tbuckley/cabot-search huggingface dataset:
Classification of <i>Parabacteroides distasonis</i> and other <i>Bacteroidetes</i> using O- antigen virulence gene: <i>RfbA</i> -Typing and hypothesis for pathogenic vs. probiotic strain differentiation
Authors: Nicholas C. Bank, Vaidhvi Singh, Alex Rodriguez-Palacios
Journal: Gut Microbes (2022)

Parabacteroides distasonis (Pdis) is the type species for the new Parabacteroides genus, and a gut commensal of the Bacteroidetes phylum. Emerging reports (primarily based on reference strain/ATCC-8503) concerningly propose that long-known opportunistic pathogen Pdis is a probiotic. We posit there is an urgent need to characterize the pathogenicity of Pdis strain-strain variability. Unfortunately, no methods/insights exist to classify Bacteroidetes for this purpose. Herein, we developed a virulence gene-based classification system for Pdis and Bacteroidetes to facilitate pathogenic-vs-probiotic characterization. We used DNA in silico methods to develop a system based on the virulence (lipopolysaccharide/bacterial wall) 'rfbA O-antigen-synthesis gene'. We then performed phylogenetic analysis of rfbA from fourteen Pdis complete genomes (21 genes), other Parabacteroides, Bacteroidetes, and Enterobacteriaceae; and proposed a PCR-based Restriction-Fragment Length Polymorphism method. Cluster analysis revealed that Pdis can be classified into four lineages (based on gene gaps/insertions) which we designated rfbA-Types I, II, III, and IV. In context, we found 14 additional rfbA-types (I–XVIII) interspersed with numerous Bacteroidetes and pathogenic Enterobacteriaceae forming three major "rfbA-superclusters." For laboratory rfbA-Typing implementation, we developed a PCR-primer strategy to amplify Pdis rfbA genes (100%-specificity) to conduct MboII-RFLP and sub-classify Pdis. In-silico primers for other Bacteroidetes are proposed/discussed. Comparative analysis of lipopolysaccharide/lipid-A gene lpxK confirmed rfbA as highly discriminant. In conclusion, rfbA-Typing classifies Bacteroidetes/Pdis into unique clusters/superclusters given rfbA copy/sequence variability. Analysis revealed that most pathogenic Pdis strains are single-copy rfbA-Type I . The relevance of the rfbA strain variability in disease might depend on their hypothetical modulatory interactions with other O-antigens/lipopolysaccharides and TLR4 lipopolysaccharide-receptors in human/animal cells.
Why doctors have a moral imperative to prescribe and support medical cannabis—an essay by David Nutt
Authors: David Nutt
Journal: BMJ (2022)

Medical cannabis has been legal to prescribe since 2018—yet just a handful of prescriptions have been made in three years. The reasons: stigma, fear, and an entrenched resistance in the medical profession that is harming patients, writes <b>David Nutt</b>
Association of Tramadol vs Codeine Prescription Dispensation With Mortality and Other Adverse Outcomes
Authors: Hsin-Yi Shu, Yung-Heng Lee, James Wei
Journal: JAMA (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 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
Brain Structural Changes During Juvenile Fibromyalgia: Relationships With Pain, Fatigue, and Functional Disability
Authors: Maria Suñol, Michael F. Payne, Han Tong, Thomas C. Maloney, Tracy V. Ting, Susmita Kashikar‐Zuck, Robert C. Coghill, Marina López‐Solà
Journal: Arthritis & Rheumatology (2022)

Juvenile fibromyalgia (FM) is a prevalent chronic pain condition affecting children and adolescents worldwide during a critical period of brain development. To date, no published studies have addressed the pathophysiology of juvenile FM. This study was undertaken to characterize gray matter volume (GMV) alterations in juvenile FM patients for the first time, and to investigate their functional and clinical relevance.Thirty-four female adolescents with juvenile FM and 38 healthy adolescents underwent a structural magnetic resonance imaging examination and completed questionnaires assessing core juvenile FM symptoms. Using voxel-based morphometry, we assessed between-group GMV differences and associations between GMV and functional disability, fatigue, and pain interference in juvenile FM. We also studied whether validated brain patterns predicting pain, cognitive control, or negative emotion were amplified/attenuated in juvenile FM patients and whether structural alterations reported in adult FM were replicated in adolescents with juvenile FM.Compared to controls, juvenile FM patients showed GMV reductions in the anterior midcingulate cortex (aMCC) region (family-wise error corrected P [PFWE-corr ] = 0.04; estimated with threshold-free cluster enhancement [TFCE]; n = 72) associated with pain. Within the juvenile FM group, patients reporting higher functional disability had larger GMV in inferior frontal regions (PFWE-corr = 0.006; TFCE estimated; n = 34) linked to affective, self-referential, and language-related processes. Last, GMV reductions in juvenile FM showed partial overlap with findings in adult FM, specifically for the anterior/posterior cingulate cortices (P = 0.02 and P = 0.03, respectively; n = 72).Pain-related aMCC reductions may be a structural hallmark of juvenile FM, whereas alterations in regions involved in emotional, self-referential, and language-related processes may predict disease impact on patients' well-being. The partial overlap between juvenile and adult FM findings strengthens the importance of early symptom identification and intervention to prevent the transition to adult forms of the disease.
Manuscripts Approved for JNCI, August 15 to September 15, 1960
Journal: JNCI Journal of the National Cancer Institute (1960)

Manuscripts Approved for JNCI, August 15 to September 15, 1960 Get access JNCI: Journal of the National Cancer Institute, Volume 25, Issue 4, October 1960, Pages 890–891, https://doi.org/10.1093/jnci/25.4.890 Published: 01 October 1960
Nicholas Matthew Wharton
Authors: Lucy Bushby, Malcolm Wharton
Journal: BMJ (2022)

As a student at St Andrews, he was president of the Bute (Medical Students') Society and later safety officer of the scuba diving club.He stayed for a fourth year BSc course.He was a keen fell walker and had respectable times in two Karrimor marathons.At the end of each year at St. Andrews he went with family members for a week scrambling in the Cuillin hills on Skye.While still a student he undertook two treks to the Karakorum Mountains in Pakistan; firstly to the K2 base camp at 16 400 ft and secondly, trekking over the Baltoro/Hisper glacier, reaching 17 000 ft.His anaesthetic training was mainly in the South West with a specialist year in New Zealand.As a consultant in Bristol, he undertook upper airway surgery, thoracic anaesthesia, and obstetric anaesthesia.He was a supervisor and college tutor for trainees.His main achievement
Molecular Evolution across Mouse Spermatogenesis
Authors: Emily E K Kopania, Erica L Larson, Colin Callahan, Sara Keeble, Jeffrey M Good
Journal: Molecular Biology and Evolution (2022)

Genes involved in spermatogenesis tend to evolve rapidly, but we lack a clear understanding of how protein sequences and patterns of gene expression evolve across this complex developmental process. We used fluorescence-activated cell sorting (FACS) to generate expression data for early (meiotic) and late (postmeiotic) cell types across 13 inbred strains of mice (Mus) spanning ∼7 My of evolution. We used these comparative developmental data to investigate the evolution of lineage-specific expression, protein-coding sequences, and expression levels. We found increased lineage specificity and more rapid protein-coding and expression divergence during late spermatogenesis, suggesting that signatures of rapid testis molecular evolution are punctuated across sperm development. Despite strong overall developmental parallels in these components of molecular evolution, protein and expression divergences were only weakly correlated across genes. We detected more rapid protein evolution on the X chromosome relative to the autosomes, whereas X-linked gene expression tended to be relatively more conserved likely reflecting chromosome-specific regulatory constraints. Using allele-specific FACS expression data from crosses between four strains, we found that the relative contributions of different regulatory mechanisms also differed between cell types. Genes showing cis-regulatory changes were more common late in spermatogenesis, and tended to be associated with larger differences in expression levels and greater expression divergence between species. In contrast, genes with trans-acting changes were more common early and tended to be more conserved across species. Our findings advance understanding of gene evolution across spermatogenesis and underscore the fundamental importance of developmental context in molecular evolutionary studies.
Nuclear Medicine
Authors: Henry N. Wagner
Journal: JAMA (1989)

In vivo chemistry has become a major focus of nuclear medicine. By means of positron- and γ-emittingradioactive tracers, the regional chemistry of body organs can now be measured with the same sensitivity as hormones in body fluids by radioimmunoassay. Nuclear medicine focuses on molecules, as well as cells, as a basic unit of study. Many new nuclear medicine procedures are still at the interface between research and clinical practice, but it is becoming increasingly clear that positron emission tomography (PET) examinations can help care for patients with epilepsy, cancer, dementia, and heart disease. It is somewhat unfortunate that technological advances such as PET and single photon emission computed tomography (SPECT), have occurred when cost containment is a major focus of medical practice. However, knowledge about a patient can help decrease the overall cost of medical care. For example, detection of occult coronary heart disease in a patient being considered for
An Open-label Trial With Plasma Prekallikrein Oligonucleotide Antisense Therapy To Control Angioedema Attacks In Hereditary Angioedema Patients With Normal C1-inhibitor
Authors: Danny Cohn, Laura Bordone, Lauré Fijen, Veronica Alexander, Kenneth Newman, Eugene Schneider, Marc Riedl, Jason Raasch, Michael Manning
Journal: Journal of Allergy and Clinical Immunology (2022)
Potential of BAFF in Nasal Secretions as a Marker of Allergic Rhinitis Severity in Children
Authors: Toshiko Itazawa, Yutaka Ueda, Takeshi Koga, Keisuke Okada, Takahiro Shimizu, Eiji Morita, Kenichi Tokuyama
Journal: Journal of Allergy and Clinical Immunology (2022)
Intrauterine contraceptive device and ovarian thecoma
Authors: M. S. Piver
Journal: JAMA (1966)

DESPITE the widespread universal use of intrauterine contraceptive devices, serious complications are infrequent. This report is of a patient whose pelvic pain and excessive uterine bleeding, thought to be due to an intrauterine device, were caused by a functioning thecoma that became evident after the device had been in use for more than a year. Furthermore, from the findings at operation, the device (a Birnberg bow) lay outside the uterus. <h3>Report of a Case</h3> A 26-year-old Negro woman was seen in the Family Planning Clinic of the Pennsylvania Hospital in November 1964, six weeks after the delivery of her fourth child. The past history was notable only for nephrectomy at age 11 for renal cell carcinoma. The findings of both general, physical, and pelvic examinations were normal; a No. 5 Birnberg bow was inserted without difficulty on the third day of the menstrual period. A stained cervical smear (Papanicolaou class
Editorial: Sir Rickard Christophers.
Journal: BMJ (1973)

or four times a week.But, in addition to the problems that a transplant operation presents to any patient, children are liable to suffer serious impairment of growth.They often remain short.1 2 A usefil report has been published recently from Los Angeles on this problem.C. M. Grushkin and R. N. Fine3 report on the growth of 26 children who have survived at least one to four years after a kidney transplant.The patients were aged 1-to 17, and most of them had cadaver grafts.Only six of the 26 achieved a normal linear growth rate, and a further five had some useful growth at about half the normal rate.These figures sound more depressing than they really are because many of the children were rather old at the time of the transplant.In those who had a bone age of under 12 years and whose distal femoral and proximal tibial epiphyses had not fuEed by the time of transplant 40% achieved normal growth and 30% useful growth subsequently.The Los Angeles workers concluded that the most critical factor in predicting whether or not growth would occur after trans-
Receptor tyrosine kinase co-amplification and benefit from HER2 inhibitors in biliary tract cancers
Authors: Raffaella Casolino, Francesco Amato, Colin Rae, Srikanth Puttagunta, Chiara Braconi, Tamsin Nash, Martin MacLeod, Paula Sanchon-Sanchez, Patricia Roxburgh, Jeff Evans, Janet Graham, Fraser Duthie, Nicola Valeri, Pawel Herzyk, Julie Galbraith
Journal: Journal of Hepatology (2022)
LONG TERM EFFECT OF BOSENTAN THERAPY ON CARDIAC FUNCTION AND SYMPTOMATIC BENEFITS IN PATIENTS WITH EISENMENGER SYNDROME
Authors: Mehmet Kaya, Yat Yin Lam, Betul Erer, Selim Ayhan, Mehmet A. Vatankulu, Zekeriya Nurkalem, Mehmet Eren, Namik K. Eryol
Journal: Journal of the American College of Cardiology (2010)
Diagnosis and Management of Multiple Myeloma
Authors: Andrew J. Cowan, Damian J. Green, Mary Kwok, Sarah Lee, David G. Coffey, Leona A. Holmberg, Sherilyn Tuazon, Ajay K. Gopal, Edward N. Libby
Journal: JAMA (2022)

<h3>Importance</h3> Multiple myeloma is a hematologic malignancy characterized by presence of abnormal clonal plasma cells in the bone marrow, with potential for uncontrolled growth causing destructive bone lesions, kidney injury, anemia, and hypercalcemia. Multiple myeloma is diagnosed in an estimated 34 920 people in the US and in approximately 588 161 people worldwide each year. <h3>Observations</h3> Among patients with multiple myeloma, approximately 73% have anemia, 79% have osteolytic bone disease, and 19% have acute kidney injury at the time of presentation. Evaluation of patients with possible multiple myeloma includes measurement of hemoglobin, serum creatinine, serum calcium, and serum free light chain levels; serum protein electrophoresis with immunofixation; 24-hour urine protein electrophoresis; and full-body skeletal imaging with computed tomography, positron emission tomography, or magnetic resonance imaging. The Revised International Staging System combines data from the serum biomarkers β<sub>2</sub>microglobulin, albumin, and lactate dehydrogenase in conjunction with malignant plasma cell genomic features found on fluorescence in situ hybridization—t(4;14), del(17p), and t(14;16)—to assess estimated progression-free survival and overall survival. At diagnosis, 28% of patients are classified as having Revised International Staging stage I multiple myeloma, and these patients have a median 5-year survival of 82%. Among all patients with multiple myeloma, standard first-line (induction) therapy consists of a combination of an injectable proteasome inhibitor (ie, bortezomib), an oral immunomodulatory agent (ie, lenalidomide), and dexamethasone and is associated with median progression-free survival of 41 months, compared with historical reports of 8.5 months without therapy. This induction therapy combined with autologous hematopoietic stem cell transplantation followed by maintenance lenalidomide is standard of care for eligible patients. <h3>Conclusions and Relevance</h3> Approximately 34 920 people in the US and 155 688 people worldwide are diagnosed with multiple myeloma each year. Induction therapy with an injectable proteasome inhibitor, an oral immunomodulatory agent and dexamethasone followed by treatment with autologous hematopoietic stem cell transplantation, and maintenance therapy with lenalidomide are among the treatments considered standard care for eligible patients.
Abstracts Appearing in JAMA
Journal: JAMA (1969)

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
Résumés in Oncology—II
Journal: JNCI Journal of the National Cancer Institute (1970)

Résumés in Oncology—II Get access JNCI: Journal of the National Cancer Institute, Volume 44, Issue 6, June 1970, Page 1321, https://doi.org/10.1093/jnci/44.6.1321 Published: 01 June 1970
Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction
Authors: Anastasia Ignatieva, Jotun Hein, Paul A Jenkins
Journal: Molecular Biology and Evolution (2022)

The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa and find evidence of ongoing recombination.
Bacteria-enabled oral delivery of a replicon-based mRNA vaccine candidate protects against ancestral and delta variant SARS-CoV-2
Authors: Vijayakumar Jawalagatti, Perumalraja Kirthika, Chamith Hewawaduge, Myeon-Sik Yang, Ji-Young Park, Byungkwan Oh, John Hwa Lee
Journal: Molecular Therapy (2022)

The ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolution has resulted in many variants, contributing to the striking drop in vaccine efficacy and necessitating the development of next-generation vaccines to tackle antigenic diversity. Herein we developed a multivalent Semliki Forest virus replicon-based mRNA vaccine targeting the receptor binding domain (RBD), heptad repeat domain (HR), membrane protein (M), and epitopes of non-structural protein 13 (nsp13) of SARS-CoV-2. The bacteria-mediated gene delivery offers the rapid production of large quantities of vaccine at a highly economical scale and notably allows needle-free mass vaccination. Favorable T-helper (Th) 1-dominated potent antibody and cellular immune responses were detected in the immunized mice. Further, immunization induced strong cross-protective neutralizing antibodies (NAbs) against the B.1.617.2 delta variant (clade G). We recorded a difference in induction of immunoglobulin (Ig) A response by the immunization route, with the oral route eliciting a strong mucosal secretory IgA (sIgA) response, which possibly has contributed to the enhanced protection conferred by oral immunization. Hamsters immunized orally were completely protected against viral replication in the lungs and the nasal cavity. Importantly, the vaccine protected the hamsters against SARS-CoV-2-induced pneumonia. The study provides proof-of-principle findings for the development of a feasible and efficacious oral mRNA vaccine against SARS-CoV-2 and its variants.Graphical abstract
Endothelin ET 8 receptors are functionally important in mediating vasoconstriction in the systemic circulation in patients with left ventricular dysfunction
Authors: P.J. Cowburn, J.J. Morton, J.D. McArthur, M.R. MacLean, H.J. Dargie, J.J.V. McMurray, J.G.F. Cleland
Journal: Journal of the American College of Cardiology (1998)