tbuckley/cabot-search huggingface dataset:
Insights into the design and interpretation of iCLIP experiments
Authors: Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W. Hentze, Andreas E. Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R. Sibley, Kathi Zarnack, Jernej Ule
Journal: Genome biology (2017)

Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis. This variety of approaches can create challenges for a novice user and can hamper insights from multi-study comparisons. Here, we produce data with multiple variants of CLIP and evaluate the data with various computational methods to better understand their suitability. We perform experiments for PTBP1 and eIF4A3 using individual-nucleotide resolution CLIP (iCLIP), employing either UV-C or photoactivatable 4-thiouridine (4SU) combined with UV-A crosslinking and compare the results with published data. As previously noted, the positions of complementary DNA (cDNA)-starts depend on cDNA length in several iCLIP experiments and we now find that this is caused by constrained cDNA-ends, which can result from the sequence and structure constraints of RNA fragmentation. These constraints are overcome when fragmentation by RNase I is efficient and when a broad cDNA size range is obtained. Our study also shows that if RNase does not efficiently cut within the binding sites, the original CLIP method is less capable of identifying the longer binding sites of RBPs. In contrast, we show that a broad size range of cDNAs in iCLIP allows the cDNA-starts to efficiently delineate the complete RNA-binding sites. We demonstrate the advantage of iCLIP and related methods that can amplify cDNAs that truncate at crosslink sites and we show that computational analyses based on cDNAs-starts are appropriate for such methods.
Abstract 14: Estrone Is Neuroprotective in Rats Following Traumatic Brain Injury
Authors: Joshua Gatson, Ming-Mei Liu, Kareem Abdelfattah, Jane G Wigginton, James Simpkins, Joseph P Minei
Journal: Circulation (2011)

Introduction: In various animal and human studies, early administration of 17 beta-estradiol, a strong anti-oxidant, anti-inflammatory, and anti-apoptotic agent significantly decreases the severity...
Abstract 2124: Accuracy of T2-weighted Cardiac Magnetic Resonance in Detecting Myocardial Edema in Acute Myocardial Infarction is Strongly Influenced by Microvascular Obstruction.
Authors: Yoko Mikami, Hajime Sakuma, Motonori Nagata, Nanaka Ishida, Tairo Kurita, Takashi Tanigawa, Katsuya Onishi, Issei Komuro, Kan Takeda, Masaaki Ito
Journal: Circulation (2007)

Background: High signal intensity (SI) on T2-weighted Cardiac Magnetic Resonance (CMR) indicates infarct-associated myocardial edema in patients with acute myocardial infarction (MI). However, erythrocytes leaking from capillaries in infarct tissue may result in reduced signal on T2W CMR due to T2 shortening. The purpose of this study was to determine if detection of myocardial edema with T2-weighted CMR is influenced by microvascular obstruction (MO- ). Methods: Thirty-seven patients underwent black blood T2 weighted MRI with a spectral presaturation with inversion recovery fat saturation method, rest perfusion MRI and late gadolinium enhanced (LGE) MRI 5.4±3.1 days after onsets. The presence and transmural extent of LGE and MO were analyzed based on a 16-segment model. The relative SI compared with remote normal myocardium was determined in the infarction and peri-infarction zones on T2 weighted MRI, by using the mean + 2SD of the SI in normal segments as a threshold. Results: LGE was observed in 37 (100%) of 37 patients and MO in 19 (51%) of 37 patients. The SI in LGE segments without MO and the SI in periinfarct zones were significantly higher than those in normal segments (relative SI 1.84±0.5, p&lt;0.001 and 1.69±0.18, p&lt;0.001, respectively). However, no significant difference was found between the SI in MO segments and the SI in normal segments (relative SI 1.12±0.24, p=N.S.). The sensitivity of T2 weighted MRI for detecting edema in acute MI was 95% (73/77) in the LGE segments without MO, but was reduced to 30% (22/73) in the segments with MO. Myocardial edema was completely missed on T2 weighted MRI in 2 patients with severe MO. Conclusions: Although T2-weighted CMR is highly sensitive in detecting myocardial edema in the segments without MO, reduced T2 signal intensity in MO segments can be an important pitfall in characterizing the area of the acute event.
Childhood Blood Lead Levels in Children Aged &lt;5 Years — United States, 2009–2014
Authors: Jaime Raymond, Mary Jean Brown
Journal: MMWR Surveillance Summaries (2017)

This report provides data concerning childhood blood lead levels (BLLs) in the United States during 2009-2014. These data were collected and compiled from raw data extracts sent by state and local health departments to CDC's Childhood Blood Lead Surveillance (CBLS) system. These raw data extracts have been de-identified and coded into a format specifically for childhood blood lead reporting. The numbers of children aged <5 years for 2014 are reported with newly confirmed BLLs ≥10 µg/dL by month (Table 1) and geographic location (Table 2). The incidence of BLLs ≥10 µg/dL is reported by age group for 2009-2014 (Table 3). The numbers of children aged <5 years are reported by the prevalence of BLLs 5-9 µg/dL by age group and sample type during 2009-2014 (Tables 4 and 5). For the period 2009-2014, the numbers of children newly confirmed with BLLs ≥70 µg/dL are summarized (Figure 1) as well as the percentage of children with BLLs ≥5 µg/dL (Figure 2).
Pharmacodynamic and Pharmacokinetic Properties of a Novel and Selective HDAC6 Inhibitor, ACY-1215, in Combination with Bortezomib in Multiple Myeloma
Authors: Loredana Santo, Teru Hideshima, Andrew L. Kung, Jen-Chieh Tseng, David Tamang, Min Yang, Matthew Jarpe, John H. van Duzer, Ralph Mazitschek, Walter C Ogier, Diana D. Cirstea, Scott Rodig, Homare Eda, Tyler A. Scullen, Miriam Canavese, James E. Bradner, Kenneth C Anderson, Simon Jones, Noopur S. Raje
Journal: Blood (2011)
PCSK9 inhibitors for hypercholesterolaemia
Authors: Patricia McGettigan, Robin E Ferner
Journal: BMJ (2017)

New drugs, old problems

Statins (hydroxymethyl-glutaryl coenzyme A reductase inhibitors) reduce “bad” low density lipoprotein (LDL) cholesterol concentrations and cardiovascular risk. So too, do better diet and more exercise, which together almost halve rates of coronary event rates when compared with an “unfavourable lifestyle.”3 For some people, though, statins and other medicines cause unacceptable adverse effects or are inadequate to control LDL cholesterol even when combined with lifestyle changes.45 People with familial hypercholesterolaemia have particularly high concentrations of LDL cholesterol, and a new generation of drugs promises to help control this.

The drugs derived from the discovery that a few people with very low LDL cholesterol concentrations have gene mutations that cause loss of function of the enzyme PCSK9 (proprotein convertase-subtilisin/kexin type 9).67 LDL receptors on the surface of hepatocytes bind circulating LDL cholesterol and are then endocytosed. Within the cell, receptors are either recycled or degraded. We now know that PCSK9 switches this process towards degradation, and if PCSK9 is inhibited, more LDL receptors are recycled to the cell surface, where they can take up more LDL cholesterol.

This mechanistic insight has led to two …
Single Institution Experience with Two High-Dose Chemotherapy (HDC) Conditioning Regimens Prior to Autologous Stem Cell Transplant (ASCT) for Multiple Myeloma (MM).
Authors: Don M. Benson, Patrick J. Elder, Thomas Lin, William Blum, Sam Penza, Belinda Avalos, John C. Byrd, Edward Copelan, Sherif S. Farag
Journal: Blood (2004)
Diagnosis and management of an acute knee injury
Authors: Duncan Steele, William Morley
Journal: BMJ (2017)

A 47 year old presented to the emergency department with a severely painful left knee after she was hit while skiing by a fellow skier who approached at high speed from behind. The pain occurred immediately after impact with the skier, with marked general swelling of the joint and she was unable to bear weight. On examination, the limb was neurovascularly intact and the skin was not broken. She had no relevant medical, family, or social history. Anteroposterior (AP) and lateral x rays of her left knee were taken (fig 1⇓).



Fig 1  Anteroposterior radiograph of patient’s left knee



1. What does the radiograph show and what is the diagnosis?

2. How would you classify this injury?

3. How would you manage this patient?

### 1. What does the radiograph show and what is the diagnosis?

#### Short answer

The AP radiograph shows a fracture line extending from the medial proximal tibia border and a vertical fracture line extending into the joint. The lateral image shows some posterior displacement of the segment. The diagnosis is tibial plateau fracture.

#### Discussion

Tibial plateau fractures are intra-articular fractures that show extension of the fracture line into the joint surface of the proximal tibia. They can exist in isolation or be accompanied by other injuries either to local structures of the knee or elsewhere on the patient. Identifying extension into the joint is vital as it affects the urgency and decision making process for treatment, as well as the prognosis. Neurovascular status is a key component in evaluation of the injury, as the common peroneal nerve …
Influence of Platelet and White Blood Cell Counts until Major Thrombosis: Analysis from a Patient Registry in Essential Thrombocythemia
Authors: Veronika Buxhofer-Ausch, Michael Steurer, Siegfried Sormann, Ernst Schloegel, Wolfgang Schimetta, Bettina Gisslinger, Reinhard Ruckser, Martin Schalling, Guenther A. Gastl, Heinz Gisslinger
Journal: Blood (2015)
Anaemia Management in Patients on Peritoneal Dialysis in Portugal: A Nationwide Multicenter Survey.
Authors: Patrícia Q. Branco, Cristina P. Abreu, Pedro Pessegueiro, Manuel Amoedo, Anabela Rodrigues, Antonio Cabrita, Margarida Bruges, Edgar de Almeida, Mateus Martins Prata
Journal: Blood (2005)
Azacitidine in Patients with Acute Myeloid Leukemia: Assessing the Potential Negative Impact of Elevated Baseline White Blood Cell Count on Outcome
Authors: Lisa Pleyer, Sonja Burgstaller, Reinhard Stauder, Michael Girschikofsky, Werner Linkesch, Michael Pfeilstöcker, Eva Maria Autzinger, Christoph Tinchon, Thamer Sliwa, Alois Lang, Wolfgang R. Sperr, Dietmar Geissler, Peter Krippl, Daniela Voskova, Dieter H. Rossmann, Konstantin Schlick, Josef Thaler, Britta Halter, Sigrid Machherndl-Spandl, Georg Theiler, Peter Valent, Otto Eckmüllner, Richard Greil
Journal: Blood (2014)
Albert Montgomery Kligman—Remembering a Pioneer of Topical Treatment
Authors: Christos C. Zouboulis
Journal: JAMA Dermatology (2017)

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 Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast 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) 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 Dermatology journal
Molecular network analysis of signaling pathways in metastatic breast cancer in patients treated with erlotinib
Authors: R. Speer, D. Wallwiener, S. X. Yang, S. M. Swain, J. D. Wulfkuhle, L. A. Liotta, E. F. Petricoin
Journal: Journal of Clinical Oncology (2006)

10064 Erlotinib, an epidermal growth factor receptor tyrosine kinase inhibitor, is under active clinical investigation. It may have profound effects on the cellular molecular network by affecting downstream signaling and inhibiting tumor cell proliferation. Knowledge about the specificity of drug effects on the signaling pathways might enable therapy tailored specifically for each patient’s defect. We examined the activation of cellular signaling pathways involved in cell survival and proliferation in response to erlotinib treatment using a biopsy study set that comprised patient-matched breast cancer metastases from 8 women obtained prior to treatment with erlotinib and after 1 month of therapy. We procured pure cancer cell lysates from very small amounts of frozen tissue by Laser Capture Microdissection (about 60,000 cells). Matching lysates were printed on nitrocellulose and incubated with antibodies against the endpoints of interest. Using the Reverse Phase Protein Microarray technology we were able to generate a portrait of 18 phosphorylated kinase substrate endpoints as well as total expression levels of ERK, EGFR, Her2/neu, and IGF1R that revealed an upregulation of pro-survival pathway signaling in the post-erlotinib treatment set. Especially the measurement of the pro-survival, apoptosis-inhibiting signal transduction pAkt (S473) protein alone showed a statistically significant stronger staining in post-erlotinib treatment samples (p=0.019) in each of the individual patient-matched specimens as well as the entire post-treatment group, showing concordance with the clinical data of the trial, i.e. progressive disease observed for all participating patients. The results indicate the feasibility of this approach to monitor signaling events and molecular pathways in clinical specimens taken during targeted therapy trials. No significant financial relationships to disclose.
Acute pulmonary embolism: mortality prediction by the 2014 European Society of Cardiology risk stratification model
Authors: Savas Ozsu
Journal: European Respiratory Journal (2017)

I eagerly read the recent article by Becattini et al. [1] entitled "Acute pulmonary embolism: mortality prediction by the 2014 European Society of Cardiology risk stratification model". Those authors compared the prognosis of acute pulmonary thromboembolism in 906 patients according to the European Society of Cardiology (ESC) guidelines published in 2008 and 2014. Patients with increased troponin alone are at intermediate risk according to ESC 2014 guidelines <http://ow.ly/v2Jh304ovTw>
Abnormalities of the Hematopoietic Stem Cell Compartment in Children After in Utero Exposure to AZT
Authors: Isabelle Andre-Schmutz, Liliane Dal Cortivo, Emmanuelle M. Six, Sophie Kaltenbach, Isabelle Radford-Weiss, Nicolas Cagnard, Fabienne Cocchiarella, Alexandra Benachi, Laurent Mandelbrot, Fulvio Mavilio, Marina Cavazzana-Calvo, Stéphane Blanche
Journal: Blood (2011)
Preliminary Results from a Phase I Dose Escalation Trial of Ruxolitinib and the PI3Kδ Inhibitor TGR-1202 in Myelofibrosis
Authors: Tamara K Moyo, Andrew Sochacki, Gregory D Ayers, Michael T. Byrne, Stephen A. Strickland, Sanjay R. Mohan, Jill Harrison, Lynne D Berry, Channing V Dudley, Rachel Severs, Laura Dugger, Hari P. Miskin, Amy Cavers, Peter Sportelli, Laura C Michaelis, Ruben A. Mesa, Michael R. Savona
Journal: Blood (2016)
A Phase I Study of Bortezomib (Velcade®) Plus 90yttrium Labeled Ibritumomab Tiuxetan (Zevalin®) in Patients with Relapsed or Refractory B-Cell Non-Hodgkin Lymphoma (NHL)
Authors: Anne Beaven, Thomas C. Shea, Dominic T Moore, Tatyana Feldman, Anastasia Ivanova, Madlyn Ferraro, Peggy Ford, Judy Smith, Andre Goy
Journal: Blood (2008)
Synergistic Interaction of the Heat Shock Protein 90 Inhibitor NVP-AUY922 and the Histone Deacetylase Inhibitor NVP-LBH589 in Multiple Myeloma
Authors: Martin Kaiser, Britta Lamottke, Michael R. Jensen, Cornelia Quadt, Carlos Garcia-Echeverria, Maren Mieth, Ulrike Heider, Orhan Sezer
Journal: Blood (2008)
Allogeneic Stem Cell Transplantation for Acquired Aplastic Anemia: Better Outcome with Bone Marrow as Compared to Peripheral Blood in HLA-Matched Sibling Donor Transplantation and Improved Outcome Over Time After Matched Unrelated Donor Transplantation. A Retrospective Analysis of Transplants Reported to the German Registry for Stem Cell Transplantation (DRST).
Authors: Hubert Schrezenmeier, Ulrike Feldmann, Hellmut Ottinger, Matthias Eder, Monika Führer, Hans-Jochem Kolb, Axel Zander, Karin Kolbe, Dietger Niederwieser, Donald W. Bunjes, Rainer Schwerdtfeger, Rupert Handgretinger, Karl Welte, Carlheinz Müller, Gerhard Ehninger, Jürgen Finke, Dietrich Beelen
Journal: Blood (2009)
Combining standard clinical blood values for improving survival prediction in patients with newly diagnosed brain metastases—development and validation of the LabBM score
Authors: Anna S. Berghoff, Fabian Wolpert, Tim Holland-Letz, Romina Koller, Georg Widhalm, Brigitte Gatterbauer, Karin Dieckmann, Peter Birner, Rupert Bartsch, Christoph C. Zielinski, Michael Weller, Matthias Preusser
Journal: Neuro-Oncology (2016)

We aimed to investigate the potential of standard hematologic and serum biochemical parameters to provide an independent and substantial contribution to the prediction of survival in patients with newly diagnosed brain metastases (BM).Hemoglobin, white blood cell count, platelet count, serum albumin, creatinine, lactate dehydrogenase (LDH), and C-reactive protein (CRP) were assessed at diagnosis of BM in a discovery cohort of 1200 cancer patients. A multivariable Cox regression model was used to derive the LabBM score. The LabBM score was externally validated in an independent cohort consisting of 366 patients.Hemoglobin below lower limit of normal (<LLN; hazard ratio [HR] 1.28; P = .001), platelet count <LLN (HR: 1.36; P = .013), albumin <LLN (HR: 1.19; P = .038), LDH above upper limit of normal (>ULN; HR: 1.51; P < .001), and CRP >ULN (HR: 1.52; P < .001) were associated with survival in a multivariable Cox regression model and were included in the calculation of the LabBM score. Multivariable analysis including the LabBM score and graded prognostic assessment class revealed an independent and significant association of the LabBM score with overall survival (OS) (HR: 1.42; 95% CI: 1.29-1.57; P < .001). The strong and independent association of LabBM score (HR: 1.93; 95% CI: 1.54-2.42) with OS prognosis was confirmed in the validation cohort.Standard clinical blood parameters, combined in the easy-to-calculate LabBM score, provide strong and independent prognostic information in patients with BM. The LabBM score is an objective, inexpensive, and reproducible tool to plan clinical management strategies in BM patients and to improve patient selection and stratification for clinical trials.
Adenosine A2A and Beta-2 Adrenergic Receptor Agonism: Novel Selective and Synergistic Multiple Myeloma Targets Discovered through Systematic Combination Screening
Authors: Richard J. Rickles, Laura Pierce, Thomas Giordano, Winnie F. Tam, William Avery, Melissa Farwell, David Crowe, Mei Chen, Alexander Brown, Vikram Kansra, Steffan T. Nawrocki, Jennifer S Carew, Francis J Giles, Margaret S Lee
Journal: Blood (2008)
Detection of Recurrent Uniparental Disomy and Cryptic Chromosomal Abnormalities in MDS/MPD-U and MDS/MPD-Derived Secondary AML
Authors: Lukasz P. Gondek, Andrew J. Dunbar, Michael A. McDevitt, Hadrian Szpurka, Mikkael A. Sekeres, Jaroslaw P. Maciejewski
Journal: Blood (2007)
ZRSR2 Mutations Cause Dysregulated RNA Splicing in MDS
Authors: Vikas Madan, Deepika Kanojia, Li Jia, Ryoko Okamoto, Aiko Sato-Otsubo, Alexander Kohlmann, Masashi Sanada, Vera Grossmann, Janani Sundaresan, Yuichi Shiraishi, Satoru Miyano, Felicitas Thol, Arnold Ganser, Henry Yang, Torsten Haferlach, Seishi Ogawa, H. Phillip Koeffler
Journal: Blood (2014)
Pathophysiological Significances of Serotonin in Pulmonary Circulation
Authors: Katsura Yoshitake
Journal: Circulation (1967)

The estimation of whole blood serotonin and the related substances and analysis of the haemodynamic effects in serotonin administration were made in man and dog. In cardiac patients with pulmonary hypertension, notwithstanding their elevated reactivity of pulmonary circulation to serotonin, whole blood serotonin levels were markedly lowered. Prominent decrease of whole blood serotonin and blood platelet, increase of urinary excretion of 5-hydroxyindole acetic acid and the rise of the pulmonary arterial pressure were noted in the experimental pulmonary embolism with auto-clot in dogs. Active serotonin seemed to be released from the circulating blood platelet to play some roles in the pulmonary circulatory disturbances.
Therapy of Early Stage Myelodysplastic Syndrome (MDS) with Anti-Thymocyte Globulin (ATG) and Etanercept.
Authors: Bart L. Scott, Aaron L. Holsinger, Aaravind Ramakrishnan, Barry Storer, Pamela S. Becker, Stephen Petersdorf, H. Joachim Deeg
Journal: Blood (2007)
Incidence, Etiology and Outcome of Pleural Effusions in Patients Undergoing Allogeneic Stem Cell Transplantation
Authors: Dipenkumar Modi, Abhinav Deol, Divaya Bhutani, Lawrence G. Lum, Lois Ayash, Voravit Ratanatharathorn, Hyejeong Jang, Seongho Kim, Richard Manasa, Kendra Mellert, Joseph P. Uberti
Journal: Blood (2015)
The MMSET Histone Methyl Transferase Alters Chromatin Structure and Gene Expression in t(4;14) Multiple Myeloma Cells.
Authors: Eva Martinez-Garcia, Relja Popovic, Dong-Joon Min, Christine Will, Julia Meyer, Louis M. Staudt, Laurence Lamy, Josh Lauring, Zhongjun Cheng, Dinshaw Patel, Jonathan D. Licht
Journal: Blood (2009)
Late side-effects and cosmetic results of accelerated partial breast irradiation with interstitial brachytherapy versus whole-breast irradiation after breast-conserving surgery for low-risk invasive and in-situ carcinoma of the female breast: 5-year results of a randomised, controlled, phase 3 trial
Authors: Csaba Polgár, Oliver J Ott, Guido Hildebrandt, Daniela Kauer-Dorner, Hellen Knauerhase, Tibor Major, Jaroslaw Lyczek, José Luis Guinot, Jürgen Dunst, Cristina Gutierrez Miguelez, Pavel Slampa, Michael Allgäuer, Kristina Lössl, Bülent Polat, György Kovács, Arnt-René Fischedick, Rainer Fietkau, Alexandra Resch, Anna Kulik, Leo Arribas, Peter Niehoff, Ferran Guedea, Annika Schlamann, Richard Pötter, Christine Gall, Wolfgang Uter, Vratislav Strnad
Journal: The Lancet Oncology (2017)