tbuckley/cabot-search huggingface dataset:
Optimising predictive models to prioritise viral discovery in zoonotic reservoirs
Authors: Daniel J Becker, Gregory F Albery, Anna R Sjodin, Timothée Poisot, Laura M Bergner, Binqi Chen, Lily E Cohen, Tad A Dallas, Evan A Eskew, Anna C Fagre, Maxwell J Farrell, Sarah Guth, Barbara A Han, Nancy B Simmons, Michiel Stock, Emma C Teeling, Colin J Carlson
Journal: The Lancet Microbe (2022)

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host–virus associations and developed priority sampling recommendations for potential bat reservoirs of betacoronaviruses and bridge hosts for SARS-CoV-2. During a time frame of more than a year, we tracked the discovery of 47 new bat hosts of betacoronaviruses, validated the initial predictions, and dynamically updated our analytical pipeline. We found that ecological trait-based models performed well at predicting these novel hosts, whereas network methods consistently performed approximately as well or worse than expected at random. These findings illustrate the importance of ensemble modelling as a buffer against mixed-model quality and highlight the value of including host ecology in predictive models. Our revised models showed an improved performance compared with the initial ensemble, and predicted more than 400 bat species globally that could be undetected betacoronavirus hosts. We show, through systematic validation, that machine learning models can help to optimise wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.
“Super massive” intrahepatic cholangiocarcinoma: Potential role of radiation therapy.
Authors: Joseph Abi Jaoude, Brian De, Humberto R Nieves Jiménez, Rituraj Upadhyay, Cullen M. Taniguchi, Eugene Jon Koay, Ethan B. Ludmir
Journal: Journal of Clinical Oncology (2022)

567 Background: Intrahepatic cholangiocarcinoma (ICC) is a cancer of the bile ducts within the liver. Most patients have unresectable disease and die of tumor-related liver failure (TRLF); prior data suggest that radiation therapy (RT) may play an important role in decreasing TRLF and improving survival. However, for patients with exceptionally large liver tumors, the role of RT is uncertain. Here, we present our experience using hypofractionated RT for so-called “super-massive” ICC (gross tumor volume &gt; 800cc). Methods: We retrospectively collected data from ICC patients treated at the University of Texas MD Anderson Cancer Center. We included inoperable patients (both M0 and M1) who were treated with RT, identified those with a gross tumor volume of 800cc or more (median: 1,300cc IQR: 900-1,900). We analyzed overall survival (OS), local and distant recurrence, tumor-related liver failure (TRLF), and treatment toxicity. Results: A total of 12 patients were included. The median age was 60 (IQR: 55-67). The average maximal tumor diameter was 14.1cm (IQR: 12.6-15.8). All but 1 patient received pre-RT systemic therapy. Eight patients (67%) were treated with IMRT, and 4 patients (33%) with proton RT. RT was delivered to a median of 67.5Gy (IQR: 60-73.1) over 15 fractions. At a median follow up of 17.4 months, 5 patients were still alive (2-year OS: 41.7%). Median OS, local recurrence, and distant metastasis from RT were 20.0, 20, and 11.3 months, respectively. Two patients (16.7%) died from TRLF. No grade 2 or higher toxicities were noted. No radiation-induced liver toxicity was present. Conclusions: Hypofractionated RT was safe and showed promising clinical outcomes for patients with “super massive” inoperable ICC, compared to historical data. Future studies are still needed to better assess the role of RT in this patient population.
We risk letting a new threat expose us to old enemies
Authors: None The Lancet Microbe
Journal: The Lancet Microbe (2020)

The impact of COVID-19 is reaching far beyond the direct consequences of SARS-CoV-2 infection. The wholesale repurposing of resources to tackle the pandemic has left little room for ongoing efforts to control other infectious diseases—eg, HIV, malaria, and tuberculosis. Particularly concerning is the impact this shift in resource allocation is having on tuberculosis, with its unenviable status as the infectious disease responsible for the most deaths worldwide each year. Adding to this concern is the progression of the COVID-19 pandemic to nations with large burdens of tuberculosis, where changes in the response to tuberculosis will be most keenly felt.
REVISED NOTATION FOR CHEMICAL ISOTOPES
Journal: JAMA (1964)

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
LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion
Authors: Federica Marasca, Shruti Sinha, Rebecca Vadalà, Benedetto Polimeni, Valeria Ranzani, Elvezia Maria Paraboschi, Filippo Vittorio Burattin, Marco Ghilotti, Mariacristina Crosti, Maria Luce Negri, Susanna Campagnoli, Samuele Notarbartolo, Andrea Sartore-Bianchi, Salvatore Siena, Daniele Prati, Giovanni Montini, Giuseppe Viale, Olga Torre, Sergio Harari, Renata Grifantini, Giulia Soldà, Stefano Biffo, Sergio Abrignani, Beatrice Bodega
Journal: Nature Genetics (2022)
The diagnosis of multiple sclerosis
Authors: S. Gilman
Journal: JAMA (1981)

Multiple sclerosis is an acquired disease of the CNS, characterized by neuropathologic changes in the white matter of the brain and spinal cord in random and multiple sites.<sup>1</sup>The disease essentially never affects the peripheral nervous system. The neuropathologic changes consist of loss of the myelin covering of axons in the form of demyelinative plaques.<sup>2</sup>The sites frequently affected account for the characteristic symptoms and signs, with disease of the optic nerves and chiasm causing visual disturbances, involvement of the cerebellum leading to gait and limb ataxia, and spinal cord lesions causing limb paresthesias and weakness as well as urinary and sexual disturbances. Many other sites commonly are affected as well. The disease is known to occur at as young an age as 6 years and at as old an age as 65 years. The onset occurs most frequently, however, during the second and third decades of life.
Error in Results Data
Authors: Srishti Saha, Piyush Nathani, Arjun Gupta
Journal: JAMA Internal Medicine (2021)

to their use. 5If and when PAMORAs are used for OIC prophylaxis (especially in patients with cancer), developing constipation would need a thorough evaluation (history, physical examination, and assessment of accompanying symptoms such as nausea and abdominal pain, as well as other workup, such as laboratory and/or imaging studies) to evaluate biochemical, structural, or other causes of constipation, vs just assuming the constipation is related to OIC.Ongoing long-term PAMORA use in a patient with possible obstruction or a luminal lesion could be dangerous.Naloxegol and naldemedine, 2 PAMORAs, are only approved for use in patients with noncancer-related pain and OIC.PAMO-RAs are also more costly compared with traditional laxatives, and payers often encourage step therapy (ie, a failure of traditional laxatives) before covering PAMORAs.As an example, the cash price of a 3-day supply of oral methylnaltrexone (another PAMORA) at the recommended dose of 450 mg once daily ranges from $206 to $221 on GoodRx.com.Recent studies have demonstrated lower rates of bowel dysfunction and OIC with long-acting opioid/naloxone medication combinations (vs opioid alone), but these formulations are not routinely available and do not qualify as PAMORAs per se. 4,6Ongoing clinical trials are evaluating PAMORAs for preventing OIC (eg, ClinicalTrials.govidentifiers NCT02946580, NCT02977286) and we eagerly await their publication.In summary, PAMORAs are useful agents to treat laxative refractory OIC, but traditional laxatives, which are well tolerated, widely available (often over the counter), and inexpensive agents, remain first-line pharmacologic options for preventing and treating OIC.
JAMA Dermatology
Journal: JAMA Dermatology (2020)

Mission Statement JAMA Dermatology publishes information concerning the skin, its diseases, and their treatment.Its mission is to explicate the structure and function of the skin and its diseases and the art of using this information to deliver optimal medical and surgical care to the patient.We attempt to enhance the understanding of cutaneous pathophysiology and improve the clinician's ability to diagnose and treat skin disorders.This journal has a particular interest in publishing clinical and laboratory studies that reveal new information pertinent to the interests and needs of the medical dermatologist, dermatologic surgeon, and all those concerned with state-of-the-art care of cutaneous disease.We believe that knowledge derived from well-designed clinical trials and studies of cost-eff ectiveness are especially important for improving the practice of dermatology.Studies that increase the understanding of the outcome of treatment or the means by which the burden of dermatologic disease can be measured and reduced to promote the health of patients with skin disease will receive special priority.The journal regularly publishes reports on clinical investigations, editorials, and reviews.It also features reports and discussions on clinicopathologic correlations; clinical disorders of unique didactic value; pharmacologic, medical and surgical therapeutics; and ethical, moral, socioeconomic, and political issues.
PLoS Medicine Issue Image | Vol. 7(8) August 2010
Journal: PLoS Medicine (2010)

The Editorial this month argues for the need to fundamentally rethink how societies can look beyond the "medical" causes of disease in an effort to promote health and well-being. This follows a systematic review and a meta-analysis by Julianne Holt-Lunstad and colleagues published in PLoS Medicine in July finding that individuals' social relationships have as much influence on mortality risk as other well-established risk factors for mortality, such as smoking. Such a level of risk deserves attention at the highest possible level in determination of health policy, says the Editorial. Despite the fact that many governments have decided to cut to public spending drastically in order to reduce deficits, findings such as those by Holt-Lunstad and colleagues offer an opportunity to reorganize services to meet the needs of an increasingly complex society. Image Credit: Shahram Sharif
Food Allergies
Authors: Hugh A. Sampson
Journal: JAMA (1992)

THE TERMS<i>food allergy</i>and<i>food hypersensitivity</i>are synonymous when applied to a group of diseases that are characterized by an abnormal or exaggerated immunologic response to specific food allergens resulting in disease. Food allergy can be subdivided into two broad categories: disorders that are mediated by IgE, which are generally rapid in onset, and those that occur by non-IgE—mediated mechanisms.<i>Food intolerance</i>is a term used to describe an abnormal physiological response to an ingested food or food additive. Such reactions are not immunologic in nature and may include idiosyncratic, metabolic, pharmacological, or toxic responses.<sup>1</sup> The public perception of the importance of allergic reactions to foods substantially exceeds the prevalence of such reactions identified in clinical studies. Reports from prospective surveys have shown that at least one in four atopic adults believe that they have experienced adverse reactions following the ingestion or handling of foods. Similarly, parents believe
End compulsory drug treatment in the Asia-Pacific region
Authors: Claudia Stoicescu, Quinten Lataire, Karen Peters, Joseph J Amon, Adeeba Kamarulzaman, Robert Ali, Apinun Aramrattana, Ivanhoe C Escartin, Ma Inez Feria, Sangeeth Kaur, Riza Sarasvita, Sam Nugraha
Journal: The Lancet (2022)
Society Proceedings
Journal: JAMA (1934)

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
18F-GP1 Positron Emission Tomography and Bioprosthetic Aortic Valve Thrombus
Authors: Rong Bing, Marcus-André Deutsch, Stephanie L. Sellers, Carlos Alcaide Corral, Jack P.M. Andrews, Edwin J.R. van Beek, Sabine Bleiziffer, Wolfgang Burchert, Tim Clark, Damini Dey, Kai Friedrichs, Jan F. Gummert, Norman Koglin, Jonathon A. Leipsic, Oliver Lindner, Mark G. MacAskill, Hendrik Milting, Renzo Pessotto, Rainer Preuss, Jennifer B. Raftis, Tanja K. Rudolph, Volker Rudolph, Piotr Slomka, Andrew W. Stephens, Adriana Tavares, Evangelos Tzolos, Nick Weir, Audrey C. White, Michelle C. Williams, Reinhard Zabel, Marc R. Dweck, Verena Hugenberg, David E. Newby
Journal: JACC. Cardiovascular imaging (2022)
Secretory leukocyte proteinase inhibitor: A key player in the dialogue between the tumor and its microenvironment in pancreatic cancer patients.
Authors: Eduardo Chuluyan, Nella Ambrosi, Nicolas Fraunhoffer, Fiorella Caro, Carla Remolins, Macarena Reiteri, Diego Guerrieri, Philippe Soubeyran, Odile Gayet, Julie Roques, Dusetti J. Nelson, Claudio A. Incardona, Juan Iovanna
Journal: Journal of Clinical Oncology (2022)

592 Background: Secretory leukocyte proteinase inhibitor (SLPI) is a non-glycosylated pleiotropic protein with anti-protease, microbicidal, healing, anti-inflammatory and immunomodulatory activity. Previous studies have shown that SLPI is associated with pancreatic tumor progression by promoting cancer cell survival and proliferation. However, SLPI can also act on the tumor microenvironment to affect the local immune response. In the present work we evaluate the role of SLPI in patients with pancreatic cancer and its activity as a tumor escape factor from the immune response. Methods: Serum levels of SLPI was measured in pancreatic cancer patients by sandwich ELISA. RNA-seq was performed on 76 patient-derived xenografts (PDX) and we computed independent component analysis focusing the study on the component that best correlated with SLPI gene. Secretome analysis was performed on 38 different cell lines cells culture derived from PDX. Human monocytes were isolated and differentiated into immature dendritic cells in the presence or absence of SLPI or in the presence of a pancreatic tumor cell line that did or did not express SLPI. Results: The frequency distribution of serum SLPI values showed patients with low and high SLPI value (cut-off value 61.5 ng/ml). Most patients with high serum SLPI concentration had unresectable tumors. There was an indirect association between serum SLPI levels and the time of disease recurrence. The transcriptome analysis showed that expression of SLPI is associated with immune and cancer functional clusters. The analysis of the secretome showed that SLPI was present in all cell lines from PDX. The heat map of the secretome exhibited that SLPI was directly associated with factors described in tumor microenvironment and related with tumor immune evasion mechanisms, such as CSF1, SECTM1, LGALS3, IL1RN, CD59, CD55, CD46, Fas, PVR, PVRL2. Remarkably, the closest group associated with SLPI was CSF1. The latter contributes to the depressed function of antigen-presenting cells, as a result of skewed differentiation of monocytes towards macrophage-like cells rather than dendritic cells. Furthermore, in vitro experiments demonstrated that SLPI or SLPI-producing pancreatic tumor cell lines impaired the differentiation of human monocytes towards dendritic cells and their immunostimulatory capacity. Conclusions: These results suggest that SLPI may contribute to the immunosuppressive microenvironment of pancreatic cancer by acting as a tumor immune evasion factor. Clinically, this SLPI activity could be reflected in the association of the serum SLPI value with disease recurrence or progression.
Massachusetts Medical Society
Authors: John Figgis Jewett, Robert W. Buck
Journal: New England Journal of Medicine (1956)

COMMITTEE ON MATERNAL WELFAREOvarian Cystadenoma, with MetastasesA twenty-seven-year-old gravida I had no gynecologic complaints before pregnancy. Pelvic examination is said to have been negative early in pregnancy, which was uneventful until the twenty-eighth week, when she was hospitalized after fainting at work. She complained of pressure pains, marked dyspnea and constipation. Examination of the blood revealed a red-cell count of 3,100,000, with a hemoglobin of 8.1 gm. per 100 ml., and a white-cell count of 11,000. She was discharged four days later with a diagnosis of "anemia of pregnancy." An iron-and-vitamin preparation was prescribed. Because of dyspnea, digitalis . . .
Cancer Research
Authors: Michael Shimkin, Sidney Weinhouse
Journal: CA A Cancer Journal for Clinicians (1972)

â€oe¿ For many years the biochemist has been asking whether there is some unique biochemical feature that characterizes the neoplastic cell: a key to its disorderly growth.its lack of regularity, its invasiveness.Itisbecomingevermore clear that this is a simplistic question that admits no useful answers at this time.If we ask whether allcancers differ in some single.unique feature from allnormal tissues, the answer is simply no.Paradoxically, however, if we ask whether a par ticular neoplasm differs from its particular tissue of origin.the answer is that there are SOmany differences that causal re lationships are thoroughly obscured.The spectacular ad
ON THE PIGMENT OF THE NEGRO'S SKIN AND HAIR
Authors: John J. Abel, Walter S. Davis
Journal: The Journal of Experimental Medicine (1896)

The pigmentary granules of the negro's skin and hair can be freed in several ways from the cells in which they are lodged and collected in any desired amount. As thus obtained, these granules are found to be insoluble in dilute alkalies, dilute hydrochloric acid (hot or cold), alcohol, or other organic solvents when applied in the order named. If, after they have been subjected to the action of dilute hydrochloric acid, they are again treated with dilute alkalies, they are found to give up their pigment, and, on the continued application of heat, the granules dissolve entirely in the alkaline solution, leaving only an insignificant residue. The pigmentary granules are composed of a colourless ground substance or substratum, a pigment, and much inorganic matter. Their inorganic constituents, as thus far determined, are calcium, magnesium, iron, and silicic, phosphoric, and sulphuric acids; and these constituents possibly play an important part in the deposition and fixation of the colouring matter in the granules. The pigment isolated from the granules, and sufficiently freed from adherent inorganic matter, contains only the merest trace of iron—so little, in fact, that we must think of it when entirely pure as free of iron. Heating the isolated pigment with barium hydrate at a temperature of 260° C. entirely frees it from the closely adherent ground substance, and it is then found that the vapours of pyrrol are no longer emitted when it is subjected to dry distillation, and the odour of burnt feathers is no longer discerned, although nitrogen is still present. We can not conclude as the result of our work that the pigment is a derivative of hæmoglobin; it seems to us more probable that it is ultimately derived from the proteids of the parenchymatous juices. The total quantity of soluble pigment in the skin of a negro of average size is found to weigh about 1 gramme; the weight of the pigmentary granules is about 3.3 grammes, if we are right in our assumption that they contain sixty-five per cent of water and five per cent of mineral constituents in their natural state in the epidermis. The pigments of the epidermis and hair of the negro are very likely identical. In the present state of our knowledge we can only say that it seems highly probable that the pigment of the negro's hair is not different from the dark pigment found in the hair of the white races, and we may infer that the pigment of the black skin differs only in amount and not in kind from that deposited in the skin of the white man.
In Brief
Journal: JAMA (1975)

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