tbuckley/cabot-search huggingface dataset:
Outcome of Patients With Early-Stage Infradiaphragmatic Hodgkin Lymphoma: A Comprehensive Analysis From the German Hodgkin Study Group
Authors: Stephanie Sasse, Helen Goergen, Annette Plütschow, Boris Böll, Dennis A. Eichenauer, Michael Fuchs, Karolin Behringer, Joseé M. Zijlstra, Richard Greil, Jana Markova, Max S. Topp, Julia Meissner, Andreas Neubauer, Christian Baues, Andreas Engert, Peter Borchmann, Bastian von Tresckow
Journal: Journal of Clinical Oncology (2018)

Purpose The prognostic effect of isolated infradiaphragmatic involvement in Hodgkin lymphoma (HL) is controversial, and there are little data about patients treated with current therapies. Therefore, we performed a risk factor analysis to focus on isolated nodal infradiaphragmatic disease in patients treated within the German Hodgkin Study Group trials HD13 (clinical trial information: ISRCTN63474366) and HD14 (clinical trial information: ISRCTN04761296) for early-stage HL. Patients and Methods Characteristics and outcomes of patients who had infradiaphragmatic HL were compared with patients who had supradiaphragmatic disease. Progression-free survival (PFS) and overall survival (OS) were estimated according to Kaplan-Meier methods and were compared between groups using the log-rank test and Cox proportional hazards regression, which was also applied for multivariable analyses that adjusted for relevant baseline characteristics. Results Of 2,903 qualified patients, 223 (7.7%) were diagnosed with isolated nodal infradiaphragmatic disease. In general, these patients were older, had a poorer performance status, were more often male, and had the nodular sclerosis subtype less often than those with supradiaphragmatic disease. After a median follow-up time of 51 months, PFS and OS were significantly worse in patients with infradiaphragmatic disease (5-year PFS and OS, 80.1% and 91.5% v 91.2% and 97.6% in patients with supradiaphragmatic disease; each P < .001). In multivariable analyses, infradiaphragmatic HL remained a significant risk factor in terms of PFS (hazard ratio [HR], 1.5; 95% CI, 1.04 to 2.2; P = .03) and OS (HR, 2.0; 95% CI, 1.2 to 3.5; P = .01). However, inferior PFS and OS could not be observed among those patients treated with the more intensive chemotherapy (two cycles of doxorubicin, bleomycin, vinblastine, and dacarbazine [ABVD] in HD13, and two cycles of escalated bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone [BEACOPPescalated] plus two cycles of ABVD in HD14; all patients received 30 Gy of involved-field radiotherapy). Conclusion Early-stage HL that presents with infradiaphragmatic disease only represents a distinct patient group with an inferior outcome. However, this adverse outcome can be outweighed by appropriate combined modality treatment.
Poor Glycemic Control Is Associated With Increased Extracellular Volume Fraction in Diabetes
Authors: Ahmed Al-Badri, Zeba Hashmath, Garrett H. Oldland, Rachana Miller, Khuzaima Javaid, Amer Ahmed Syed, Bilal Ansari, Swetha Gaddam, Walter R. Witschey, Scott R. Akers, Julio A. Chirinos
Journal: Diabetes Care (2018)

OBJECTIVE We assessed whether poor glycemic control is associated with an increase in myocardial fibrosis among adults with diabetes. RESEARCH DESIGN AND METHODS We studied 47 adults with type 2 diabetes and stratified them into three groups according to their hemoglobin A1c (HbA1c) level: &amp;lt;6.5% (group 1; n = 12), 6.5–7.5% (group 2; n = 20), and &amp;gt;7.5% (group 3; n = 15). Left ventricular (LV) mass was assessed using cardiac MRI. The extracellular volume fraction (ECVF), an index of myocardial fibrosis, was measured by using myocardial T1 mapping before and after the administration of a gadolinium-based contrast agent. RESULTS Mean HbA1c was 5.84 ± 0.16%, 6.89 ± 0.14%, and 8.57 ± 0.2% in groups 1, 2, and 3, respectively. LV mass was not significantly different between the groups. The myocardial ECVF was significantly greater in groups 2 (mean 27.6% [95% CI 24.8–30.3]) and 3 (27.6% [24.4–30.8]) than in group 1 (21.1% [17.5–24.7]; P = 0.015). After adjusting for age, sex, BMI, blood pressure, and estimated glomerular filtration rate, the myocardial ECVF was significantly greater in groups 2 (27.4% [24.4–30.4]) and 3 (28% [24.5–31.5]) than in group 1 (20.9% [17.1–24.6]; P = 0.0156, ANCOVA). CONCLUSIONS An increased myocardial ECVF, suggesting myocardial fibrosis, is independently associated with poor glycemic control among adults with diabetes. Further research should assess whether tight glycemic control can revert fibrosis to healthy myocardium or ameliorate it and its adverse clinical consequences.
Use of dual-energy CT to detect and depict bone marrow oedema in rheumatoid arthritis: is it ready to substitute MRI?
Authors: Haijun Wu, Guangfeng Zhang, Xiaoyu Huang, Changhong Liang
Journal: Annals of the Rheumatic Diseases (2018)

MRI can visualise and depict bone marrow oedema, which is known to be a strong independent predictor for radiographic progression in patients with rheumatoid arthritis (RA).1 2 Recent advances in dual-energy CT have enabled the direct visualisation of traumatic bone marrow oedema with high sensitivity and specificity through implementation of virtual non-calcium (VNCa) images.3–7

We have recently read Jans and colleagues’ letter8 entitled, ‘Dual-energy CT: a new imaging modality for bone marrow edema in rheumatoid arthritis,’ published online this June, which mentioned the use of dual-energy CT to visualise bone marrow oedema of the hand and wrist in patients with active RA and deduced that the colour-coded VNCa images could differentiate normal bone marrow from bone marrow oedema and corresponded well to bone …
Complete response to ipilimumab and nivolumab therapy in a patient with extensive extrapulmonary high-grade small cell carcinoma of the pancreas and HIV infection
Authors: Muhammad Husnain, Wungki Park, Juan Carlos Ramos, Thomas E. Johnson, Joseph Chan, Arvind Dasari, Raja Mudad, Peter J. Hosein
Journal: Journal for ImmunoTherapy of Cancer (2018)

<h3>Background</h3> Immune checkpoint inhibitors (CPIs) have shown promising results in many solid tumors. There are limited data on the safety and efficacy of these drugs in HIV infected patients as they have traditionally been excluded from CPIs clinical trials. <h3>Case presentation</h3> We present a case of an HIV-positive patient with extensive extrapulmonary high-grade small cell carcinoma who was treated with dual CPIs (nivolumab and ipilimumab) with a complete response to therapy and with a manageable safety profile. We performed a comprehensive literature review identifying 62 total HIV positive cases treated with CPIs showing this to be a potentially safe option in HIV-positive patients. <h3>Conclusion</h3> HIV infection is not an absolute contraindication to CPI therapy. Our case and others provide justification for ongoing trials of CPI therapy in patients with HIV infection, a group that has traditionally been excluded from clinical trials.
Evaluating latent tuberculosis infection diagnostics using latent class analysis
Authors: Jason E Stout, Yanjue Wu, Christine S Ho, April C Pettit, Pei-Jean Feng, Dolly J Katz, Smita Ghosh, Thara Venkatappa, Ruiyan Luo
Journal: Thorax (2018)

Background Lack of a gold standard for latent TB infection has precluded direct measurement of test characteristics of the tuberculin skin test and interferon-γ release assays (QuantiFERON Gold In-Tube and T-SPOT.TB). Objective We estimated test sensitivity/specificity and latent TB infection prevalence in a prospective, US-based cohort of 10 740 participants at high risk for latent infection. Methods Bayesian latent class analysis was used to estimate test sensitivity/specificity and latent TB infection prevalence among subgroups based on age, foreign birth outside the USA and HIV infection. Results Latent TB infection prevalence varied from 4.0% among foreign-born, HIV-seronegative persons aged &lt;5 years to 34.0% among foreign-born, HIV-seronegative persons aged ≥5 years. Test sensitivity ranged from 45.8% for the T-SPOT.TB among foreign-born, HIV-seropositive persons aged ≥5 years to 80.7% for the tuberculin skin test among foreign-born, HIV-seronegative persons aged ≥5 years. The skin test was less specific than either interferon-γ release assay, particularly among foreign-born populations (eg, the skin test had 70.0% specificity among foreign-born, HIV-seronegative persons aged ≥5 years vs 98.5% and 99.3% specificity for the QuantiFERON and T-SPOT.TB, respectively). The tuberculin skin test’s positive predictive value ranged from 10.0% among foreign-born children aged &lt;5 years to 69.2% among foreign-born, HIV-seropositive persons aged ≥5 years; the positive predictive values of the QuantiFERON (41.4%) and T-SPOT.TB (77.5%) were also low among US-born, HIV-seropositive persons aged ≥5 years. Conclusions These data reinforce guidelines preferring interferon-γ release assays for foreign-born populations and recommending against screening populations at low risk for latent TB infection. Trial registration number NCT01622140 .
Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human
Authors: Karol Szlachta, Ryan G. Thys, Naomi D. Atkin, Levi C. T. Pierce, Stefan Bekiranov, Yuh-Hwa Wang
Journal: Genome biology (2018)

Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of high propensity to form stable DNA secondary structure across the human genome using Mfold and ViennaRNA programs with parameters for analyzing DNA.The promoter-proximal regions of genes with paused transcription are significantly and energetically more favorable to form DNA secondary structure than non-paused genes or genes without RNA polymerase II (Pol II) binding. Using Pol II ChIP-seq, GRO-seq, NET-seq, and mNET-seq data, we arrive at a robust set of criteria for Pol II pausing, independent of annotation, and find that a highly stable secondary structure is likely to form about 10-50 nucleotides upstream of a Pol II pausing site. Structure probing data confirm the existence of DNA secondary structures enriched at the promoter-proximal regions of paused genes in human cells. Using an in vitro transcription assay, we demonstrate that Pol II pausing at HSPA1B, a human heat shock gene, is affected by manipulating DNA secondary structure upstream of the pausing site.Our results indicate alternative DNA secondary structure formation as a mechanism for how GC-rich sequences regulate RNA Pol II promoter-proximal pausing genome-wide.
Resultados del tratamiento endoscópico en pacientes con pancreas divisum sintomático
Authors: S López, J Carrascosa, D Oyón, A Elosua, L Aburruza, G González, F Juanmartiñena, J Eguaras, JJ Vila
Journal: Endoscopy (2017)

Las indicaciones de tratamiento endoscópico del páncreas divisum (PD) incluyen la pancreatitis recurrente, dolor pancreático y pancreatitis crónica.
Estudio de la eficacia y seguridad del drenaje transmural de la vesícula biliar (DTVB) combinado con CPRE en una sola sesión
Authors: R Torres Yuste, FJ García Alonso, N Mora Cuadrado, M Cimavilla Román, AY Carbajo López, I Péñas Herrero, R Sánchez-Ocaña Hernández, S Sevilla Ribota, C De La Serna Higuera, M Pérez-Miranda Castillo
Journal: Endoscopy (2017)

Cada vez se usan con más frecuencia procedimientos endoscópicos combinados con CPRE (ecoendoscopia de estadificación, prótesis duodenal). El abordaje de la vesícula en un tiempo es preferible al abordaje diferido en los pacientes con coledocolitiasis. La ecoendoscopia permite el DTVB, pero no se ha descrito todavía el uso combinado del DTVB con la CPRE.
Epidemiology, diagnosis, and course of brief psychoses
Authors: E Susser, S Fennig, L Jandorf, X Amador, E Bromet
Journal: American Journal of Psychiatry (1995)

This study investigated acute and nonacute brief psychoses. On the basis of previous work, the authors proposed that 1) acute brief psychoses occur predominantly in females, 2) they often do not conform to the diagnoses of DSM-III-R, 3) they are temporally stable, and 4) nonacute brief psychoses do not share these distinctive features.The data are from a follow-up study of 221 first-admission patients with affective and nonaffective psychoses. Patients were given extensive assessments at initial evaluation, 6-month follow-up, and 24-month follow-up. The research team made consensus ratings of the presence of psychosis, DSM-III-R diagnosis, mode of onset of disorder, and course of disorder. Brief psychoses were defined by a diagnosis of nonaffective psychosis at the initial evaluation and a rating of full remission at 6-month follow-up; acute brief psychoses met the additional criterion of acute onset as defined by ICD-10.Twenty (9%) of the 221 psychoses were brief psychoses. Only seven (3%) were acute brief psychoses, but among these, six occurred in women, five were undiagnosable, and none had evolved into an affective disorder or a chronic disorder by the time of the 24-month follow-up. The 13 nonacute brief psychoses did not exhibit distinctive features, and five of them later evolved into chronic disorders.Acute brief psychoses emerged as a highly distinctive and temporally stable form of psychosis that may merit a separate diagnostic classification. The more numerous nonacute brief psychoses may represent mild forms of nonaffective psychoses such as schizophrenia.
LESS THAN IT MEETS THE EYE
Authors: C Ghaoui, A Ferreira, E Mahfouz, H Piessevaux, P Deprez
Journal: Endoscopy (2018)

A 78-year-old patient with previous history of coronary artery disease presented to the emergency department with recent onset abdominal pain and fever. He was diagnosed with cholecystitis and treated medically. Two weeks later, he presented with cholestasis and dilated intrahepatic bile ducts on abdominal US. An EUS was then performed, showing a thickened gallbladder and common hepatic duct compatible with cholecystitis and inflammation due to spontaneous calculus migration. The patient was discharged without cholecystectomy. Due to persistent icteric cholestasis and elevated serum Ca19.9, a second EUS was done showing a thickening of the cystic duct and the common hepatic duct, with an irregular hypoechoic lesion, measuring 1.6 cm probably invading the duodenal wall. An ERCP demonstrated a stricture of the common hepatic duct. Exploration with SpyGlass™ showed a 3 cm long stricture extending to the cystic duct, with a nodular mucosa and irregular dilated vessels. The hepatic hilum was normal. The guided biopsies taken using SpyBite™ forceps and the brush cytology showed signs of inflammation and were negative for neoplasia. The CT-scan showed a thickening of the common hepatic duct extending to the right hepatic and cystic ducts with encasement of the common hepatic artery, right hepatic artery, and the distal portal vein and an abutment of the left hepatic artery. A PET-CT showed a suspicious, hypermetabolic thickening of the common hepatic duct without regional lymph node metastases nor distant metastases. The findings were considered suggestive of a Klatskin IIIA tumor. The patient had a cholecystectomy with resection of the common hepatic and bile duct above the pancreas with right and left hepatico-jejunal anastomosis. The histopathology results were negative for neoplastic tissue. The findings were compatible with a severe chronic inflammation of the gallbladder with severe fibrosis.
Abstract 16005: Highly Efficient Derivation of Human Pacemaker Cells From Pluripotent Stem Cells in Chemically Defined Conditions
Authors: Zaniar Ghazizadeh, Seyedeh Faranak Fattahi, Mehdi Sharifi-tabar, Shahab Mirshahvaladi, Parisa Shabani, Hananeh Fonoudi, Hossein Baharvand, Bong Hee Lee, Nasser Aghdami, Todd Evans, Shuibing Chen, Ghasem H Salekdeh
Journal: Circulation (2015)

The cardiac conduction system is a complex network of cells that together orchestrate the rhythmic and coordinated depolarization of the heart. Dysfunction of the cardiac conduction system plays a central role in the pathogenesis of arrhythmia. While much progress has been made understanding cardiomyocyte differentiation, the molecular mechanisms regulating the specification and patterning of cells that form this conductive network is largely unknown. The LIM-homeodomain transcription factor ISL1 is highly expressed in the secondary heart field (SHF) progenitor population that makes a substantial contribution to the developing heart, comprising most cells in the right ventricle, both atria and pacemaker cells. Pacemaker cells comprise the most proximal component of the cardiac conduction system, which have been proposed as the source of most arrhythmogenic events. Their dominance on other spontaneous beating cell types makes them a suitable target for pharmacologic compounds, making access to this cell lineage necessary for the study of new therapeutic agents. To identify the signaling pathways that control the differentiation of human embryonic stem cell (hESC)-derived SHF cells into pacemaker cells, we performed RNA sequencing to compare the hESC-derived ISL1 + population, non-enriched population and undifferentiated hESCs. Furthermore, using a small molecule screen we identified compounds that can improve differentiation of hESCs toward pacemaker cells. Pathway analysis identified the Wnt pathway as the most significant regulator of SHF specification. Further differentiation of human pluripotent stem cells by stage-specific activation of BMP and WNT signaling pathways resulted in phenotypic pacemaker cells, which display morphological characteristics. More than 80% of these cells stained positively for HCN4, Contactin2(CNTN2) and GATA6, key markers of pacemaker cells. The differentiated cells express pacemaker markers, including CNTN2, TBX2, TBX3, HCN4, TBX18, GATA6 indicated by qRT-PCR. They show inward potassium currents through HCN channels in patch clamp experiments. Our data provides a new strategy to obtain human cardiac conduction cells in large scale for disease modeling, drug screening and cell therapy.
Ankle-Brachial Index Screening and Improving Peripheral Artery Disease Detection and Outcomes
Authors: Mary M. McDermott, Michael H. Criqui
Journal: JAMA (2018)

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Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia
Authors: Ruben Garrido-Oter, Ryohei Thomas Nakano, Nina Dombrowski, Ka-Wai Ma, Alice C. McHardy, Paul Schulze-Lefert
Journal: Cell Host & Microbe (2018)

Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is a characteristic trait of Rhizobiales in Arabidopsis thaliana, whereas interference with plant immunity constitutes a separate, strain-specific phenotype of root commensal Alphaproteobacteria. Additional studies with a tripartite gnotobiotic plant system reveal that these traits operate in a modular fashion and thus might be relevant to microbial homeostasis in healthy roots.
Letter by Kikkert et al Regarding Article, “Effect of Intravenous Fentanyl on Ticagrelor Absorption and Platelet Inhibition Among Patients Undergoing Percutaneous Coronary Intervention: The PACIFY Randomized Clinical Trial (Platelet Aggregation With Ticagrelor Inhibition and Fentanyl)”
Authors: Wouter J. Kikkert, Ronak Delewi, Bimmer E.P.M. Claessen
Journal: Circulation (2018)
Margaret McCartney: If screening is worth doing, it’s worth doing well
Authors: Margaret McCartney
Journal: BMJ (2018)

GlasgowAtrial fibrillation is common, strokes resulting from it are often preventable, it's often diagnosed coincidentally, and some people have the condition but no diagnosis.Screening for atrial fibrillation, therefore, should get under way without delay: on the face of it, like so much in medicine, such thinking seems to make sense.After all, we have gadgets to make the diagnosis quickly and cheaply in primary care (or anywhere, if you have a smartphone).And a range of anticoagulants don't require monitoring and are coming down in price.This line of argument is also popular, especially with the political classes.As a result we see numerous "innovation" projects pushing screening, with few people standing in the way.NICE has proposed documenting pulse rhythm as a quality indicator in patients with conditions including hypertension and ischaemic heart disease. 1 A report for the Scottish parliament's Cross Party Group on Heart Disease and Stroke recommended "case finding" for at-risk groups, including all over 65s. 2 There's a push to screen more people, through the Academic Health Science Networks (one of whose aims is "fostering opportunities for industry"), 3 and pilot studies claim "lifesaving" pathways for atrial fibrillation screening in people attending pharmacies. 4 But what might seem to make logical sense is challenged by evidence and the gaps in it.
Abstract 12104: Prospective Study Using a New Formula Incorporating Contact Force, Radiofrequency Power and Application Time (Force-Power-Time Index) for Quantifying Lesion Formation to Guide Long Continuous Atrial lesions in the Beating Canine Heart
Authors: Hiroshi Nakagawa, Atsushi Ikeda, Assaf Govari, Thanassis Papaioannou, Garth Constantine, Meir Bar-Tal, Erez Silberschein, Eitan Saba-Keren, Assaf Rubissa, Tushar Sharma, Jan V Pitha, Ralph Lazzara, Warren M Jackman
Journal: Circulation (2013)

Introduction: In a previous study on radiofrequency (RF) ablation in the canine right and left ventricle, we found that lesion depth was predicted accurately (± 1mm) by a logarithmic function of co...
Genomic and outcome analyses of Ph-like ALL in NCI standard-risk patients: a report from the Children’s Oncology Group
Authors: Kathryn G. Roberts, Shalini C. Reshmi, Richard C. Harvey, I-Ming Chen, Kinnari Patel, Eileen Stonerock, Heather Jenkins, Yunfeng Dai, Marc Valentine, Zhaohui Gu, Yaqi Zhao, Jinghui Zhang, Debbie Payne-Turner, Meenakshi Devidas, Nyla A. Heerema, Andrew J. Carroll, Elizabeth A. Raetz, Michael J. Borowitz, Brent L. Wood, Leonard A. Mattano, Kelly W. Maloney, William L. Carroll, Mignon L. Loh, Cheryl L. Willman, Julie M. Gastier-Foster, Charles G. Mullighan, Stephen P. Hunger
Journal: Blood (2018)