tbuckley/cabot-search huggingface dataset:
Plasma Matrix Metalloproteinase-9 Level Is Better than Serum Matrix Metalloproteinase-9 Level to Predict Gastric Cancer Evolution
Authors: Chun-Ying Wu, Ming-Shiang Wu, En-Pei Chiang, Yi-Ju Chen, Chien-Jen Chen, Nai-Hui Chi, Ying-Ting Shih, Gran-Hum Chen, Jaw-Town Lin
Journal: Clinical Cancer Research (2007)

Abstract Purpose: Matrix metalloproteinase-9 (MMP-9) in blood is a promising new tumor marker. The aims of the present study are to compare the usefulness of plasma and serum MMP-9 levels for predicting gastric cancer development, invasion, and survival. Experimental Design: In this nested case-control study, 114 gastric cancer patients and 87 healthy controls were enrolled. MMP-9 levels and activities were quantitatively measured by ELISA assay and zymography. The results were compared with the occurrence, clinicopathologic features, and outcomes of gastric cancer patients. The follow-up time for all patients was at least 5 years. Results: Serum MMP-9 levels were significantly higher than plasma MMP-9 levels. Both plasma and serum MMP-9 levels correlated significantly with active MMP-9 identified by zymography (P = 0.002 and P = 0.048, respectively). Plasma MMP-9 level was significantly elevated in gastric cancer patients when compared with control subjects (P &amp;lt; 0.001). Serum MMP-9 levels did not differ between the groups. Receiver-operator characteristics analysis showed the values of sensitivity (82.5%) and specificity (65.5%) at the maximum accuracy for plasma MMP-9 at ≥60 ng/mL (P &amp;lt; 0.001). Elevated plasma MMP-9 correlated significantly with lymph node metastasis [odds ratio (OR), 3.43; P = 0.019], lymphatic invasion (OR, 7.58; P = 0.009), and venous invasion (OR, 4.14; P = 0.033). Patients with elevated plasma MMP-9 levels had poorer survival rates than those with normal plasma MMP-9 levels (P = 0.038). Serum MMP-9 level did not correlate well with gastric cancer–invasive phenotypes or survival. Conclusion: Our results suggest plasma MMP-9 level is a better marker than serum MMP-9 level for predicting gastric cancer development and progression.
Microscopic observation drug susceptibility assay for the diagnosis of TB and MDR-TB in HIV-infected patients: a systematic review and meta-analysis
Authors: Philip Wikman-Jorgensen, Jara Llenas-García, Michael Hobbins, Jochen Ehmer, Rosa Abellana, Alessandra Queiroga Gonçalves, Tomàs Maria Pérez-Porcuna, Carlos Ascaso
Journal: European Respiratory Journal (2014)

The objective of the present study was to assess the diagnostic accuracy of the microscopic observation drug susceptibility (MODS) assay for tuberculosis (TB) diagnosis in HIV-infected patients. MEDLINE, EMBASE, LILACS, the Cochrane Central Register of Controlled Trials, African Index Medicus, ResearchGate, SciELO, and the abstracts of the main conferences on infectious diseases and tropical medicine were searched, and other sources investigated. Only studies including HIV-infected patients evaluating MODS for the diagnosis of TB and using culture-based diagnostic tests as a gold standard were analysed. Summary sensitivity and specificity were calculated with a bivariate model. 3259 citations were found, 29 were selected for full-text review and 10 studies including 3075 samples were finally analysed. Overall diagnostic accuracy of MODS for the diagnosis of TB was a sensitivity of 88.3% (95% CI 86.18–90.2%) and specificity 98.2% (95% CI 97.75–98.55%). For multidrug-resistant (MDR)-TB, sensitivity was 89% (95% CI 66.07–97%) and specificity was 100% (95 CI 94.81–100%). For smear-negative pulmonary TB, a sensitivity of 88.2% (95% CI 86.1–89.9%) and specificity of 98.2% (95% CI 96.8–98.9%) were found. Costs varied between USD 0.72 and 7.31 per sample. Mean time to positivity was 8.24 days. MODS was found to have a good accuracy for the diagnosis of TB and MDR-TB in HIV-infected patients with low cost and fast results.
Pre-operative evaluation of lung function test results
Authors: B. Houltz, J. Olofson, B. Bake
Journal: European Respiratory Journal (2010)

To the Editors: 

The European Respiratory Society/European Society of Thoracic Surgeons joint clinical guidelines on fitness for radical therapy in lung cancer patients (surgery and chemo-radiotherapy) were published in the July 2009 issue of the European Respiratory Journal 1. This comprehensive and very important document provides guidelines for the risk evaluation of candidates for lung cancer surgery. We fully agree that the lung function variables forced expiratory volume in 1 s (FEV …
Apoptosis and Necrosis in the Liver: A Tale of Two Deaths?
Authors: Harmeet Malhi, Gregory J. Gores, John J. Lemasters
Journal: Hepatology (2006)

Death of hepatocytes and other hepatic cell types is a characteristic feature of liver diseases as diverse as cholestasis, viral hepatitis, ischemia/reperfusion, liver preservation for transplantation and drug/toxicant-induced injury. Cell death typically follows one of two patterns: oncotic necrosis and apoptosis. Necrosis is typically the consequence of acute metabolic perturbation with ATP depletion as occurs in ischemia/reperfusion and acute drug-induced hepatotoxicity. Apoptosis, in contrast, represents the execution of an ATP-dependent death program often initiated by death ligand/death receptor interactions, such as Fas ligand with Fas, which leads to a caspase activation cascade. A common event leading to both apoptosis and necrosis is mitochondrial permeabilization and dysfunction, although the mechanistic basis of mitochondrial injury may vary in different settings. Prevention of these modes of cell death is an important target of therapy, but controversies still exist regarding which mode of cell death predominates in various forms of liver disease and injury. Resolution of these controversies may come with the recognition that apoptosis and necrosis frequently represent alternate outcomes of the same cellular pathways to cell death, especially for cell death mediated by mitochondrial permeabilization. An understanding of processes leading to liver cell death will be important for development of effective interventions to prevent hepatocellular death leading to liver failure and to promote cancer and stellate cell death in malignancy and fibrotic disease.
Does This Patient Have a Torn Meniscus or Ligament of the Knee?
Authors: Daniel H. Solomon, David L. Simel, David W. Bates, Jeffrey N. Katz, Jonathan L. Schaffer
Journal: JAMA (2001)

ContextWhile most meniscal or ligamentous knee injuries heal with nonoperative treatments, a subset should be treated with arthroscopic or open surgery.ObjectiveTo analyze the accuracy of the clinical examination for meniscal or ligamentous knee injuries.Data SourcesMEDLINE (1966-December 31, 2000) and HealthSTAR (1975-December 31, 2000) databases were searched for English-language articles describing the diagnostic accuracy of individual examination items for the knee and a combination of physical examination items (composite examination). Other data sources included reference lists from relevant articles.Study SelectionStudies selected for data extraction were those that compared the performance of the physical examination of the knee with a reference standard, such as arthroscopy, arthrotomy, or magnetic resonance imaging. Eighty-eight articles were identified, of which 23 (26%) met inclusion criteria.Data ExtractionA rheumatologist and an orthopedic surgeon independently reviewed each article using a standardized rating scale that scored the assembly of the study, the relevance of the patients enrolled, the appropriateness of the reference standard, and the blinding of the examiner.Data SynthesisSummary likelihood ratios (LRs) were estimated from random effects models. The summary LRs for physical examination for tears of the anterior cruciate ligament, using the anterior drawer test, were 3.8 (95% confidence interval [CI], 0.7-22.0) for a positive examination and 0.30 (95% CI, 0.05-1.50) for a negative examination; the Lachman test, 25.0 (95% CI, 2.7-651.0) and 0.1 (95% CI, 0.0-0.4); and the composite assessment, 25.0 (95% CI, 2.1-306.0) and 0.04 (95% CI, 0.01-0.48), respectively. The LRs could not be generated for any specific examination maneuver for a posterior cruciate ligament tear, but the composite assessment had an LR of 21.0 (95% CI, 2.1-205.0) for a positive examination and 0.05 (95% CI, 0.01-0.50) for a negative examination. Determination of meniscal lesions, using McMurray test, had an LR of 1.3 (95% CI, 0.9-1.7) for a positive examination and 0.8 (95% CI, 0.6-1.1) for a negative examination; joint line tenderness, 0.9 (95% CI, 0.8-1.0) and 1.1 (95% CI, 1.0-1.3); and the composite assessment, 2.7 (95% CI, 1.4-5.1) and 0.4 (95% CI, 0.2-0.7), respectively.ConclusionThe composite examination for specific meniscal or ligamentous injuries of the knee performed much better than specific maneuvers, suggesting that synthesis of a group of examination maneuvers and historical items may be required for adequate diagnosis.
Partial amino acid sequence homology between an heredofamilial amyloid protein and human plasma prealbumin.
Authors: M D Benson
Journal: Journal of Clinical Investigation (1981)

Amyloid fibril protein has been isolated from the tissues of a patient of Swedish ancestry with autosomal dominant heredofamilial amyloidosis. After solubilization in guanidine HCl, a significant amount of the protein was contained in a homogeneous low molecular weight fraction. Molecular weight of approximately 14,000, amino acid analysis, double immunodiffusion analysis and immunoelectrophoresis all supported this material being a prealbumin-related protein. Automated sequence analysis gave a mixture of amino acids at each step, suggesting an heterogeneous NH2-terminus. After cleavage of the protein with cyanogen bromide, a homogeneous peptide was obtained with the sequence Val-Val-Val-Leu-Asp-Ala-Val-Arg-Gly-Thr-Pro- corresponding in 9 of the 11 positions analyzed with the known sequence of human prealbumin, starting with position 14. Antiserum raised to the amyloid protein reacted with normal human prealbumin. After absorption with normal human serum, this antiserum continued to detect a determinant in the amyloid patient's serum, suggesting an abnormal serum prealbumin, which may be the precursor of the fibril protein in this type of heredo-familial amyloidosis. Indirect immunohistochemical studies on kidney tissue from the patient with amyloidosis showed marked staining with anti-prealbumin and anti-heredofamilial amyloid protein, but not with anti-AA or anti-kappa antisera. No genetic association between this family and amyloidosis and Portuguese families with familial amyloid polyneuropathy is known.
Bmp Signaling Exerts Opposite Effects on Cardiac Differentiation
Authors: Emma de Pater, Metamia Ciampricotti, Florian Priller, Justus Veerkamp, Ina Strate, Kelly Smith, Anne Karine Lagendijk, Thomas F. Schilling, Wiebke Herzog, Salim Abdelilah-Seyfried, Matthias Hammerschmidt, Jeroen Bakkers
Journal: Circulation Research (2012)

Rationale: The importance for Bmp signaling during embryonic stem cell differentiation into myocardial cells has been recognized. The question when and where Bmp signaling in vivo regulates myocardial differentiation has remained largely unanswered. Objective: To identify when and where Bmp signaling regulates cardiogenic differentiation. Methods and Results: Here we have observed that in zebrafish embryos, Bmp signaling is active in cardiac progenitor cells prior to their differentiation into cardiomyocytes. Bmp signaling is continuously required during somitogenesis within the anterior lateral plate mesoderm to induce myocardial differentiation. Surprisingly, Bmp signaling is actively repressed in differentiating myocardial cells. We identified the inhibitory Smad6a, which is expressed in the cardiac tissue, to be required to inhibit Bmp signaling and thereby promote expansion of the ventricular myocardium. Conclusion: Bmp signaling exerts opposing effects on myocardial differentiation in the embryo by promoting as well as inhibiting cardiac growth.
S101 Pathogen associated molecular patterns in cystic fibrosis pathogens: Analysis of peptidoglycan structure
Authors: SC Carnell, J Biboy, G Cerardi, B Ville, C Deleuse, R Samain, D Vollmer, CMA Khan, J Gray, W Vollmer, A De Soyza
Journal: Thorax (2013)

<h3>Background</h3> Pathogen associated molecular patterns (PAMPS) are key virulence determinants in triggering immune mediated damage in cystic fibrosis. The lipopolysaccharide (LPS) in <i>Pseudomonas aeruginosa</i> strains isolated from CF-lungs has “CF specific” structural motifs not seen in other clinical isolates nor environmental strains. We have shown these motifs are also present in <i>Burkholderia</i> cepacia complex (BCC) species. We hypothesised that another key virulence determinant, peptidoglycan (PG), may show similar CF specific changes. PG is essential for bacterial cell wall stability and is the principle target for many antibiotics and for antimicrobial hydrolases of the innate immune system. Soluble PG fragments show biological activity interacting with NOD receptors. <h3>Methods</h3> <i>Burkholderia</i> cepacia complex strains of interest were selected from the BCC international reference panel (n = 8), <i>P. aeruginosa </i>from a novel international reference panel and local repository (n = 6) and <i>Achromobacter</i><i>xylosoxidans</i> from a local repository (n = 6). After growth in LB media and SDS extraction the PG was digested and the resulting muropeptides were analysed by HPLC and MS. The profiles were compared to the well characterised <i>E. coli</i> PG. <h3>Results</h3> <i>P. aeruginosa</i> PG was similar to the archetypical PG from <i>E. coli</i>. Strikingly, BCC spp. PG contained amidated muropeptides that have previously been described only in some Gram-positive bacteria. The extent of amidation varied between strains and did not map to either CF, other clinical or environmental origins. It was not linked to LPS chemotype nor BCC genomovars. <i>A. xylosoxidans </i>PG also contained novel muropeptide structures different to those seen in BCC. <h3>Conclusions</h3> We describe for the first time novel and unexpected modifications in the PG of BCC and <i>Achromobacter</i>, which were present in all strains tested so far. These modifications may offer either a biological advantage against PG hydrolases or may be linked with modulating the host immune responses. Immunostimulatory data are presently being collected to investigate this aspect.
A Perivascular Niche for Brain Tumor Stem Cells
Authors: Christopher Calabrese, Helen Poppleton, Mehmet Kocak, Twala L. Hogg, Christine Fuller, Blair Hamner, Eun Young Oh, M. Waleed Gaber, David Finklestein, Meredith Allen, Adrian Frank, Ildar T. Bayazitov, Stanislav S. Zakharenko, Amar Gajjar, Andrew Davidoff, Richard J. Gilbertson
Journal: Cancer Cell (2007)
Involvement of E-selectin in recruitment of endothelial progenitor cells and angiogenesis in ischemic muscle
Authors: Il-Young Oh, Chang-Hwan Yoon, Jin Hur, Ji-Hyun Kim, Tae-Youn Kim, Choon-Soo Lee, Kyung-Woo Park, In-Ho Chae, Byung-Hee Oh, Young-Bae Park, Hyo-Soo Kim
Journal: Blood (2007)
THE ANEMIA OF SCURVY
Authors: Stacy R. Mettier, William B. Chew
Journal: The Journal of Experimental Medicine (1932)

1. Weight loss, progressive anemia, and a moderate increase in reticulated red blood cells occurred in seventeen guinea pigs on a diet deficient in vitamin C. 2. The histological changes of the bone marrow removed from guinea pigs with scurvy showed large numbers of erythrogenic cells, but scant evidence of active maturation to the adult erythrocyte. 3. A reticulocyte response was induced in guinea pigs with scurvy when fed orange juice daily. 4. The histological changes of the bone marrow removed from guinea pigs during the reticulocyte response showed large numbers of mitotic figures and relatively more adult red blood cells than in the bone marrow from guinea pigs with scurvy that had not been treated with orange juice. 5. It is concluded from this study that the anemia of experimentally induced scurvy in the guinea pig is largely dependent upon vitamin C deficiency resulting in retarded maturation of the red blood cell.
Long term efficacy and safety of cyclosporin versus parenteral gold in early rheumatoid arthritis: a three year study of radiographic progression, renal function, and arterial hypertension
Authors: T K Kvien, H K Zeidler, P Hannonen, F A Wollheim, Ø Førre, I Hafström, J P Kaltwasser, M Leirisalo-Repo, B Manger, L Laasonen, H Prestele, P Kurki
Journal: Annals of the Rheumatic Diseases (2002)

Objective: To compare the three year safety and efficacy of cyclosporin and parenteral gold in the treatment of early, active, severe rheumatoid arthritis (RA), and to study the reversibility of cyclosporin associated renal dysfunction in patients who discontinued cyclosporin treatment. Methods: The patients continued to receive cyclosporin or parenteral gold in an 18 month open extension to an 18 month randomised, parallel group study. The main efficacy variable was blinded evaluation of radiographic progression of joint damage. Safety variables included serum creatinine, calculated creatinine clearance, and blood pressure. Results: Radiographic progression during follow up was similar in both groups. About 60% of the patients in the intention to treat groups (n=272) and about half of the patients in the completer groups (n=114) had definite radiographic progression in joint damage (increases &gt;6 in the Larsen-Dale score), and about one in three also had substantial progression (&gt;18 increase in Larsen-Dale score). Both systolic and diastolic blood pressure were significantly increased in the cyclosporin group compared with the gold group, and 12/139 (9%) versus 3/139 (2%) (p=0.03) had notably raised blood pressure. The mean serum creatinine increased by 28% at the treatment end point in the cyclosporin group as compared with 7% in the gold group. The mean calculated creatinine clearance was reduced by 16% and increased by 1% in the cyclosporin and gold groups, respectively, at the end of the study. At the final follow up visit after discontinuation of cyclosporin (at least three months after treatment was stopped) the mean serum creatinine was increased by 15% and creatinine clearance reduced by 16%. Sustained increases in serum creatinine at this post-treatment end point were mostly seen in patients with a raised serum creatinine during treatment of at least 50%. Conclusion: Three year changes in radiographic damage during cyclosporin and parenteral gold were similar in patients with early, active RA. Abnormal renal function and raised blood pressure were often seen in the cyclosporin treated patients.
Phage Display–Derived Peptides for Osteosarcoma Imaging
Authors: Xilin Sun, Gang Niu, Yongjun Yan, Min Yang, Kai Chen, Ying Ma, Nicholas Chan, Baozhong Shen, Xiaoyuan Chen
Journal: Clinical Cancer Research (2010)

Abstract Purpose: Osteosarcoma represents the most common malignant primary bone tumor in childhood; however, the survival rate has remained unchanged for the past 20 years. To improve existing diagnosis and treatment methods and broaden the spectrum of imaging agents that can be used for early detection and assessment of tumor response to therapy, we performed a phage display–based screening for peptide sequences that bind specifically to osteosarcoma cells. Experimental Design: From the Ph.D.-12 phage display peptide library composed of 2.7 × 109 different displayed peptides, one peptide was enriched after four rounds of in vitro selection in 143B osteosarcoma tumor cells with 293T human embryonic kidney cells as a control. Both the peptide and the phage clone displaying the peptide were conjugated with fluorescent dyes for in vitro cell and ex vivo tumor tissue stainings. The peptide was further labeled with 18F for positron emission tomography imaging studies. Cell uptake and efflux and ex vivo biodistribution were also done with 18F-labeled osteosarcoma specific peptide. Results: ASGALSPSRLDT was the dominant sequence isolated from biopanning and named as OSP-1. OSP-1 shares a significant homology with heparinase II/III family protein, which binds and reacts with heparan sulfate proteoglycans. The fluorescence staining showed that FITC-OSP-1-phage or Cy5.5-OSP-1 had high binding with a panel of osteosarcoma cell lines, much less binding with UM-SCC1 human head and neck squamous cell carcinoma cells, and almost no binding with 293T cells, whereas the scrambled peptide OSP-S had virtually no binding to all the cell lines. 18F-OSP-1 had significantly higher accumulation in 143B tumor cells both in vitro and in vivo than 18F-OSP-S. 18F-OSP-1 also had higher uptake in 143B tumors than in UM-SCC-1 tumors. Conclusions: Our data suggest that OSP-1 peptide is osteosarcoma specific, and the binding site of OSP-1 might be related to heparan sulfate proteoglycans. Appropriately labeled OSP-1 peptide has the potential to serve as a novel probe for osteosarcoma imaging. Clin Cancer Res; 16(16); 4268–77. ©2010 AACR.
Polyarthritis and pitting oedema
Authors: J. Dudler, J.-C. Gerster, A. So
Journal: Annals of the Rheumatic Diseases (1999)

### CASE 1

A 74 year old white man presented with an abrupt onset of metacarpophalangeal (MCP) and interphalangeal (IP) joint pains associated with swelling of both hands. He had two hours of morning stiffness but no other joint complaints or history of constitutional symptoms. Past medical history was unremarkable except for diabetes mellitus type 2 treated with oral antidiabetic drugs.#### Key points

Examination showed gross pitting oedema of the dorsum of both hands with swollen and tender MCPs, severe tenosynovitis of the flexor tendons, and swollen and limited wrist movements. Both knees had painless small effusions. Other joints showed no signs of inflammation and no nodules were palpated.

The erythrocyte sedimentation rate was increased at 55 mm in the first hour. Except for a mild inflammatory anaemia and hyperglycaemia between 8 to 10 mmol/l, the full blood count, renal, liver and thyroid function tests were within normal limits. Electrophoresis demonstrated an acute and subacute inflammatory pattern without monoclonal peak and rheumatoid factor and ANA were negative. Four millilitres of clear synovial fluid were aspirated from the left knee. Cell count was 198/mm3 with no crystals.

The patient was treated with prednisone with a rapid clinical response. Maximal dose was 20 mg per day, slowly tapered over four months to zero. No flare up was observed and after two years the patient was still …
Regulation of Tumor Angiogenesis by EZH2
Authors: Chunhua Lu, Hee Dong Han, Lingegowda S. Mangala, Rouba Ali-Fehmi, Christopher S. Newton, Laurent Ozbun, Guillermo N. Armaiz-Pena, Wei Hu, Rebecca L. Stone, Adnan Munkarah, Murali K. Ravoori, Mian M.K. Shahzad, Jeong-Won Lee, Edna Mora, Robert R. Langley, Amy R. Carroll, Koji Matsuo, Whitney A. Spannuth, Rosemarie Schmandt, Nicholas B. Jennings, Blake W. Goodman, Robert B. Jaffe, Alpa M. Nick, Hye Sun Kim, Eylem Ozturk Guven, Ya-Huey Chen, Long-Yuan Li, Ming-Chuan Hsu, Robert L. Coleman, George A. Calin, Emir B. Denkbas, Jae Yun Lim, Ju-Seog Lee, Vikas Kundra, Michael J. Birrer, Mien-Chie Hung, Gabriel Lopez-Berestein, Anil K. Sood
Journal: Cancer Cell (2010)