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  1. Article ; Online: SHRiMP2: sensitive yet practical SHort Read Mapping.

    David, Matei / Dzamba, Misko / Lister, Dan / Ilie, Lucian / Brudno, Michael

    Bioinformatics (Oxford, England)

    2011  Volume 27, Issue 7, Page(s) 1011–1012

    Abstract: Unlabelled: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space ... ...

    Abstract Unlabelled: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures.
    Availability: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.
    MeSH term(s) Algorithms ; Chromosome Mapping ; Genomics/methods ; Polymorphism, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Software
    Language English
    Publishing date 2011-04-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btr046
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Surgical and endoscopic management options for patients with GERD based on proton pump inhibitor symptom response: recommendations from an expert U.S. panel.

    Gawron, Andrew J / Bell, Reginald / Abu Dayyeh, Barham K / Buckley, F P / Chang, Kenneth / Dunst, Christy M / Edmundowicz, Steven A / Jobe, Blair / Lipham, John C / Lister, Dan / Canto, Marcia Irene / Smith, Michael S / Starpoli, Anthony A / Triadafilopoulos, George / Watson, Thomas J / Wilson, Erik / Pandolfino, John E / Kaizer, Alexander / Van De Voorde, Zoe /
    Yadlapati, Rena

    Gastrointestinal endoscopy

    2020  Volume 92, Issue 1, Page(s) 78–87.e2

    Abstract: Background and aims: The objective of this study was to examine expert opinion and agreement on the treatment of distinct GERD profiles from surgical and therapeutic endoscopy perspectives.: Methods: We used the RAND/University of California, Los ... ...

    Abstract Background and aims: The objective of this study was to examine expert opinion and agreement on the treatment of distinct GERD profiles from surgical and therapeutic endoscopy perspectives.
    Methods: We used the RAND/University of California, Los Angeles Appropriateness Method over 6 months (July 2018 to January 2019) to assess the appropriateness of antireflux interventions among foregut surgeons and therapeutic gastroenterologists. Patients with primary atypical or extraesophageal symptoms were not considered. Patient scenarios were grouped according to their symptom response to proton pump inhibitor (PPI) therapy. The primary outcome was appropriateness of an intervention.
    Results: Antireflux surgery with laparoscopic fundoplication (LF) and magnetic sphincter augmentation (MSA) were ranked as appropriate for all complete and partial PPI responder scenarios. Transoral incisionless fundoplication was ranked as appropriate in complete and partial PPI responders without a hiatal hernia. Radiofrequency energy was not ranked as appropriate for complete or partial responders. There was lack of agreement between surgery and interventional gastroenterology groups on the appropriateness of LF and MSA for PPI nonresponders. Rankings for PPI nonresponders were similar when results from impedance-pH testing on PPI therapy were available, except that LF and MSA were not ranked as appropriate for PPI nonresponders if the impedance-pH study was negative.
    Conclusions: This work highlights areas of agreement for invasive therapeutic approaches for GERD and provides impetus for further interdisciplinary collaboration and trials to compare and generate novel and effective treatment approaches and care pathways, including the role of impedance-pH testing in PPI nonresponders.
    MeSH term(s) Adult ; Aged ; Endoscopy ; Endoscopy, Gastrointestinal ; Female ; Fundoplication ; Gastroesophageal Reflux/drug therapy ; Gastroesophageal Reflux/surgery ; Humans ; Laparoscopy ; Los Angeles ; Male ; Middle Aged ; Proton Pump Inhibitors/therapeutic use ; Treatment Outcome
    Chemical Substances Proton Pump Inhibitors
    Language English
    Publishing date 2020-01-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 391583-9
    ISSN 1097-6779 ; 0016-5107
    ISSN (online) 1097-6779
    ISSN 0016-5107
    DOI 10.1016/j.gie.2020.01.037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Magnetic Sphincter Augmentation Superior to Proton Pump Inhibitors for Regurgitation in a 1-Year Randomized Trial.

    Bell, Reginald / Lipham, John / Louie, Brian E / Williams, Valerie / Luketich, James / Hill, Michael / Richards, William / Dunst, Christy / Lister, Dan / McDowell-Jacobs, Lauren / Reardon, Patrick / Woods, Karen / Gould, Jon / Buckley, F Paul / Kothari, Shanu / Khaitan, Leena / Smith, C Daniel / Park, Adrian / Smith, Christopher /
    Jacobsen, Garth / Abbas, Ghulam / Katz, Philip

    Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association

    2019  Volume 18, Issue 8, Page(s) 1736–1743.e2

    Abstract: Background & aims: Regurgitative gastroesophageal reflux disease (GERD) refractive to medical treatment is common and caused by mechanical failure of the anti-reflux barrier. We compared the effects of magnetic sphincter augmentation (MSA) with those of ...

    Abstract Background & aims: Regurgitative gastroesophageal reflux disease (GERD) refractive to medical treatment is common and caused by mechanical failure of the anti-reflux barrier. We compared the effects of magnetic sphincter augmentation (MSA) with those of proton-pump inhibitors (PPIs) in a randomized trial.
    Methods: Patients with moderate to severe regurgitation (assessed by the foregut symptom questionnaire) despite once-daily PPI therapy (n = 152) were randomly assigned to groups given twice-daily PPIs (n = 102) or laparoscopic MSA (n = 50) at 20 sites, from July 2015 through February 2017. Patients answered questions from the foregut-specific reflux disease questionnaire and GERD health-related quality of life survey about regurgitation, heartburn, dysphagia, bloating, diarrhea, flatulence, and medication use, at baseline and 6 and 12 months after treatment. Six months after PPI therapy, MSA was offered to patients with persistent moderate to severe regurgitation and excess reflux episodes during impedance or pH testing on medication. Regurgitation, foregut scores, esophageal acid exposure, and adverse events were evaluated at 1 year.
    Results: Patients in the MSA group and those who crossed over to the MSA group after PPI therapy (n = 75) had similar outcomes. MSA resulted in control of regurgitation in 72/75 patients (96%); regurgitation control was independent of preoperative response to PPIs. Only 8/43 patients receiving PPIs (19%) reported control of regurgitation. Among the 75 patients who received MSA, 61 (81%) had improvements in GERD health-related quality of life improvement scores (greater than 50%) and 68 patients (91%) discontinued daily PPI use. Proportions of patients with dysphagia decreased from 15% to 7% (P < .005), bloating decreased from 55% to 25%, and esophageal acid exposure time decreased from 10.7% to 1.3% (P < .001) from study entry to 1-year after MSA (Combined P < .001). Seventy percent (48/69) of patients had pH normalization at study completion. MSA was not associated with any peri-operative events, device explants, erosions, or migrations.
    Conclusions: In a prospective study, we found MSA to reduce regurgitation in 95% of patients with moderate to severe regurgitation despite once-daily PPI therapy. MSA is superior to twice-daily PPIs therapy in reducing regurgitation. Relief of regurgitation is sustained over 12 months. ClinicalTrials.gov no: NCT02505945.
    MeSH term(s) Electric Impedance ; Esophageal Sphincter, Lower/surgery ; Humans ; Prospective Studies ; Proton Pump Inhibitors ; Quality of Life ; Treatment Outcome
    Chemical Substances Proton Pump Inhibitors
    Language English
    Publishing date 2019-09-10
    Publishing country United States
    Document type Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2119789-1
    ISSN 1542-7714 ; 1542-3565
    ISSN (online) 1542-7714
    ISSN 1542-3565
    DOI 10.1016/j.cgh.2019.08.056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Laparoscopic magnetic sphincter augmentation versus double-dose proton pump inhibitors for management of moderate-to-severe regurgitation in GERD: a randomized controlled trial.

    Bell, Reginald / Lipham, John / Louie, Brian / Williams, Valerie / Luketich, James / Hill, Michael / Richards, William / Dunst, Christy / Lister, Dan / McDowell-Jacobs, Lauren / Reardon, Patrick / Woods, Karen / Gould, Jon / Buckley, F Paul / Kothari, Shanu / Khaitan, Leena / Smith, C Daniel / Park, Adrian / Smith, Christopher /
    Jacobsen, Garth / Abbas, Ghulam / Katz, Philip

    Gastrointestinal endoscopy

    2018  Volume 89, Issue 1, Page(s) 14–22.e1

    Abstract: Background and aims: GERD patients frequently complain of regurgitation of gastric contents. Medical therapy with proton-pump inhibitors (PPIs) is frequently ineffective in alleviating regurgitation symptoms, because PPIs do nothing to restore a weak ... ...

    Abstract Background and aims: GERD patients frequently complain of regurgitation of gastric contents. Medical therapy with proton-pump inhibitors (PPIs) is frequently ineffective in alleviating regurgitation symptoms, because PPIs do nothing to restore a weak lower esophageal sphincter. Our aim was to compare effectiveness of increased PPI dosing with laparoscopic magnetic sphincter augmentation (MSA) in patients with moderate-to-severe regurgitation despite once-daily PPI therapy.
    Methods: One hundred fifty-two patients with GERD, aged ≥21 years with moderate-to-severe regurgitation despite 8 weeks of once-daily PPI therapy, were prospectively enrolled at 21 U.S. sites. Participants were randomized 2:1 to treatment with twice-daily (BID) PPIs (N = 102) or to laparoscopic MSA (N = 50). Standardized foregut symptom questionnaires and ambulatory esophageal reflux monitoring were performed at baseline and at 6 months. Relief of regurgitation, improvement in foregut questionnaire scores, decrease in esophageal acid exposure and reflux events, discontinuation of PPIs, and adverse events were the measures of efficacy.
    Results: Per protocol, 89% (42/47) of treated patients with MSA reported relief of regurgitation compared with 10% (10/101) of the BID PPI group (P < .001) at the 6-month primary endpoint. By intention-to-treat analysis, 84% (42/50) of patients in the MSA group and 10% (10/102) in the BID PPI group met this primary endpoint (P < .001). Eighty-one percent (38/47) of patients with MSA versus 8% (7/87) of patients with BID PPI had ≥50% improvement in GERD-health-related quality of life scores (P < .001), and 91% (43/47) remained off of PPI therapy. A normal number of reflux episodes and acid exposures was observed in 91% (40/44) and 89% (39/44) of MSA patients, respectively, compared with 58% (46/79) (P < .001) and 75% (59/79) (P = .065) of BID PPI patients at 6 months. No significant safety issues were observed. In MSA patients, 28% reported transient dysphagia; 4% reported ongoing dysphagia.
    Conclusion: Patients with GERD with moderate-to-severe regurgitation, especially despite once-daily PPI treatment, should be considered for minimally invasive treatment with MSA rather than increased PPI therapy. (Clinical trial registration number: NCT02505945.).
    MeSH term(s) Adult ; Aged ; Cross-Over Studies ; Esophageal Sphincter, Lower/surgery ; Esophageal pH Monitoring ; Female ; Gastroesophageal Reflux/therapy ; Humans ; Laparoscopy ; Laryngopharyngeal Reflux/therapy ; Magnets ; Male ; Middle Aged ; Omeprazole/administration & dosage ; Proton Pump Inhibitors/administration & dosage ; Quality of Life ; Treatment Outcome ; Young Adult
    Chemical Substances Proton Pump Inhibitors ; Omeprazole (KG60484QX9)
    Language English
    Publishing date 2018-07-18
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Randomized Controlled Trial
    ZDB-ID 391583-9
    ISSN 1097-6779 ; 0016-5107
    ISSN (online) 1097-6779
    ISSN 0016-5107
    DOI 10.1016/j.gie.2018.07.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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