, rats received infusions of saline, the dopamine antagonist flupenthixol (100 mM), or the GABA agonists baclofen and muscimol (0.5 mM baclofen/0.05 mM muscimol) into the nucleus accumbens core or the dorsal lateral striatum. Dopamine antagonism within the nucleus accumbens core attenuated sign-tracking, whereas reversible inactivation did not affect sign-tracking but increased non-specific food cup checking behaviors. Neither drug in the dorsal lateral striatum affected sign-tracking behavior. Critically, extended training did not alter these effects. Though extended experience with an incentive stimulus may reduce cue-evoked dopamine in the nucleus accumbens core, this does not alter the function of dopamine in this region to promote Pavlovian cue approach nor result in the recruitment of dorsal lateral striatal systems for this behavior. These data support the notion that dopamine within the mesoaccumbal system, but not the nigrostriatal system, contributes critically to incentive motivational processes independent of the length of training. Abbreviations DLS dorsal lateral striatum GT goal-tracker IN intermediate responder NAcC nucleus accumbens core ST sign-tracker
Age and apolipoprotein E*4 allele effects on cerebrospinal fluid beta-amyloid 42 in adults with normal cognition.

BACKGROUND Decreased cerebrospinal fluid (CSF) beta-amyloid 42 (A beta 42) concentration, but not A beta 40 concentration, is a biomarker for Alzheimer disease. This A beta 42 concentration decrease in CSF likely reflects precipitation of A beta 42 in amyloid plaques in brain parenchyma. This pathogenic plaque deposition begins years before the clinical expression of dementia in Alzheimer disease. Normal aging and the presence of the apolipoprotein E (APOE*4) allele are the most important known risk factors for Alzheimer disease. OBJECTIVE To estimate the interactive effects of normal aging and presence of the APOE*4 allele on CSF A beta 42 concentration in adults with normal cognition across the life span. DESIGN The CSF was collected in the morning after an overnight fast using Sprotte 24-g atraumatic spinal needles. The CSF A beta 42 and A beta 40 concentrations were measured in the 10th milliliter of CSF collected by sandwich enzyme-linked immunosorbent assay. The APOE genotype was determined by a restriction digest method. Subjects One hundred eighty-four community volunteers with normal cognition aged 21 to 88 years. RESULTS The CSF A beta 42, but not the A beta 40, concentration decreased significantly with age. There was a sharp decrease in CSF A beta 42 concentration beginning in the sixth decade in subjects with the APOE*4 allele. This age-associated decrease in CSF A beta 42 concentration was significantly and substantially greater in subjects with the APOE*4 allele compared with those without the APOE*4 allele. CONCLUSION These CSF A beta 42 findings are consistent with acceleration by the APOE*4 allele of pathogenic A beta 42 brain deposition starting in later middle age in persons with normal cognition.
Susceptibility loci for the defective foreign protein‐induced tolerance in New Zealand Black mice: Implication of epistatic effects of Fcgr2b and Slam family genes

In contrast to normal mice, autoimmune‐prone New Zealand Black (NZB) mice are defective in susceptibility to tolerance induced by deaggregated bovine γ globulin (DBGG). To examine whether this defect is related to the loss of self‐tolerance in autoimmunity, susceptibility loci for this defect were examined by genome‐wide analysis using the F2 intercross of nonautoimmune C57BL/6 (B6) and NZB mice. One NZB locus on the telomeric chromosome 1, designated Dit (Defective immune tolerance)‐1, showed a highly significant linkage. This locus overlapped with a locus containing susceptibility genes for autoimmune disease, namely Fcgr2b and Slam family genes. To investigate the involvement of these genes in the defective tolerance to DBGG, we took advantage of two lines of Fcgr2b‐deficient B6 congenic mice: one carries autoimmune‐type, and the other carries B6‐type, Slam family genes. Defective tolerance was observed only in Fcgr2b‐deficient mice with autoimmune‐type Slam family genes, indicating that epistatic effects of both genes are involved. Thus, common genetic mechanisms may underlie the defect in foreign protein antigen‐induced tolerance and the loss of self‐tolerance in NZB mouse‐related autoimmune diseases.
Altered developmental toxicity caused by three carrier solvents

Many aquatic bioassays rely on chemical solvents to solubilize water‐insoluble test materials. Interactions between solvents and test materials can lead to false positive or negative results. For this reason, tests for interactions between solvents and test materials were performed. The Frog Embryo Teratogenesis Assay–Xenopus (FETAX) was chosen because of its capacity to assess three different endpoints; mortality, malformation and embryo growth. Three solvents–dimethylsulfoxide (DMSO), acetone and triethylene glycol (TG)–were tested with two teratogens–methylmercury chloride (MMC) and trichloroethylene (TCE). DMSO potentiated the lethal effect of both teratogens but did not alter significantly the rate of malformation. Acetone increased the mortality for both teratogens, but only increased the MMC malformation greater than the additive effects. TG only increased the mortality and malformation with TCE. There were additive effects for growth for all solvents with the teratogens. The carrier solvents caused interactions even at their no‐observable‐effect concentration (NOEC). Therefore, the choice of carrier solvent should be made with caution. This study shows that different results can occur depending on the solvent used, and that a difference in one endpoint does not necessarily change the other endpoints.
Matrilin-3 Is Dispensable for Mouse Skeletal Growth and Development

ABSTRACT Matrilin-3 belongs to the matrilin family of extracellular matrix (ECM) proteins and is primarily expressed in cartilage. Mutations in the gene encoding human matrilin-3 (MATN-3) lead to autosomal dominant skeletal disorders, such as multiple epiphyseal dysplasia (MED), which is characterized by short stature and early-onset osteoarthritis, and bilateral hereditary microepiphyseal dysplasia, a variant form of MED characterized by pain in the hip and knee joints. To assess the function of matrilin-3 during skeletal development, we have generated Matn-3 null mice. Homozygous mutant mice appear normal, are fertile, and show no obvious skeletal malformations. Histological and ultrastructural analyses reveal endochondral bone formation indistinguishable from that of wild-type animals. Northern blot, immunohistochemical, and biochemical analyses indicated no compensatory upregulation of any other member of the matrilin family. Altogether, our findings suggest functional redundancy among matrilins and demonstrate that the phenotypes of MED disorders are not caused by the absence of matrilin-3 in cartilage ECM.
Panchromatic spectral energy distributions of Herschel sources

Combining far-infrared Herschel photometry from the PACS Evolutionary Probe (PEP) and Herschel Multi-tiered Extragalactic Survey (HerMES) guaranteed time programs with ancillary datasets in the GOODS-N, GOODS-S, and COSMOS fields, it is possible to sample the 8–500 μm spectral energy distributions (SEDs) of galaxies with at least 7–10 bands. Extending to the UV, optical, and near-infrared, the number of bands increases up to 43. We reproduce the distribution of galaxies in a carefully selected restframe ten colors space, based on this rich data-set, using a superposition of multivariate Gaussian modes. We use this model to classify galaxies and build median SEDs of each class, which are then fitted with a modified version of the magphys code that combines stellar light, emission from dust heated by stars and a possible warm dust contribution heated by an active galactic nucleus (AGN). The color distribution of galaxies in each of the considered fields can be well described with the combination of 6–9 classes, spanning a large range of far- to near-infrared luminosity ratios, as well as different strength of the AGN contribution to bolometric luminosities. The defined Gaussian grouping is used to identify rare or odd sources. The zoology of outliers includes Herschel-detected ellipticals, very blue z ~ 1 Ly-break galaxies, quiescent spirals, and torus-dominated AGN with star formation. Out of these groups and outliers, a new template library is assembled, consisting of 32 SEDs describing the intrinsic scatter in the restframe UV-to-submm colors of infrared galaxies. This library is tested against L(IR) estimates with and without Herschel data included, and compared to eightother popular methods often adopted in the literature. When implementing Herschel photometry, these approaches produce L(IR) values consistent with each other within a median absolute deviation of 10–20%, the scatter being dominated more by fine tuning of the codes, rather than by the choice of SED templates. Finally, the library is used to classify 24 μm detected sources in PEP GOODS fields on the basis of AGN content, L(60)/L(100) color and L(160)/L(1.6) luminosity ratio. AGN appear to be distributed in the stellar mass (M_∗) vs. star formation rate (SFR) space along with all other galaxies, regardless of the amount of infrared luminosity they are powering, with the tendency to lie on the high SFR side of the “main sequence”. The incidence of warmer star-forming sources grows for objects with higher specific star formation rates (sSFR), and they tend to populate the “off-sequence” region of the M_∗ − SFR − z space.
The long wavelength topography of Beethoven and Tolstoj basins, Mercury

Topography derived from Mariner 10 stereo images is used to characterize the interior structure of two mercurian basins, Beethoven and Tolstoj. Beethoven and Tolstoj basins are shallow (∼2.5 km and ∼2 km deep, respectively) and relatively flat‐floored. Beethoven basin has an interior topographic rise near the northwest margin. The topography of Beethoven and Tolstoj basins is similar to that of lunar mare‐filled basins. Well‐developed basin‐concentric wrinkle ridges and arcuate graben associated with lunar mascons are absent in both Beethoven and Tolstoj basins. The lack of mascon tectonic features suggests that either 1) the mercurian basins have a relatively thin veneer of fill material, 2) Mercury's elastic lithosphere was too strong for significant lithospheric flexure and subsidence to occur, or 3) the basin fill material has little or no density contrast with the surrounding crust and thus exerts little net load on the mercurian lithosphere.