Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression profiling of metalloproteinases and their inhibitors in cartilage.

OBJECTIVE To profile the expression of all known members of the matrix metalloproteinase (MMP), ADAMTS, and tissue inhibitor of metalloproteinases (TIMP) gene families in normal cartilage and cartilage from patients with osteoarthritis (OA). METHODS Human cartilage was obtained from femoral heads at joint replacement for OA or following fracture to the femoral neck. Total RNA was purified, and gene expression was assayed using quantitative real-time polymerase chain reaction. RESULTS Several members of the above gene families were regulated in OA. Genes that showed increased expression in OA were MMP13, MMP28, and ADAMTS16 (all at P < 0.001), MMP9, MMP16, ADAMTS2, and ADAMTS14 (all at P < 0.01), and MMP2, TIMP3, and ADAMTS12 (all at P < 0.05). Genes with decreased expression in OA were MMP1, MMP3, and ADAMTS1 (all at P < 0.001), MMP10, TIMP1, and ADAMTS9 (all at P < 0.01), and TIMP4, ADAMTS5, and ADAMTS15 (all at P < 0.05). Correlation analysis revealed that groups of genes across the gene families were coexpressed in cartilage. CONCLUSION This is the first comprehensive expression profile of all known MMP, ADAMTS, and TIMP genes in cartilage. Elucidation of patterns of expression provides a foundation with which to understand mechanisms of gene regulation in OA and potentially to refine the specificity of antiproteolytic therapies.
Nivolumab and pembrolizumab as immune-modulating monoclonal antibodies targeting the PD-1 receptor to treat melanoma

Malignant melanoma is an important issue in oncology due to its high incidence, high mortality, and resistance to systemic therapy; however, targeted immunotherapy has noticeably improved the survival rates of melanoma patients. Promising targeted immunotherapies for malignant melanoma include the blockade of immune checkpoints with antibodies targeting cytotoxic T lymphocyte-associated antigen 4 and the programmed cell death protein 1 pathway. The US FDA-approved antibody ipilimumab targets cytotoxic T lymphocyte-associated antigen 4; however, it was limited by toxicity and a low response. Nivolumab and pembrolizumab (formerly lambrolizumab), the two FDA-approved anti-programmed death-1 monoclonal antibodies, show highly durable response rates and long-term safety, validating the importance of the programmed cell death protein 1 pathway blockade for treatment of malignant melanoma.
Immune Cross-Reactivity in Celiac Disease: Anti-Gliadin Antibodies Bind to Neuronal Synapsin I1

Celiac disease is an immune-mediated disorder triggered by ingestion of wheat gliadin and related proteins in genetically susceptible individuals. In addition to the characteristic enteropathy, celiac disease is associated with various extraintestinal manifestations, including neurologic complications such as neuropathy, ataxia, seizures, and neurobehavioral changes. The cause of the neurologic manifestations is unknown, but autoimmunity resulting from molecular mimicry between gliadin and nervous system proteins has been proposed to play a role. In this study, we sought to investigate the immune reactivity of the anti-gliadin Ab response toward neural proteins. We characterized the binding of affinity-purified anti-gliadin Abs from immunized animals to brain proteins by one- and two-dimensional gel electrophoresis, immunoblotting, and peptide mass mapping. The major immunoreactive protein was identified as synapsin I. Anti-gliadin Abs from patients with celiac disease also bound to the protein. Such cross-reactivity may provide clues into the pathogenic mechanism of the neurologic deficits that are associated with gluten sensitivity.
Testing for Blood Glucose by Office-Based Physicians in the U.S.

A national sample of 2879 physicians were surveyed to ascertain characteristics of patient visits for diabetes including whether any test had been ordered or provided or a specimen taken to assess the patient's blood glucose level. Based on survey data, an estimated 21.3 million visits were made for diabetes in 1985. Of these, 16.8 million were for continuing care of diabetes by primary-care physicians, an average of 2.7 visits/yr for the 6.1 million U.S. residents diagnosed as having diabetes. A test for blood glucose was associated with 69% of these visits, an average of 1.9 times/yr per patient with diabetes in the U.S. Rates of testing for blood glucose varied by source of payment for the visit and were higher when diabetes was the primary diagnosis and when the number of physicians practicing together was greater, such as in health maintenance organizations or group practices. Rates of testing did not differ by age, race, or sex of the patient; location of the physician/s practice; whether insulin or oral agents were prescribed; or a number of other characteristics. Other studies indicate that self-monitoring of blood glucose is performed by <10% of diabetic patients. Hence, the physician's office remains an important location for assessment of diabetes control by measurement of blood glucose levels.
Histamine-2-Receptor Antagonist Administration and Gastrointestinal Bleeding When Used for Stress Ulcer Prophylaxis in Patients With Severe Sepsis or Septic Shock

Background: The Surviving Sepsis Campaign suggests that proton pump inhibitors (PPIs) be considered over histamine-2-receptor antagonists (H2RA) for stress ulcer prophylaxis (SUP), but there are no studies demonstrating superiority with PPIs in this population. Objective: To determine if H2RAs are associated with an increased risk for gastrointestinal (GI) bleeding in patients with severe sepsis or septic shock. Methods: This study queried the Multiparameter Intelligent Monitoring in Intensive Care II database to identify adult patients with severe sepsis or septic shock requiring mechanical ventilation for at least 48 hours. Patients were excluded if they had GI bleeding as a primary diagnosis, variceal bleeding, received both PPIs and H2RAs or no acid suppression. Demographic characteristics, medication use and potential confounders for GI bleeding were recorded. ICD-9 coding was used to identify GI bleeding listed as a secondary diagnosis. Multivariate analysis was performed to assess the role of H2RAs as an independent risk factor for GI bleeding. Results: There were 686 patients evaluated. The incidence of GI bleeding was 9.5%. Patients who received H2RAs had a bleeding incidence of 2.3% versus 10% with PPIs (P = 0.111). On controlling for confounding variables, drug selection (H2RA or PPI) was not associated with an increased risk for bleeding. Acute or chronic liver disease was the only independent risk factor identified: odds ratio [OR] (95% CI) = 3.75 (2.19-6.44); P < 0.001. Conclusion: H2RAs are not associated with an increased risk for GI bleeding in patients with severe sepsis or septic shock who require mechanical ventilation. These data do not support the Surviving Sepsis Campaign recommendation of PPIs as the preferred agent in this population.
Detection and quantification of five major periodontal pathogens by single copy gene-based real-time PCR

Periodontitis is a common chronic multibacterial infection in the tooth-supporting tissues. It has been shown that periodontitis patients carry higher number of disease-associated bacteria than healthy ones. The aim of this study was to generate a novel, single copy gene-based quantitative real-time PCR (qPCR) assay for five major periodontal pathogens — Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Treponema denticola, and Tannerella forsythia. The primer/probe sets were designed for conservative lipopolysaccharide-coding gene regions. They proved to be sensitive and able to detect strains representing different serotypes of the target bacteria. The specificity of designed primers was tested using 49 selected bacterial species and no false positive or negative results were observed. We validated the assay with a case-control population, including 165 saliva samples, and proved the diagnostic accuracy by Receiver Operating Characteristic (ROC) curves. All quantified pathogens alone were able to distinguish significantly between the subjects with and without periodontitis, and provided areas under the ROC curve larger than 0.5. The total pathogen burden comprising all five species associated with periodontitis with an area of 0.821 (95% CI, 0.758—0.885, P50.001). Our prominently sensitive and specific assay may have major importance in the diagnosis, prevention, and treatment of periodontitis.
Association of ABO(H) and I blood group system development with von Willebrand factor and Factor VIII plasma levels in children and adolescents

BACKGROUND: The modulation of Factor (F)VIII activity (FVIII : C), von Willebrand factor antigen (VWF : Ag), and von Willebrand factor ristocetin cofactor (VWF : RCo) by the ABO(H) blood group is well established in adults. Expression of ABH antigens on N‐linked glycans of VWF protects plasma VWF from proteolysis and clearance. Protection by H antigens is less effective than by AB antigens, resulting in approximately 25% lower VWF plasma levels in adults with blood group O compared to non‐O. Given the reduced branching of ABO(H) bearing structures (I blood group system) with lower numbers of H, A, and B antigen sites during the first 18 months of life, we reasoned that if the relationship between ABO(H) blood group and VWF levels were causal, the difference of ABO(H) blood group–dependent VWF levels should be marginal or not be observed in the first months of life.
Developmental expression and regulation of the gap junction protein and transcript in rat ovaries

The extensively developed network of cell‐to‐cell communication, generated by gap junctions, mediates transmission of small molecules between the cells of the ovarian follicle. Our study aimed at the analysis of the ontogeny and regulation of connexin43 (Cx43) the ovarian gap junction protein and its gene expression throughout folliculogenesis. Developmental analysis was performed using ovaries of immature rats at different ages and selected ovarian follicles of sexually mature female rats at different phases of their estrous cycle. In order to establish the effect of hormones involved in regulation of folliculogenesis on Cx43 modulation, the experimental animal model of sexually immature female rats administered with exogenous gonadotropins was employed. Developmental and hormonal modulations of Cx43 protein and its mRNA expression were studied by Western and Northern blot analysis, respectively. We found that Cx43 was undetectable in ovaries of rats on the first postnatal day, with a low level of this protein observed in 11‐day‐old rats ovaries. Some increase in the amount of Cx43 was observed at the age of 25 days with a dramatic elevation accompanied by phosphorylation of this protein that was specific to large antral follicles of sexually mature proestrous rats. Elimination of the protein was observed at estrus and could be prevented by cancellation of the preovulatory surge of luteinizing hormone (LH). This pattern of Cx43 modifications was mimicked by exogenous administration of hormones as follows: Pregnant mare's serum gonadotropin (PMSG) increased the Cx43 protein expression with a concurrent induction of its phosphorylation while a further human chorionic gonadotropin (hCG) injection resulted in a decrease of the signal. Analysis of the Cx43 mRNA showed a direct correlation between the Cx43 protein level and its gene expression. We conclude that: 1) At early folliculogenesis the ovarian gap junction protein Cx43 and its gene are developmentally regulated; and 2) After antrum formation, transcription, translation, and posttranslational modifications of Cx43 are regulated by gonadotropins. Mol. Reprod. Dev. 47:231–239, 1997. © 1997 Wiley‐Liss, Inc.
Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire.

In the bone marrow, diversity in the primary antibody repertoire is created by the combinatorial rearrangement of different gene segments and by the association of different heavy and light chains. During the secondary response in the germinal centres, antibodies are diversified by somatic mutation and possibly by further rearrangements, or "receptor editing". Here, we have analysed the pairings of heavy and light chain variable domains (VH and VL) in 365 human IgG+ B cells from peripheral blood, and established that these pairings are largely random. The repertoire is dominated by a limited number of pairings of segments and folds. Among these pairings we identified two identical mutated heavy chains in combination with two different mutated light chains (one kappa and one lambda). This shows that receptor editing occurs in the human periphery and that the same antibody lineage can be subjected to both receptor editing and somatic hypermutation. This suggests that receptor editing may be used together with somatic mutation for the affinity maturation of antibodies. We also propose that receptor editing has shaped variable gene segment use and the evolution of V gene families.
Ribosomal resistance in the gentamicin producer organism Micromonospora purpurea

The mechanism of resistance of the gentamicin-producing organism Micromonospora purpurea was analyzed. Determination of minimal inhibitory concentrations revealed high resistance to the 4,6-substituted deoxystreptamine aminoglycosides amikacin, gentamicin, kanamycin, netilmicin, sisomicin, and tobramycin and also to lividomycin A and hygromycin B, but susceptibility to streptomycin, dihydrostreptomycin, paromomycin, and neomycin during all phases of the growth cycle. The nonproducing, closely related Micromonospora melanosporea was susceptible to these compounds. In agreement with results from previous studies (R. Benveniste and J. Davies, Proc. Natl. Acad. Sci. U.S.A. 70:2276-2280, 1973), extracts from M. purpurea showed no activity of enzymes specifically modifying gentamicin. 70S ribosomes from M. purpurea but not from M. melanosporea were resistant to inhibition by gentamicin, kanamycin, tobramycin, and lividomycin in a polyuridylic acid-dependent polyphenylalanine synthesis system and susceptible to those compounds which were inhibitory in vivo. The former antibiotics were also unable to induce misreading. Subunit exchange experiments between M. purpurea and M. melanosporea showed that the main site for inhibition and induction of misreading is the 30S subunit (up to gentamicin concentrations of 10 micrograms/ml).
Gene escape model: transfer of heavy metal resistance genes from Escherichia coli to Alcaligenes eutrophus on agar plates and in soil samples

Conjugal transfer from Escherichia coli to Alcaligenes eutrophus of the A. eutrophus genes coding for plasmid-borne resistance to cadmium, cobalt, and zinc (czc genes) was investigated on agar plates and in soil samples. This czc fragment is not expressed in the donor strain, E. coli, but it is expressed in the recipient strain, A. eutrophus. Hence, expression of heavy metal resistance by cells plated on a medium containing heavy metals represents escape of the czc genes. The two plasmids into which this DNA fragment has been cloned previously and which were used in these experiments are the nonconjugative, mobilizable plasmid pDN705 and the nonconjugative, nonmobilizable plasmid pMOL149. In plate matings at 28 to 30 degrees C, the direct mobilization of pDN705 occurred at a frequency of 2.4 x 10(-2) per recipient, and the mobilization of the same plasmid by means of the IncP1 conjugative plasmids RP4 or pULB113 (present either in a third cell [triparental cross] or in the recipient strain itself [retromobilization]) occurred at average frequencies of 8 x 10(-4) and 2 x 10(-5) per recipient, respectively. The czc genes cloned into the Tra- Mob- plasmid pMOL149 were transferred at a frequency of 10(-7) to 10(-8) and only by means of plasmid pULB113. The direct mobilization of pDN705 was further investigated in sandy, sandy-loam, and clay soils. In sterile soils, transfer frequencies at 20 degrees C were highest in the sandy-loam soil (10(-5) per recipient) and were enhanced in all soils by the addition of easily metabolizable nutrients. (ABSTRACT TRUNCATED AT 250 WORDS)
Effects of Melanin upon Susceptibility of Cryptococcus to Antifungals

Melanin is a recognized virulence factor in Cryptococcus neoformans; several pathogenetic mechanisms have been suggested. We studied melanin as an antifungal resistance factor. The growth of laccase‐active strains of C. neoformans and C. albidus in L‐DOPA resulted in the production of black pigment. The formal minimal inhibitory concentrations (MICs) of amphotericin B and fluconazole were not changed by melanization. However, when we examined those wells which contained inhibited cells, we found live cells only in wells containing melanized C. neoformans. In contrast, melanization did not protect C. albidus from killing by amphotericin B. In an amphotericin B time‐kill study of C. neoformans, significantly more melanized cells than non‐melanized survived for the first few hours. Fluorescence microscopy and flow cytometry analyses showed that fewer melanized cells were stained with the fluorescent dye MitoRed. Incubation of MitoRed (the model) or amphotericin B with melanin extracted from C. neoformans decreased the free concentrations of these substances. Fluconazole, in contrast, was not removed from solution by melanin. This suggests that neoformans cryptococcal melanin deposited amphotericin B in the cell wall binds, reducing its effective concentrations.
Characterization of novel akermanite:poly‐ϵ‐caprolactone scaffolds for human adipose‐derived stem cells bone tissue engineering

In this study, three different akermanite:poly‐ϵ‐caprolactone (PCL) composite scaffolds (wt%: 75:25, 50:50, 25:75) were characterized in terms of structure, compression strength, degradation rate and in vitro biocompatibility to human adipose‐derived stem cells (hASC). Pure ceramic scaffolds [CellCeramTM, custom‐made, 40:60 wt%; β‐tricalcium phosphate (β‐TCP):hydroxyapatite (HA); and akermanite] and PCL scaffolds served as experimental controls. Compared to ceramic scaffolds, the authors hypothesized that optimal akermanite:PCL composites would have improved compression strength and comparable biocompatibility to hASC. Electron microscopy analysis revealed that PCL‐containing scaffolds had the highest porosity but CellCeramTM had the greatest pore size. In general, compression strength in PCL‐containing scaffolds was greater than in ceramic scaffolds. PCL‐containing scaffolds were also more stable in culture than ceramic scaffolds. Nonetheless, mass losses after 21 days were observed in all scaffold types. Reduced hASC metabolic activity and increased cell detachment were observed after acute exposure to akermanite:PCL extracts (wt%: 75:25, 50:50). Among the PCL‐containing scaffolds, hASC cultured for 21 days on akermanite:PCL (wt%: 75:25) discs displayed the highest viability, increased expression of osteogenic markers (alkaline phosphatase and osteocalcin) and lowest IL‐6 expression. Together, the results indicate that akermanite:PCL composites may have appropriate mechanical and biocompatibility properties for use as bone tissue scaffolds. Copyright © 2012 John Wiley & Sons, Ltd.
The Type II Secretion System of Legionella pneumophila Dampens the MyD88 and Toll-Like Receptor 2 Signaling Pathway in Infected Human Macrophages

ABSTRACT Previously, we reported that mutants of Legionella pneumophila lacking a type II secretion (T2S) system elicit higher levels of cytokines (e.g., interleukin-6 [IL-6]) following infection of U937 cells, a human macrophage-like cell line. We now show that this effect of T2S is also manifest upon infection of human THP-1 macrophages and peripheral blood monocytes but does not occur during infection of murine macrophages. Supporting the hypothesis that T2S acts to dampen the triggering of an innate immune response, we observed that the mitogen-activated protein kinase (MAPK) and nuclear transcription factor kappa B (NF-κB) pathways are more highly stimulated upon infection with the T2S mutant than upon infection with the wild type. By using short hairpin RNA to deplete proteins involved in specific pathogen-associated molecular pattern (PAMP) recognition pathways, we determined that the dampening effect of the T2S system was not dependent on nucleotide binding oligomerization domain (NOD)-like receptors (NLRs), retinoic acid-inducible protein I (RIG-I)-like receptors (RLRs), double-stranded RNA (dsRNA)-dependent protein kinase receptor (PKR), or TIR domain-containing adaptor inducing interferon beta (TRIF) signaling or an apoptosis-associated speck-like protein containing a CARD (ASC)- or caspase-4-dependent inflammasome. However, the dampening effect of T2S on IL-6 production was significantly reduced upon gene knockdown of myeloid differentiation primary response 88 (MyD88), TANK binding kinase 1 (TBK1), or Toll-like receptor 2 (TLR2). These data indicate that the L. pneumophila T2S system dampens the signaling of the TLR2 pathway in infected human macrophages. We also document the importance of PKR, TRIF, and TBK1 in cytokine secretion during L. pneumophila infection of macrophages.
The SNF2 family ATPase LSH promotes cell-autonomous de novo DNA methylation in somatic cells

Methylation of DNA at carbon 5 of cytosine is essential for mammalian development and implicated in transcriptional repression of genes and transposons. New patterns of DNA methylation characteristic of lineage-committed cells are established at the exit from pluripotency by de novo DNA methyltransferases enzymes, DNMT3A and DNMT3B, which are regulated by developmental signaling and require access to chromatin-organized DNA. Whether or not the capacity for de novo DNA methylation of developmentally regulated loci is preserved in differentiated somatic cells and can occur in the absence of exogenous signals is currently unknown. Here, we demonstrate that fibroblasts derived from chromatin remodeling ATPase LSH (HELLS)-null mouse embryos, which lack DNA methylation from centromeric repeats, transposons and a number of gene promoters, are capable of reestablishing DNA methylation and silencing of misregulated genes upon re-expression of LSH. We also show that the ability of LSH to bind ATP and the cellular concentration of DNMT3B are critical for cell-autonomous de novo DNA methylation in somatic cells. These data suggest the existence of cellular memory that persists in differentiated cells through many cell generations and changes in transcriptional state.
MDR1 gene polymorphisms and risk of recurrence in patients With hepatocellular carcinoma after liver transplantation

Recurrence of hepatocellular carcinoma (HCC) after liver transplantation (LT) remains a major cause of post‐LT death. However, currently there is still lacking the markers to reliably predict recurrence. This study was undertaken to evaluate the association between three polymorphisms (C1236T, G2677A/T, C3435T) of Multidrug resistance 1 (MDR1) gene and the risk of recurrence after LT.