tbuckley/cabot-search huggingface dataset:
Untangling and segmenting the small intestine in 3D cine-MRI using deep learning
Authors: Louis D. van Harten, Catharina S. de Jonge, Kim J. Beek, Jaap Stoker, Ivana Išgum
Journal: Medical Image Analysis (2022)

Cine-MRI of the abdomen is a non-invasive imaging technique allowing assessment of small intestinal motility. This is valuable for the evaluation of gastrointestinal disorders. While 2D cine-MRI is increasingly used for this purpose in both clinical practice and in research settings, the potential of 3D cine-MRI has been largely underexplored. In the absence of image analysis tools enabling investigation of the intestines as 3D structures, the assessment of motility in 3D cine-images is generally limited to the evaluation of movement in separate 2D slices. Furthermore, while a segmentation map of the small intestine would be required for a number of automatic analysis tasks, deep learning based segmentation of the small intestine generally performs poorly due to the large variety in shapes, sizes and locations in the abdomen among different patients. Using a data set of 3D cine-MRI scans from 14 healthy volunteers, we developed a multi-task method that automatically tracks individual segments of the small intestine in a time-point from 3D cine-MRI scans, using a stochastic tracker built on top of a CNN-based orientation classifier. The method additionally performs segmentation, conditioned on the locations of intestinal centerlines. We demonstrate the benefit of our stochastic tracking strategy and we show that our proposed segmentation method performs significantly better than an identical network without centerline conditioning. Furthermore, we assess the robustness of the method through evaluation on a set of patients with severe bowel disease. In terms of centerline tracking, our method achieves a recall of 0.74±0.07, a precision of 0.80±0.06 and an F1 score of 0.77±0.05 in the set of healthy volunteers. In the set of patients, it achieves a recall of 0.76±0.12, a precision of 0.86±0.11 and an F1 score of 0.80±0.08. Segmentation achieves a Dice coefficient of 0.88±0.03 in the set of healthy volunteers and 0.79±0.09 in the set of patients. By extracting a structural representation of the small intestine, the presented method provides a major first step towards automatic detailed quantitative assessment of small intestinal motility in abdominal 3D cine-MRI.
Impact of surgical versus endoscopic management of complex nonmalignant polyps in a colorectal cancer screening program
Authors: Maaike Buskermolen, Steffie K. Naber, Esther Toes-Zoutendijk, Miriam P. van der Meulen, Wilhelmina M. U. van Grevenstein, Monique E. van Leerdam, Manon C. W. Spaander, Iris Lansdorp-Vogelaar
Journal: Endoscopy (2022)

When complex nonmalignant polyps are detected in colorectal cancer (CRC) screening programs, patients may be referred directly to surgery or may first undergo additional endoscopy for attempted endoscopic removal by an expert. We compared the impact of both strategies on screening effectiveness and costs.We used MISCAN-Colon to simulate the Dutch screening program, and projected CRC deaths prevented, quality-adjusted life-years (QALYs) gained, and costs for two scenarios: 1) surgery for all complex nonmalignant polyps; 2) attempted removal by an expert endoscopist first. We made the following assumptions: 3.9 % of screen-detected large nonmalignant polyps were complex; associated surgery mortality was 0.7 %; the rate of successful removal by an expert was 87 %, with 0.11 % mortality.The screening program was estimated to prevent 11.2 CRC cases (-16.7 %) and 10.1 CRC deaths (-27.1 %), resulting in 32.9 QALYs gained (+ 17.2 %) per 1000 simulated individuals over their lifetimes compared with no screening. The program would also result in 2.1 surgeries for complex nonmalignant polyps with 0.015 associated deaths per 1000 individuals. If, instead, these patients were referred to an expert endoscopist first, only 0.2 patients required surgery, reducing associated deaths by 0.013 at the expense of 0.003 extra colonoscopy deaths. Compared with direct referral to surgery, referral to an expert endoscopist gained 0.2 QALYs and saved €12 500 per 1000 individuals in the target population.Referring patients with complex polyps to an expert endoscopist first reduced some surgery-related deaths while substantially improving cost-effectiveness of the screening program.
THE FOOD CHAIN AND THE MONARCH BUTTERFLY
Journal: JAMA (1967)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Single-cell isoform analysis in human immune cells
Authors: Roger Volden, Christopher Vollmers
Journal: Genome biology (2022)

High-throughput single-cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a transcript is encoded at its 5' or 3' end. Here, we used R2C2 to sequence and demultiplex 12 million full-length cDNA molecules generated by the 10X Genomics platform from ~3000 peripheral blood mononuclear cells. We use these reads, independent from Illumina data, to identify B cell, T cell, and monocyte clusters and generate isoform-level transcriptomes for cells and cell types. Finally, we extract paired adaptive immune receptor sequences unique to each T and B cell.
Therapeutics
Journal: JAMA (1910)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Disentangling Workflow Paradigms and Treatment Decision-Making in Acute Ischemic Stroke—Reply
Authors: Marc Ribo, Manuel Requena
Journal: JAMA Neurology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Neurology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Neurology journal
Homosexuality
Authors: Samuel Friedman
Journal: JAMA (1968)

In the interesting chapter on legal problems, the reader notes that, in England, "indecent assault" may bring a maximum penalty of two years if the victim is a girl, but ten years if a boy. Sexual intercourse with a girl under 12 may incur a penalty of life imprisonment; with a female under 16, two years. However, buggery with boys, regardless of age or the degree of their consent, may bring a life sentence. In this area, then, the male is "deadlier" than the female. West realistically upholds the increasingly accepted concept that intercourse between two consenting adult males, in privacy, should not constitute a matter for criminal law. He emphasizes also the thought that imprisonment of homosexual offenders merely increases their stresses and temptations. We learn, too, that there is more homosexuality in women's prisons than in men's. With respect to etiology, Dr. West appears to discount constitutional factors.
DERMOID CYSTS OR EMBRYOMAS OF THE OVARY.
Journal: JAMA (1901)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
State Boards of Registration.
Journal: JAMA (1904)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
British Surgical Practice
Journal: JAMA (1949)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Sic Transit...
Authors: Faye C. Lewis
Journal: JAMA (1974)

SOME scruffy new growth at the base of a lilac bush hides the numerals on Old Bailey's tombstone, which tell when he was born and when he died, and the lilac bush itself has cut off the front part of his first name. It ends in "ed," so it may very well have been Fred. A man called Fred in our town need not have been christened Frederick. We are a straight-laced community, comparatively speaking. There is less bastardy in our lives than in our names. Many of our Doloreses, for example, were born—or christened, I should say—without the aegis of the parental dolor, and have turned out to be Deloris or Delores. We have as many Debras as Deborahs, and we have Cathies and Kathies who were never Catherine or Katherine, or even Kathryn. In taking a medical history and striving for accuracy of record, we may ask a
Leads from the MMWR. Perspectives in disease prevention and health promotion: Report of the Secretary's Task Force on Black and Minority Health
Journal: JAMA (1986)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Opportunities for milk and milk-related systems as ‘new’ low-cost excipient drug delivery materials
Authors: Malinda Salim, Thomas Eason, Ben J. Boyd
Journal: Advanced Drug Delivery Reviews (2022)

Milk is well recognised as an amazing delivery system for essential lipids, poorly soluble nutrients, sugars, amino acids and delivery of critical biological molecules to sustain the infant and adult alike. It is also a safe and abundant resource with potential to act as a low-cost material for formulation of medicines, especially for paediatric patients and those in low economy settings. However, its use in low cost formulations has never developed beyond preclinical evaluation. Reasons for this are several-fold including variable composition and therefore regulatory challenges, as well as a lack of clear understanding around when milk or milk-related materials like infant formula could best be deployed by linking drug properties with excipient composition attributes, especially when taking digestion into account. This review collects the current understanding around these issues. It is apparent from the evolving understanding that while milk may be a bridge too far for translation as an excipient, infant formula is positioned to play a key role in the future because, as a powder-based excipient, it has the performance benefits of milk powder together with the controlled specifications during manufacture and versatility of application to function as a low cost lipid excipient to enable potential translation for the oral delivery of poorly water soluble drugs for key populations including paediatrics and low economy medicines.
Troubled waters
Authors: M. T. Southgate
Journal: JAMA (1970)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
CD8<sup>+</sup>PD-1<sup>+</sup> to CD4<sup>+</sup>PD-1<sup>+</sup> ratio (PERLS) is associated with prognosis of patients with advanced NSCLC treated with PD-(L)1 blockers
Authors: Boris Duchemann, Marie Naigeon, Edouard Auclin, Roberto Ferrara, Lydie Cassard, Jean-Mehdi Jouniaux, Lisa Boselli, Jonathan Grivel, Aude Desnoyer, François-Xavier Danlos, Laura Mezquita, Caroline Caramella, Aurelien Marabelle, Benjamin Besse, Nathalie Chaput
Journal: Journal for ImmunoTherapy of Cancer (2022)

Programmed cell death protein-1 (PD-1) expression has been associated with activation and exhaustion of both the CD4 and CD8 populations in advanced non-small cell lung cancer (aNSCLC). Nevertheless, the impact of the balance between circulating CD8+PD-1+ and CD4+PD-1+ in patients treated with immune checkpoint blockers (ICB) is unknown. The CD8+PD-1+ to CD4+PD-1+ ratio (PD-1-Expressing Ratio on Lymphocytes in a Systemic blood sample, or 'PERLS') was determined by cytometry in fresh whole blood from patients with aNSCLC before treatment with single-agent ICB targeting PD-1 or programmed cell death-ligand 1 (PD-L1 (discovery cohort). A PERLS cut-off was identified by log-rank maximization. Patients treated with ICB (validation cohort) or polychemotherapy (control cohort) were classified as PERLS+/- (above/below cut-off). Circulating immune cell phenotype and function were correlated with PERLS. A composite score (good, intermediate and poor) was determined using the combination of PERLS and senescent immune phenotype as previously described in aNSCLC. In the discovery cohort (N=75), the PERLS cut-off was 1.91, and 11% of patients were PERLS+. PERLS + correlated significantly with median progression-free survival (PFS) of 9.63 months (95% CI 7.82 to not reached (NR)) versus 2.69 months (95% CI 1.81 to 5.52; p=0.03). In an independent validation cohort (N=36), median PFS was NR (95% CI 7.9 to NR) versus 2.00 months (95% CI 1.3 to 4.5; p=0.04) for PERLS + and PERLS-, respectively; overall survival (OS) followed a similar but non-significant trend. In the pooled cohort (N=111), PERLS + correlated significantly with PFS and OS. PERLS did not correlate with outcome in the polychemotherapy cohort. PERLS did not correlate with clinical characteristics but was significantly associated with baseline circulating naïve CD4+ T cells and the increase of memory T cells post-ICB treatment. Accumulation of memory T cells during treatment was linked to CD4+ T cell polyfunctionality. The composite score was evaluated in the pooled cohort (N=68). The median OS for good, intermediate and poor composite scores was NR (95% CI NR to NR), 8.54 months (95% CI 4.96 to NR) and 2.42 months (95% CI 1.97 to 15.5; p=0.001), respectively. The median PFS was 12.60 months (95% CI 9.63 to NR), 2.58 months (95% CI 1.74 to 7.29) and 1.76 months (95% CI 1.31 to 4.57; p<0.0001), respectively. Elevated PERLS, determined from a blood sample before immunotherapy, was correlated with benefit from PD-(L)1 blockers in aNSCLC.
Determinants of isolated systolic hypertension
Authors: S. V. Wilking
Journal: JAMA (1988)

<i>Isolated systolic hypertension</i>(ISH), defined as systolic blood pressure of 160 mm Hg or greater when the diastolic pressure is less than 95 mm Hg, is a common form of hypertension among the elderly. We collected incidence and prevalence data on ISH and evaluated several potential factors for its occurrence in the Framingham Heart Study during 16 biennial examinations. The factors evaluated were age, sex, all components of the blood pressure (systolic and diastolic blood pressure, pulse pressure, and mean arterial pressure), Metropolitan relative weight, serum cholesterol level, serum uric acid level, cigarette smoking, ventricular heart rate, glucose intolerance, and hematocrit. The population at risk (1687 men and 1992 women) were those members of the Framingham cohort with a systolic blood pressure less than 160 mm Hg in the first four biennial examinations. Results showed ISH in 14.4% of the men and 22.8% of the women. Cumulative incidence rates were 418 per 1000 in men and 533 per 1000 in women. Significant risk factors for ISH were age, sex, all components of the blood pressure, and increased relative weight in women. We conclude that ISH is a highly prevalent disorder. Its major determinants are age, sex, increasing levels of blood pressure, and obesity in women. (<i>JAMA</i>1988;260:3451-3455)