tbuckley/cabot-search huggingface dataset:
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Authors: Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
Journal: Genome biology (2017)

Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes. We have carried out an unbiased global analysis of m5C in total and nuclear poly(A) RNA of mouse embryonic stem cells and murine brain. We show that there are intriguing differences in these samples and cell compartments with respect to the degree of methylation, functional classification of methylated transcripts, and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences, and mixed patterns of enrichment in the 3′ UTR. Degree and pattern of methylation distinguish transcripts modified in both embryonic stem cells and brain from those methylated in either one of the samples. We also analyze potential correlations between m5C and micro RNA target sites, binding sites of RNA binding proteins, and N6-methyladenosine. Our study presents the first comprehensive picture of cytosine methylation in the epitranscriptome of pluripotent and differentiated stages in the mouse. These data provide an invaluable resource for future studies of function and biological significance of m5C in mRNA in mammals.
FLT3/Internal Tandem Duplication in Paired Presentation and Relapse Pediatric AML Samples.
Authors: Jacqueline Cloos, Christian M. Zwaan, Sophie L. Corthals, Bianca F. Goemans, Quinten Waisfisz, Ursula Creutzig, Dirk Reinhardt, Karel Hählen, Gertjan J.L. Kaspers
Journal: Blood (2004)
In Vivo T-Cell Depletion Does Not Improve Rates of Graft-Versus-Host Disease and Transplantation Outcomes In Patients Undergoing Peripheral Blood Hematopoietic Cell Transplant.
Authors: Abraham S Kanate, Salman Osman, Aaron Cumpston, Gerry Hobbs, Sonia Leadmon, Pamela Bunner, Laura Gibson, William Tse, Jame Abraham, Scot Remick, Michael Craig, Sayed Mehdi Hamadani
Journal: Blood (2010)
Identification of a Small Molecule Inhibitor of RAD52 to Induce Synthetic Lethality in BRCA-Deficient Leukemias
Authors: Katherine Sullivan, Kimberly Cramer-Morales, Daniel L McElroy, David Ostrov, Kimberly Haas, Margaret Nieborowska-Skorska, Wayne Childers, Alexander Mazin, Robert A Hromas, Richard Pomerantz, Tomasz Skorski
Journal: Blood (2015)
Patients with Therapy-Related Myelodysplastic Syndromes (t-MDS) Have Shorter Median Overall Survival Than De Novo MDS: Mayo Clinic Experience
Authors: Muhanad Hreh, Darci Zblewski, Mrinal M Patnaik, Firas Baidoun, Naseema Gangat, Dong Chen, Chris Hook, William J Hogan, Mark R Litzow, Aref Al-Kali
Journal: Blood (2015)
GST T1 and GST M1 Polymorphisms Are Associated with the Risk of Acute Myeloid Leukemia
Authors: Hee Nam Kim, Li Yu, Nan Young Kim, Il-Kwon Lee, Yeo-Kyeoung Kim, Deok-Hwan Yang, Je-Jung Lee, Hee-Je Kim, Woo- Sung Min, Moo-Rim Park, Deog-Yeon Jo, Jong-Ho Won, Jae-Yong Kwak, Hyeoung Joon Kim
Journal: Blood (2008)
First-Line Treatment with Rituximab Combined with Intravenous or Oral Fludarabine for Patients with Extranodal Mucosa Associated Lymphoid Tissue (MALT) Lymphoma.
Authors: Antonio Salar, Eva Domingo-Domènech, Cristina Estany, Miguel Canales, Octavio Servitge, Fernando Gallardo, Guadalupe Fraile, Carlos Montalbán
Journal: Blood (2008)
Genetic Analysis of Candidate Modifier Polymorphisms in β-Thalassemia/Hb E Patients.
Authors: Suthat Fucharoen, Pranee Winichagoon, Orapan Sripichai, Thongperm Munkongdee, Chutima Kumkhaek, Kanjana Vichitumaros, Johanna Whiacre, Ken Abel, Andreas Braun
Journal: Blood (2004)
Analysis of nocturnal actigraphic sleep measures in patients with COPD and their association with daytime physical activity
Authors: Gabriele Spina, Martijn A Spruit, Jennifer Alison, Roberto P Benzo, Peter M A Calverley, Christian F Clarenbach, Richard W Costello, David Donaire-Gonzalez, Selina Dürr, Judith Garcia-Aymerich, Arnoldus J R van Gestel, Marco Gramm, Nidia A Hernandes, Kylie Hill, Nicholas S Hopkinson, Diana Jarreta, Malcolm Kohler, Anne M Kirsten, Jörg D Leuppi, Helgo Magnussen, François Maltais, William D-C Man, Zoe J McKeough, Rafael Mesquita, David Miedinger, Fabio Pitta, Sally J Singh, Frank W J M Smeenk, Ruth Tal-Singer, Barbara Vagaggini, Benjamin Waschki, Henrik Watz, Emiel F M Wouters, Stefanie Zogg, Albertus C den Brinker
Journal: Thorax (2017)

<h3>Background</h3> Sleep disturbances are common in patients with chronic obstructive pulmonary disease (COPD) with a considerable negative impact on their quality of life. However, factors associated with measures of sleep in daily life have not been investigated before nor has the association between sleep and the ability to engage in physical activity on a day-to-day basis been studied. <h3>Aims</h3> To provide insight into the relationship between actigraphic sleep measures and disease severity, exertional dyspnoea, gender and parts of the week; and to investigate the association between sleep measures and next day physical activity. <h3>Methods</h3> Data were analysed from 932 patients with COPD (66% male, 66.4±8.3 years, FEV<sub>1</sub>% predicted=50.8±20.5). Participants had sleep and physical activity continuously monitored using a multisensor activity monitor for a median of 6 days. Linear mixed effects models were applied to investigate the factors associated with sleep impairment and the association between nocturnal sleep and patients9 subsequent daytime physical activity. <h3>Results</h3> Actigraphic estimates of sleep impairment were greater in patients with worse airflow limitation and worse exertional dyspnoea. Patients with better sleep measures (ie, non-fragmented sleep, sleeping bouts ≥225 min, sleep efficiency ≥91% and time spent awake after sleep onset &lt;57 min) spent significantly more time in light (p&lt;0.01) and moderate-to-vigorous physical activity (p&lt;0.01). <h3>Conclusions</h3> There is a relationship between measures of sleep in patients with COPD and the amount of activity they undertake during the waking day. Identifying groups with specific sleep characteristics may be useful information when designing physical activity-enhancing interventions.
Endogenous and Antipsychotic-Related Risks for Diabetes Mellitus in Young People With Schizophrenia: A Danish Population-Based Cohort Study
Authors: Anto P. Rajkumar, Henriette Thisted Horsdal, Theresa Wimberley, Dan Cohen, Ole Mors, Anders D. Børglum, Christiane Gasse
Journal: American Journal of Psychiatry (2017)

Diabetes mellitus contributes to excessive cardiovascular deaths and reduced life expectancy in schizophrenia. This population-based cohort study investigated the endogenous risk for diabetes in antipsychotic-naive schizophrenia and evaluated the risks added by starting antipsychotic treatment in people with schizophrenia.The study followed all people born in Denmark on or after Jan. 1, 1977, until Jan. 1, 2013 (N=2,736,510). The Danish Psychiatric Central Research Register ascertained schizophrenia diagnoses. The Danish National Prescription Registry provided data on prescriptions of antipsychotics. Diabetes was ascertained from the Danish National Patient Register and Danish National Prescription Registry. The authors estimated the endogenous and antipsychotic-related risks for diabetes by using Cox proportional hazards regression models, while accounting for potential confounders.Of the cohort members, 14,118 (0.52%) developed diabetes, and 8,945 (0.33%) developed schizophrenia during follow-up (49,582,279 person-years). The adjusted hazard ratio for diabetes was 3.07 (95% confidence interval [CI], 1.71-5.41) in antipsychotic-naive schizophrenia compared with the general population. The risk for diabetes after starting antipsychotic treatment was significantly higher (adjusted hazard ratio, 3.64; 95% CI, 1.95-6.82) than the risk in antipsychotic-naive schizophrenia, after adjustment for family history of diabetes and other potential confounders. First-line treatment with either first-generation antipsychotics (adjusted hazard ratio, 3.06; 95% CI, 1.32-7.05) or second-generation antipsychotics (adjusted hazard ratio, 3.44; 95% CI, 1.73-6.83) increased the risk for diabetes without a statistically significant difference. Appropriate sensitivity analyses limited to type 2 diabetes corroborated these results.Schizophrenia confers a high endogenous risk for diabetes, and the risk is further increased by both first-generation and second-generation antipsychotics. Early detection and effective treatment of diabetes should be an integral part of multidisciplinary management of schizophrenia regardless of antipsychotic drug exposure.
Guidance for Assessment of Poliovirus Vaccination Status and Vaccination of Children Who Have Received Poliovirus Vaccine Outside the United States
Authors: Mona Marin, Manisha Patel, Steve Oberste, Mark A. Pallansch
Journal: MMWR Morbidity and Mortality Weekly Report (2017)

In 1988, the World Health Assembly resolved to eradicate poliomyelitis (polio). Since then, wild poliovirus (WPV) cases have declined by >99.9%, from an estimated 350,000 cases of polio each year to 74 cases in two countries in 2015 (1). This decrease was achieved primarily through the use of trivalent oral poliovirus vaccine (tOPV), which contains types 1, 2, and 3 live, attenuated polioviruses. Since 2000, the United States has exclusively used inactivated polio vaccine (IPV), which contains all three poliovirus types (2,3). In 2013, the World Health Organization (WHO) set a target of a polio-free world by 2018 (4). Of the three WPV types, type 2 was declared eradicated in September 2015. To remove the risk for infection with circulating type 2 vaccine-derived polioviruses (cVDPV), which can lead to paralysis similar to that caused by WPV, all OPV-using countries simultaneously switched in April 2016 from tOPV to bivalent OPV (bOPV), which contains only types 1 and 3 polioviruses (5). This report summarizes current Advisory Committee on Immunization Practices (ACIP) recommendations for poliovirus vaccination and provides CDC guidance, in the context of the switch from tOPV to bOPV, regarding assessment of vaccination status and vaccination of children who might have received poliovirus vaccine outside the United States, to ensure that children living in the United States (including immigrants and refugees) are protected against all three poliovirus types. This guidance is not new policy and does not change the recommendations of ACIP for poliovirus vaccination in the United States. Children living in the United States who might have received poliovirus vaccination outside the United States should meet ACIP recommendations for poliovirus vaccination, which require protection against all three poliovirus types by age-appropriate vaccination with IPV or tOPV. In the absence of vaccination records indicating receipt of these vaccines, only vaccination or revaccination in accordance with the age-appropriate U.S. IPV schedule is recommended. Serology to assess immunity for children with no or questionable documentation of poliovirus vaccination will no longer be an available option and therefore is no longer recommended, because of increasingly limited availability of antibody testing against type 2 poliovirus.
IL-10 Contributes to the Development of Immunosuppressive CD14+HLA-DRlow/- monocytes in B-Cell Non-Hodgkin’s Lymphoma
Authors: Bing Xiu, Yi Lin, Deanna Grote, Steven Ziesmer, Michael Gustafson, Mary Maas, Zhe Zhang, Allan B Dietz, Aibin Liang, Luis F. Porrata, Anne J. Novak, Zhi-Zhang Yang, Stephen M. Ansell
Journal: Blood (2014)
Arsenic Trioxide with Ascorbic Acid and High-Dose Melphalan Is Safe and Effective for Autotransplantation for Multiple Myeloma.
Authors: Muzaffar H. Qazilbash, Rima M. Saliba, Gaurav Parikh, Chitra Hosing, Floralyn Mendoza, Suhail P. Qureshi, Donna M. Weber, Michael Wang, Thuy Flosser, Daniel R. Couriel, Partow Kebriaei, Uday Popat, Amin Alousi, Marcos de Lima, Richard E. Champlin, Sergio Giralt
Journal: Blood (2007)
Direct Antiglobulin Test, Ferritin and GPI-Negative Cell Populations in Patients with Paroxysmal Nocturnal Hemoglobinuria (PNH) during Eculizumab Therapy: Extravascular Hemolysis Unmasked by Efficient Eculizumab-Mediated Inhibition of Intravascular Hemolysis.
Authors: Bri tta Höchsmann, Markus Rojewski, Willy A Flegel, Hubert Schrezenmeier
Journal: Blood (2008)
“Antitumor Activity of Novel Anti-MM Agents and Combinations, the Proteasome Inhibitor Bortezomib and Multikinase Inhibitor Sorafenib, Both Applied as Monotherapy and in Combination in NOD/SCID-IL2-Receptor-Gamma-chain−/− (NSG) Mice Using a Intratibial Tumor Dissemination approach”.
Authors: Julia Schüler, Dagmar Wider, Dietmar Pfeifer, Josefina Udi, Heinz-Herbert Fiebig, Ralph M. Waesch, Monika Engelhardt
Journal: Blood (2009)
Light‐Mediated Activation of siRNA Release in Diblock Copolymer Assemblies for Controlled Gene Silencing
Authors: Abbygail A. Foster, Chad T. Greco, Matthew D. Green, Thomas H. Epps, Millicent O. Sullivan
Journal: Advanced Healthcare Materials (2015)

Adv. Healthcare Mater., 2015, 4, 760–770 The authors regret that Figure 1C in this article contained errors. The originally published gel image of the siRNA mobility shift assay for siRNA/mPEG-b-P(APNBMA)7.9 polyplexes included samples prepared with gel loading dye (6X, blue, New England Biolabs, Ipswich, MA), whereas all other gel images were prepared with glycerol/water solutions as reported in the experimental section. The correct and complete Figure 1 now appears here, where Figure 1C has been replaced with a new representative image of samples prepared without gel loading dye. Additionally, the corresponding table indicating percentages of free siRNA has been updated. The mPEG-b-P(APNBMA)7.9 polymer encapsulates siRNA more efficiently than reported previously, and this correction is attributed to inadvertent polyplex disassembly caused by components in the loading dye. Please note that the text in the first paragraph of Section 2.1 associated with Figure 1C is no longer relevant.
Reply
Authors: Eun‐Jeong Joo, Yoosoo Chang, Seungho Ryu
Journal: Hepatology (2017)

Potential conflict of interest: Nothing to report. Reply: We thank Dr. Lonardo et al. for their interest in our study1 and for raising important points regarding the interpretation and implication of our results. In our cohort study, we demonstrated that the presence of hepatitis B virus (HBV) infection was associated with a decreased risk of nonalcoholic fatty liver disease (NAFLD) independent of possible confounders.1 It is intriguing that a recent study by Tseng et al. has shown that HBV infection was associated with a reduced risk of acute ischemic stroke.2 Given that NAFLD is a strong and independent predictor of cardiovascular risk, our finding may explain how HBV infection influences the reduced risk of acute ischemic stroke, possibly being mediated by decreased risk of NAFLD. Furthermore, when we examined the longitudinal effects of HBV infection on changes in insulin resistance and lipids using the longitudinal linear mixed effects model,1 the total cholesterol level was found to decrease over time among hepatitis B surface antigen–positive subjects. Other studies have also suggested an inverse association between HBV infection and lipid profile including cholesterol, triglycerides, and low‐density lipoprotein cholesterol.3 Similarly, HBV infection appears to alter lipid metabolism.4 Therefore, the association between HBV infection and decreased risk of cardiometabolic risk observed in prior studies may be also explained by the effects of HBV on lipid metabolism and other as yet undetermined factors. Future studies are needed to explore the links between HBV infection, liver steatosis, and cardiometabolic risk.
Validation of International Working Group (IWG) Response Criteria in Higher-Risk Myelodysplastic Syndromes (MDS): A Report on Behalf of the MDS Clinical Research Consortium (MDS CRC)
Authors: Rami S. Komrokji, Amy E. DeZern, Katrina Zell, Najla H. Al Ali, Christopher Estling, Cassie Zimmerman, Wesley Hand, Francis Brown, Nicole Rizzo, John Barnard, Gail J Roboz, Guillermo Garcia-Manero, David P. Steensma, Mikkael A. Sekeres
Journal: Blood (2015)
Role of microRNA in acute cellular rejection
Authors: Anand V. Kulkarni, Shiv K. Sarin, Ashok Choudhury, S.M. Shashthry, Karan Kumar, Lovkesh Anand
Journal: Hepatology (2017)

Potential conflict of interest: Nothing to report. TO THE EDITOR: In the article by Shaked et al.,1 the authors have succinctly studied the role of microRNA (miRNA) in acute cellular rejection and have shown that distinct miRNA levels profiled from sera at the time of clinical allograft dysfunction can be used to noninvasively diagnose acute cellular rejection (ACR). The results are of great relevance as the incidence of ACR could be as high as 65% 1 year after transplantation.2 Empirical reduction of immunosuppresion to prevent adverse effects increases the risk of graft rejection, and identifying ACR 40 days in advance would therefore be of great benefit to physicians. There are a few concerns regarding this study, however. First, miRNA levels after the patient was started on immunosuppresive agents were not reported. Second, the use of miRNA decoys for miR‐885‐5p and miR‐483‐3p in animal models would have added more weight to the study. Finally, the study included miRNAs that are considered to be of immune cell origin. Hence, it would be worthwhile to know whether there was a correlation between the nature and extent of cellular infiltration in liver biopsy and the miRNA profile in the peripheral blood. The analysis of serum cytokines and their correlation with miRNA profile would have been more authentic and would have shed more light on the role of cytokines in cellular rejection.
Haploidentical Peripheral Blood Stem Cell Transplantation with Post-Transplantation Cyclophosphamide in Primary Refractory Acute Myeloid Leukemia
Authors: Sarita Rani Jaiswal, Sumita Chatterjee, Aditi Chakrabarti, Sneh Bhargava, Ray Kunal, Suparno Chakrabarti, Paul V. O'Donnell
Journal: Blood (2015)
Reply
Authors: Anthony Cousien, Viet Chi Tran, Sylvie Deuffic‐Burban, Marie Jauffret‐Roustide, Jean‐Stéphane Dhersin, Yazdan Yazdanpanah
Journal: Hepatology (2017)

Potential conflict of interest: Sylvie Deuffic‐Burban consults and has received grants from Janssen and MSD and consults for AbbVie, Bristol‐Myers Squibb, Gilead, HEVA, and PHE. Yazdan Yazdanpanah consults and has received grants from Abbott, Bristol‐Myers Squibb, Gilead, MSD, Pfizer, Tibotec, and Viiv and consults for Roche. In their commentary regarding our study on hepatitis C virus (HCV) epidemics in people who inject drugs (PWID) in the Paris area,1 Smith and Rich express their concern about the absence of opioid substitution therapies (OSTs) in our model. The current situation of harm reduction in France is actually implicitly included in our model. Indeed, we fitted the HCV transmission rate from an infected to a susceptible injector using prevalence data. Thus, it reflects the impact of current OST coverage, but also other characteristics, including needle/syringe programs (NSPs), injecting frequency, and products consumed on HCV transmission. A model is a simple representation of reality. When conceptualizing a model, selecting the correct level of complexity can be difficult.2 Simple models may be unable to respond to all questions regarding strategies to fight the disease, and increasing the model complexity results in less precision and more variance in the parameters estimation. The modelers need to find a compromise between complexity and robustness to obtain a model structure "consistent with, and adequate to address, the decision problem and the policy context."2 Because our study focused on the HCV cascade of care, none of the interventions assessed could modify the OST coverage that was assumed to be constant over time. Thus, we did not include this characteristic explicitly in the model structure. OST coverage in France is high: 85% of active injectors (in the last month) reported having been on OST during the last 6 months in an HCV seroprevalence survey (ANRS‐Coquelicot study, unpublished data3), and 80% of "problematic" drug users are on OST in monitoring data from French medical insurance.4 However, there are still ways to improve NSPs in France, given that 33% of PWID report difficulty in accessing sterile syringes.5 We are currently working on the integration of harm reduction in our model to assess the cost‐effectiveness of improvements in NSPs, OSTs, and HCV cascade of care in France.
Safety and Efficacy of Combined Ruxolitinib and Decitabine in Patients with Blast-Phase MPN and Post-MPN AML: Results of a Phase I Study (Myeloproliferative Disorders Research Consortium 109 trial)
Authors: Raajit K. Rampal, John O. Mascarenhas, Heidi E. Kosiorek, Dmitriy Berenzon, Elizabeth Hexner, Camille N. Abboud, Marina Kremyanskaya, Rona Singer Weinberg, Mohamed E Salama, Gianni Tognoni, Giuseppe Prosperini, Alessandra Di Lelio, Eliseo Serone, Lorenzo Marfisi, Lonette Sandy, Mark Lawrence Heaney, Ross L. Levine, Ruben A. Mesa, Amylou C. Dueck, Ronald Hoffman
Journal: Blood (2016)
Alcohol Drinking, Smoking, Past History of Gastroduodenal Ulcer, Height, and Risk of API2-MALT1 Fusion Positive and Negative Gastric MALT Lymphoma Among Japanese.
Authors: Takakazu Kawase, Keitaro Matsuo, Tsuneya Nakamura, Junya Kanda, Hidemi Ito, Satoyo Hosono, Miki Watanabe, Yasushi Yatabe, Yasuo Morishima, Kazuo Tajima, Masao Seto, Shigeo Nakamura, Hideo Tanaka
Journal: Blood (2009)
Thin, Soft, Skin‐Mounted Microfluidic Networks with Capillary Bursting Valves for Chrono‐Sampling of Sweat
Authors: Jungil Choi, Daeshik Kang, Seungyong Han, Sung Bong Kim, John A. Rogers
Journal: Advanced Healthcare Materials (2017)

Systems for time sequential capture of microliter volumes of sweat released from targeted regions of the skin offer the potential to enable analysis of temporal variations in electrolyte balance and biomarker concentration throughout a period of interest. Current methods that rely on absorbent pads taped to the skin do not offer the ease of use in sweat capture needed for quantitative tracking; emerging classes of electronic wearable sweat analysis systems do not directly manage sweat‐induced fluid flows for sample isolation. Here, a thin, soft, “skin‐like” microfluidic platform is introduced that bonds to the skin to allow for collection and storage of sweat in an interconnected set of microreservoirs. Pressure induced by the sweat glands drives flow through a network of microchannels that incorporates capillary bursting valves designed to open at different pressures, for the purpose of passively guiding sweat through the system in sequential fashion. A representative device recovers 1.8 µL volumes of sweat each from 0.8 min of sweating into a set of separate microreservoirs, collected from 0.03 cm 2 area of skin with approximately five glands, corresponding to a sweat rate of 0.60 µL min −1 per gland. Human studies demonstrate applications in the accurate chemical analysis of lactate, sodium, and potassium concentrations and their temporal variations.