tbuckley/cabot-search huggingface dataset:
Use of radiomics for the prediction of local control of brain metastases after stereotactic radiosurgery
Authors: Andrei Mouraviev, Jay Detsky, Arjun Sahgal, Mark Ruschin, Young K Lee, Irene Karam, Chris Heyn, Greg J Stanisz, Anne L Martel
Journal: Neuro-Oncology (2020)

Abstract Background Local response prediction for brain metastases (BM) after stereotactic radiosurgery (SRS) is challenging, particularly for smaller BM, as existing criteria are based solely on unidimensional measurements. This investigation sought to determine whether radiomic features provide additional value to routinely available clinical and dosimetric variables to predict local recurrence following SRS. Methods Analyzed were 408 BM in 87 patients treated with SRS. A total of 440 radiomic features were extracted from the tumor core and the peritumoral regions, using the baseline pretreatment volumetric post-contrast T1 (T1c) and volumetric T2 fluid-attenuated inversion recovery (FLAIR) MRI sequences. Local tumor progression was determined based on Response Assessment in Neuro-Oncology‒BM criteria, with a maximum axial diameter growth of &amp;gt;20% on the follow-up T1c indicating local failure. The top radiomic features were determined based on resampled random forest (RF) feature importance. An RF classifier was trained using each set of features and evaluated using the area under the receiver operating characteristic curve (AUC). Results The addition of any one of the top 10 radiomic features to the set of clinical features resulted in a statistically significant (P &amp;lt; 0.001) increase in the AUC. An optimized combination of radiomic and clinical features resulted in a 19% higher resampled AUC (mean = 0.793; 95% CI = 0.792–0.795) than clinical features alone (0.669, 0.668–0.671). Conclusions The increase in AUC of the RF classifier, after incorporating radiomic features, suggests that quantitative characterization of tumor appearance on pretreatment T1c and FLAIR adds value to known clinical and dosimetric variables for predicting local failure.
Survival, Nonrelapse Mortality, and Relapse-Related Mortality After Allogeneic Hematopoietic Cell Transplantation: Comparing 2003–2007 Versus 2013–2017 Cohorts
Authors: George B. McDonald, Brenda M. Sandmaier, Marco Mielcarek, Mohamed Sorror, Steven A. Pergam, Guang-Shing Cheng, Sangeeta Hingorani, Michael Boeckh, Mary D. Flowers, Stephanie J. Lee, Frederick R. Appelbaum, Rainer Storb, Paul J. Martin, H. Joachim Deeg, Gary Schoch, Ted A. Gooley
Journal: Annals of Internal Medicine (2020)

Allogeneic hematopoietic cell transplantation is indicated for refractory hematologic cancer and some nonmalignant disorders. Survival is limited by recurrent cancer and organ toxicity.To determine whether survival has improved over the past decade and note impediments to better outcomes.The authors compared cohorts that had transplants during 2003 to 2007 versus 2013 to 2017. Survival outcome measures were analyzed, along with transplant-related complications.A center performing allogeneic transplant procedures.All recipients of a first allogeneic transplant during 2003 to 2007 and 2013 to 2017.Patients received a conditioning regimen, infusion of donor hematopoietic cells, then immunosuppressive drugs and antimicrobial approaches to infection control.Day-200 nonrelapse mortality (NRM), recurrence or progression of cancer, relapse-related mortality, and overall mortality, adjusted for comorbidity scores, source of donor cells, donor type, patient age, disease severity, conditioning regimen, patient and donor sex, and cytomegalovirus serostatus.During the 2003-to-2007 and 2013-to-2017 periods, 1148 and 1131 patients, respectively, received their first transplant. Over the decade, decreases were seen in the adjusted hazards of day-200 NRM (hazard ratio [HR], 0.66 [95% CI, 0.48 to 0.89]), relapse of cancer (HR, 0.76 [CI, 0.61 to 0.94]), relapse-related mortality (HR, 0.69 [CI, 0.54 to 0.87]), and overall mortality (HR, 0.66 [CI, 0.56 to 0.78]). The degree of reduction in overall mortality was similar for patients who received myeloablative versus reduced-intensity conditioning, as well as for patients whose allograft came from a matched sibling versus an unrelated donor. Reductions were also seen in the frequency of jaundice, renal insufficiency, mechanical ventilation, high-level cytomegalovirus viremia, gram-negative bacteremia, invasive mold infection, acute and chronic graft-versus-host disease, and prednisone exposure.Cohort studies cannot determine causality, and current disease severity criteria were not available for patients in the 2003-to-2007 cohort.Improvement in survival and reduction in complications were substantial after allogeneic transplant. Relapse of cancer remains the largest obstacle to better survival outcomes.National Institutes of Health.
Personal tumor antigens in blood malignancies: genomics-directed identification and targeting
Authors: Livius Penter, Catherine J. Wu
Journal: Journal of Clinical Investigation (2020)

Hematological malignancies have long been at the forefront of the development of novel immune-based treatment strategies. The earliest successful efforts originated from the extensive body of work in the field of allogeneic hematopoietic stem cell transplantation. These efforts laid the foundation for the recent exciting era of cancer immunotherapy, which includes immune checkpoint blockade, personal neoantigen vaccines, and adoptive T cell transfer. At the heart of the specificity of these novel strategies is the recognition of target antigens presented by malignant cells to T cells. Here, we review the advances in systematic identification of minor histocompatibility antigens and neoantigens arising from personal somatic alterations or recurrent driver mutations. These exciting efforts pave the path for the implementation of personalized combinatorial cancer therapy.
NEUROIMAGING CLASSIFICATION OF PROGRESSION PATTERNS IN GLIOBLASTOMA: A SYSTEMATIC REVIEW
Authors: Rory Piper, Keerthi Senthil, Jiun-lin Yan, Stephen Price
Journal: Neuro-Oncology (2018)

Our objective was to report current neuroimaging classification systems of spatial patterns of progression in glioblastoma, report the terminology used to describe ‘progression’ and to assess the compliance of these studies with the Response Assessment in Neuro-Oncology (RANO) Criteria. We conducted a systematic review to identify all neuroimaging studies of glioblastoma that have employed a categorical classification system of spatial progression patterns. Our review was registered with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) registry. From the included 157 results, we identified 129 studies that used labels of spatial progression patterns that were not (Group 1) and 50 studies that used labels that were based on radiation volumes. In Group 1, we found 113 individual labels and the most frequent were: local/localised (58%), distant/distal (51%), diffuse (20%), multifocal (15%) and subependymal/subventricular zone (15%). We identified 13 different labels used to refer to ‘progression’, of which the most frequent were ‘recurrence’ (99%) and ‘progression’ (92%). We identified 37% (n=33/90) of studies published following the release of the RANO classification were adherent compliant with the RANO criteria. Our review reports significant heterogeneity in the published systems used to classify glioblastoma spatial progression patterns. Standardisation of terminology and classification systems used in studying progression with neuroimaging would increase the efficiency of our research in our attempts to more successfully treat glioblastoma.
Decision by injection without infection
Authors: Miwa Sasai, Masahiro Yamamoto
Journal: The Journal of Experimental Medicine (2020)

The protozoan pathogen Toxoplasma gondii co-opts host immunity by secreting various effector proteins into host cells. In this issue of JEM, Chen et al. (https://doi.org/10.1084/jem.20181757) report that T. gondii injects an effector called ROP16 without invasion to polarize macrophages toward M2 cells.
Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study
Authors: Sofia Moran-Ramos, Blanca E. Lopez-Contreras, Ricardo Villarruel-Vazquez, Elvira Ocampo-Medina, Luis Macias-Kauffer, Jennifer N. Martinez-Medina, Hugo Villamil-Ramirez, Paola León-Mimila, Blanca E. Del Rio-Navarro, Isabel Ibarra-Gonzalez, Marcela Vela-Amieva, Francisco J Gomez-Perez, Rafael Velazquez-Cruz, Jorge Salmeron, Zyanya Reyes-Castillo, Carlos Aguilar-Salinas, Samuel Canizales-Quinteros
Journal: Gut Microbes (2020)

Background Gut microbiota, by influencing multiple metabolic processes in the host, is an important determinant of human health and disease. However, gut dysbiosis associated with metabolic complications shows inconsistent patterns. This is likely driven by factors shaping gut microbial composition that have largely been under-evaluated, at a population level, in school-age children, especially from developing countries.Results Through characterization, by 16S sequencing, of the largest gut microbial population-based school-aged children cohort in Latin America (ORSMEC, N = 926, aged 6–12 y), we identified associations of 14 clinical and environmental covariates (PFDR<0.1), collectively explaining 15.7% of the inter-individual gut microbial variation. Extrinsic factors such as markers of socioeconomic status showed a major influence in the most abundant taxa and in the enterotypes' distribution. Age was positively correlated with higher diversity, but only in normal-weight children (rho = 0.138, P =2 × 10−3). In contrast, this correlation although not significant, was negative in overweight and obese children (rho = −0.125, P = 0.104 and rho = −0.058, P = 0.409, respectively). Finally, co-abundance groups (CAGs) were associated with the presence of metabolic complications.Conclusions Our study offers evidence that the presence of overweight and obesity could impair the microbial diversity maturation associated with age. Furthermore, it provides novel results toward a better understanding of gut microbiota in the pediatric population that will ultimately help to develop therapeutic approaches to improve metabolic status.
Disease escape with the selective loss of the Philadelphia chromosome after tyrosine kinase inhibitor exposure in Ph-positive acute lymphoblastic leukemia
Authors: Nicolas Gazeau, Coralie Derrieux, Olivier Nibourel, Céline Berthon, Nathalie Grardel, Laure Goursaud, Thomas Boyer, Florent Dumezy, Valérie Coiteux, Bruno Quesnel, Claude Preudhomme, Catherine Roche-Lestienne, Nicolas Duployez
Journal: Leukemia (2020)
Met Activation by Autocrine Loop Rescues Colon Cancer Cells From Sensitivity to EGFR Inhibition
Authors: T. Troiani, D. Vitagliano, S. Napolitano, F. Morgillo, A. Capasso, V. Sforza, A. Nappi, L. Berrino, F. Ciardiello, E. Martinelli
Journal: Annals of Oncology (2012)
Health care worker use of N95 respirators vs medical masks did not differ for workplace-acquired influenza
Authors: Aaron E. Glatt
Journal: Annals of Internal Medicine (2020)

Source Citation Radonovich LJ Jr, Simberkoff MS, Bessesen MT, et al. N95 respirators vs medical masks for preventing influenza among health care personnel: a randomized clinical trial. JAMA. 2019;322:824-33. 31479137
Children born as a result of incest.
Journal: BMJ (1981)

Children born as a result of incestAfter an address to the Medicolegal Society on the crime of incest, Sir Desmond Acknerl asked, "To what extent is it a serious eugenic risk if brother and sister marry ?"There was no response from his audience.Father-daughter and brothersister unions result in inbreeding four times as intense as in first-cousin marriages.The surveys of the extra risks of recessive disorders and congenital malformations to the children of first cousins have not, however, given enough information to permit reliable extrapolation to the children of incestuous unions.There are also obvious difficulties in following up closely children born to a random sample of incestuous unions without causing distress to the families.Nevertheless, three studies have been reported.The largest, a retrospective survey of 161 children, was from Czechoslovakia2 in 1971.Rare recessive or probably recessive disorders found in the children included homocystinuria, adiposogenital syndrome, congenital ichthyosis, retinitis pigmentosa, and deaf-mutism as well as a high incidence of mental retardation.Fewer than half the children were normal.This study might possibly have been biased by some selection in the sources from which the children were ascertained.The other two studies,3 one from England of 13 live-born children followed up for four to six years and one from Michigan of 18 live-born children followed up for six to 12 years, were prospective, with the children being ascertained during their mothers' pregnancies.Of the 31 children in these two studies-12 born to father- daughter and 19 to brother-sister matings-only 13 were normal.Two died from recessive disorders (cystic fibrosis and glycogen-storage disease) and one from an almost certainly recessive disorder causing progressive cerebral degeneration and loss of vision.Two of those alive probably had recessive disorders, both with severe mental retardation with cerebral palsy, and one a possibly recessive disorder, severe non-specific mental retardation.Two others had died in the neonatal period, a baby with very low birth weight and another with respiratorydistress syndrome.Two had congenital malformations, a lethal Fallot's tetralogy and a survivor with bilateral cleft lip.Eight other survivors were mildly mentally retarded with IQs in seven ranging from 59 to 76; the eighth, whose IQ score was not available, was in a school for the educationally subnormal.This increase in recessive disorders-between three and six cases in 31 children compared with an expected incidence5 in the general population of two or three per thousand-is in line with expectations.It is compatible with a lesser increase
Time to Include Nonalcoholic Steatohepatitis in the Management of Patients With Type 2 Diabetes
Authors: Kenneth Cusi
Journal: Diabetes Care (2020)

Nonalcoholic fatty liver disease (NAFLD) is today the most common cause of chronic liver disease and second only to viral hepatitis as a cause of liver transplantation in the U.S. (1,2). It encompasses conditions from simple steatosis (NAFL), believed to be associated with slow disease progression, to the more severe and progressive form known as nonalcoholic steatohepatitis (NASH). NASH is characterized by hepatocellular injury in the form of hepatocyte ballooning (necrosis) and predominantly lobular inflammation. The severity of hepatic fibrosis is defined in stages. They range from stage F0, or no fibrosis, to mild (stage F1), moderate (stage F2, with zone 3 sinusoidal fibrosis plus periportal fibrosis), or advanced fibrosis, with bridging fibrosis (stage F3) or cirrhosis (stage F4). NASH may lead to cirrhosis and to the development of hepatocellular carcinoma, but even moderate-to-severe fibrosis (F2-F3) is associated with higher mortality (1,2). Advanced liver fibrosis and cirrhosis occur more often in obesity but, in particular, in patients with type 2 diabetes (T2D) (3). Endocrinologists should be aware that patients with NAFLD are also at a two- to threefold increased risk of both progression from prediabetes to diabetes and development of cardiovascular disease (4,5). Taken together, there is a consensus that patients with T2D and NASH are at a much higher risk of hepatic and extrahepatic morbidity and premature death than in the absence of liver disease.

Within this context, Younossi et al. (6) report in the current issue of Diabetes Care an important study on the clinical and economic burden of NASH in patients with T2D in the U.S. This is so far the most comprehensive effort to systematically outline the magnitude of the problem in patients with diabetes. The authors used 2017 annual direct medical costs attributed to diagnosed diabetes reported by the …
Unethical International Nurse-Staffing Agencies — The Need for Legislative Action
Authors: Patricia Pittman, Adam R. Pulver
Journal: New England Journal of Medicine (2020)

A bill in the U.S. Congress would remove caps on employment-based visas for immigrants from any one country and may include a carve-out for nurses. The policy could exacerbate unfair labor practices in the staffing industry without rules preventing worker exploitation.
Can a better understanding of frailty improve the quality of life of patients with fibrotic interstitial lung diseases?
Authors: Bernard Aguilaniu
Journal: European Respiratory Journal (2020)

<b>The fate of patients with pulmonary fibrosis is also influenced by their frailty. Hence the urgent need to evaluate these patients beyond pulmonary involvement, and to consider the decline in pulmonary function as a late warning of homeostasis erosion.</b>http://bit.ly/2LehtmU
Association of Repeated Antibiotic Exposure Up to Age 4 Years With Body Mass at Age 4.5 Years
Authors: Carol Chelimo, Carlos A. Camargo, Susan M. B. Morton, Cameron C. Grant
Journal: JAMA Network Open (2020)

Antibiotic exposures in early life may affect weight by altering gut microbiota, potentially increasing the likelihood of childhood obesity.To examine whether repeated antibiotic exposure by age 48 months is associated with higher body mass index (BMI) at age 54 months.This research was undertaken within a prospective cohort study in New Zealand (Growing Up in New Zealand) that recruited 6853 children antenatally during 2009 to 2010. At the 54-month follow-up, 5734 of 6156 children (93%) had their weight and height measured. Community pharmacy antibiotic dispensing data were obtained from the New Zealand Pharmaceutical Collection database for children whose parents consented to external data linkage. The analytic sample comprised singletons with 54-month weight and height measurements, community antibiotic dispensing and birth weight data, gestational age greater than 27 weeks, and no congenital anomalies. Data analysis took place from 2017 to 2018.Antibiotic exposure (yes or no), the number of dispensings, age at first exposure, and timing (age) of exposures between birth and age 48 months.World Health Organization BMI-for-age z scores; and International Obesity Task Force overweight and obesity cutoff points that pass through adult BMI values of 25 and 30.Of the 5128 singletons (2622 [51%] male; mean [SD] birth weight of 3527 [542] g), 4886 (95%) had an antibiotic prescription by age 48 months and 437 (9%) had obesity at age 54 months. Adjusted mean (SE) BMI-for-age z scores increased significantly with the number of antibiotic dispensings for 4 to 6, 7 to 9, and more than 9 dispensings (unexposed, 0.87 [0.09]; 1-3 exposures, 0.92 [0.06] [P = .57]; 4-6 exposures, 1.06 [0.06] [P = .02]; 7-9 exposures, 1.06 [0.06] [P = .02]; >9 exposures, 1.08 [0.05] [P = .01]). Additionally, receiving more than 9 dispensings was associated with greater likelihood of obesity compared with no exposure (adjusted odds ratio, 2.41; 95% CI, 1.07-5.41). Children whose exposure began in the first year of life had a higher adjusted mean (SD) BMI-for-age z score than those not exposed (1.06 [0.05] vs 0.89 [0.09]; P = .03), whereas those whose exposure commenced after the first year of life did not (1.02 [0.06] vs 0.89 [0.09]; P = .10).In this study, repeated antibiotic exposure in early childhood was associated with higher mean BMI-for-age z score and an increased likelihood of obesity. Future research could examine whether interventions such as antibiotic stewardship programs, which are designed to reduce overprescribing of antibiotics, also reduce early childhood obesity.
The Pathogenesis of Nodding Syndrome
Authors: Tory P. Johnson, James Sejvar, Thomas B. Nutman, Avindra Nath
Journal: Annual Review of Pathology Mechanisms of Disease (2020)

Nodding syndrome is a rare, enigmatic form of pediatric epilepsy that has occurred in an epidemic fashion beginning in the early 2000s in geographically distinct regions of Africa. Despite extensive investigation, the etiology of nodding syndrome remains unclear, although much progress has been made in understanding the pathogenesis of the disease, as well as in treatment and prevention. Nodding syndrome is recognized as a defined disease entity, but it is likely one manifestation along a continuum of Onchocerca volvulus–associated neurological complications. This review examines the epidemiology of nodding syndrome and its association with environmental factors. It provides a critical analysis of the data that support or contradict the leading hypotheses of the etiologies underlying the pathogenesis of the syndrome. It also highlights the important progress made in treating and preventing this devastating neurological disease and prioritizes important areas for future research.
Lung Microbiota Predict Clinical Outcomes in Critically Ill Patients
Authors: Robert P. Dickson, Marcus J. Schultz, Tom van der Poll, Laura R. Schouten, Nicole R. Falkowski, Jenna E. Luth, Michael W. Sjoding, Christopher A. Brown, Rishi Chanderraj, Gary B. Huffnagle, Lieuwe D. J. Bos, F. M. de Beer, L. D. Bos, T. A. Claushuis, G. J. Glas, J. Horn, A. J. Hoogendijk, R. T. van Hooijdonk, M. A. Huson, M. D. de Jong, N. P. Juffermans, W. A. Lagrand, T. van der Poll, B. Scicluna, L. R. Schouten, M. J. Schultz, K. F. van der Sluijs, M. Straat, L. A. van Vught, L. Wieske, M. A. Wiewel, E. Witteveen
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

Recent studies have revealed that, in critically ill patients, lung microbiota are altered and correlate with alveolar inflammation. The clinical significance of altered lung bacteria in critical illness is unknown.
Duchenne Screening Test Is OK’d
Authors: Rebecca Voelker
Journal: JAMA (2020)

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Natural products-based polypharmacological modulation of the peripheral immune system for the treatment of neuropsychiatric disorders
Authors: Simon Wing-Fai Mok, Vincent Kam-Wai Wong, Hang-Hong Lo, Ivo Ricardo de Seabra Rodrigues Dias, Elaine Lai-Han Leung, Betty Yuen-Kwan Law, Liang Liu
Journal: Pharmacology & Therapeutics (2020)