tbuckley/cabot-search huggingface dataset:
Evolution and Variation of the SARS-CoV Genome
Authors: Jianfei Hu, Jing Wang, Jing Xu, Wei Li, Yujun Han, Yan Li, Jia Ji, Jia Ye, Zhao Xu, Zizhang Zhang, Wei Wei, Songgang Li, Jun Wang, Jian Wang, Jun Yu, Huanming Yang
Journal: Genomics Proteomics & Bioinformatics (2003)

Abstract Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us.
Inhaled β<sub>2</sub>-Agonists in the Treatment of Asthma
Authors: Paul M. O'Byrne, Huib A.M. Kerstjens
Journal: New England Journal of Medicine (1996)

The introduction of selective, potent inhaled β2-agonists more than 30 years ago revolutionized the treatment of asthma. Until that time, nonselective sympathomimetic agents, such as ephedrine and epinephrine, which stimulate both α- and β-adrenergic receptors and have a very short duration of action, were used to relieve bronchoconstriction. The selective inhaled β2-agonists, such as terbutaline and albuterol, have a longer duration of action (four to six hours), are potent bronchodilators, relieve symptoms rapidly, and protect against the acute bronchoconstriction caused by stimuli such as exercise1 or the inhalation of cold, dry air.2 For these reasons, in . . .
Long-term remissions in lymphoblastic lymphoma.
Authors: J R Bertino
Journal: Journal of Clinical Oncology (1983)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1983.1.9.515 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 6689427 Long-term remissions in lymphoblastic lymphoma. J R BertinoxJ R BertinoSearch for articles by this author https://doi.org/10.1200/JCO.1983.1.9.515 PDF "Long-term remissions in lymphoblastic lymphoma.." Journal of Clinical Oncology, 1(9), p. 515© 1983 by American Society of Clinical Oncology
The use of former phobics in the treatment of phobias
Authors: J Ross
Journal: American Journal of Psychiatry (1980)

The author describes the role of the phobia therapist, usually a former phobic or a mental health worker. The therapist works with a psychiatrist as part of an overall psychiatric treatment program that provides an effective, low-cost approach to the treatment of phobias. Case studies illustrate how the supported-exposure approach, whereby patients are confronted gradually with the fearful situation in a real-life setting, enables phobics to learn how to deal with their phobic symptoms while they are occurring.
Cost effectiveness of DVd vs VAd in newly diagnosed multiple myeloma
Authors: M. A. Hussein, M. Wildgust, J. Fastenau, C. T. Piech
Journal: Journal of Clinical Oncology (2004)

6548 Background: Pegylated liposomal doxorubicin (Doxil/Caelyx) was used in place of doxorubicin in a regimen to treat multiple myeloma. This study evaluates the cost effectiveness (CE) of the regimen. Methods: This economic model evaluates the expected treatment cost and CE of DVd (pegylated liposomal doxorubicin 40 mg/m2 IV Day 1, vincristine 1.4 mg/m2 [max 2.0 mg/m2] IV Day 1, and reduced-dose dexamethasone 40 mg PO Days 1–4) vs VAd (vincristine 0.4 mg/day and conventional doxorubicin 9 mg/m2/day by continuous IV infusion Days 1–4 and reduced-dose dexamethasone 40 mg PO Days 1–4) in patients with newly diagnosed multiple myeloma. A payer's perspective is adopted. Clinical results and resource use are drawn from a randomized, multicenter comparative trial. Resources are valued via the following: 2003 Drug Topics Red Book (drug acquisition); 2001 HCUPnet (inpatient administration fees); and 2003 National Medicare Fee Schedule (outpatient administration fees). CE is calculated as expected cost per objective response (CR/R/PR, SWOG). Results: Data on 175/198 patients (87 DVd; VAd 88) are included. Baseline characteristics are balanced across groups. The percent of patients reporting adverse events is similar, although frequency of grade 3/4 neutropenia is significantly lower for DVd vs VAd (8.0% [95%CI 2.3–13.8] vs 22.7% [14.0–31.5]). Patients in each group received similar number of chemotherapy cycles (DVd 3.4 vs VAd 3.2, P=.53), however, patients receiving DVd required significantly fewer cumulative days in the hospital or outpatient setting for drug administration (4.8 vs 21.6 days, respectively; P<.0001). 4% of the DVd cycles vs 35% of VAd cycles were administered in the hospital (P<.0001). Expected drug costs per cycle are higher for DVd compared to VAd ($3,307.80 vs $155.49), but, total expected costs per patient are lower after accounting for inpatient and outpatient administration fees ($13,972.21 vs $23,507.16). 44% of DVd compared to 39% of VAd patients had an objective response. The CE ratio for DVd is superior to VAd ($31,755.02 vs $60,274.78) due to the lower expected treatment cost. Conclusions: In this model, DVd is equally effective and less costly (dominates) than VAd. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Ortho Biotech Products, L.P. Ortho Biotech Products, L.P. Ortho Biotech Products, L.P. Alza; Ortho Biotech Products, LP
Abstract IA11: Clinical application of next-generation sequencing as a guide to treatment selection
Authors: David B. Solit
Journal: Clinical Cancer Research (2016)

Abstract Profound and durable responses are often observed in early stage clinical trials of novel cancer agents in only a small minority of patients. It has long been postulated that these responses have a definable genetic basis but until now it was not feasible to perform a comprehensive genomic analysis of such patients. Rather, at best a few candidate genes were examined. Technical feasibility thus ensured that oncology trials were designed to identify agents that have a statistically significant benefit in a genetically unselected population, a paradigm that has led to the development of many agents that have modest or no benefit in the vast majority of patients. Agents with profound activity in only a small number of patients were on the other had deemed inactive and abandoned. Our preliminary experience shows that next generation sequencing methodology can now be feasibly applied in the clinical setting to identify previously unrecognized biomarkers of response for agents that show profound responses in only a minority of patients. As an example, we explored the molecular basis of an outlier phenotype, an apparent disease cure of a 51-year old woman with recurrent metastatic small cell carcinoma. The patient was treated on a phase 1 clinical trial that combined topoisomerase I inhibition with an ATP-competitive inhibitor of checkpoint kinase 1 (Chk1). Whole genome sequencing revealed a complex but highly clonal tumor genome with a somatic, missense mutation in the Mre11 complex gene RAD50, which functions to initiate double stranded break (DSB) repair by homologous recombination or non- homologous end joining. Through modeling in yeast, we confirmed that this heterozygous RAD50 mutation, which affects a highly conserved residue and whose wild type copy was focally deleted, conferred sensitivity to topoisomerase I inhibition. Drug sensitivity was markedly enhanced upon genetic ablation of the DNA damage checkpoint pathway, suggesting a synthetic lethal interaction between checkpoint kinase inhibition and clastogenic chemotherapy. These results and additional examples to be presented demonstrate the feasibility of using whole-genome sequencing in the clinical setting to identify previously occult biomarkers of drug sensitivity that can aid in the identification of patients most likely to respond to targeted anticancer drugs. The use of novel clinical trial designs to confirm genotype-phenotype associations will also be discussed. Citation Format: David B. Solit. Clinical application of next-generation sequencing as a guide to treatment selection. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA11.
The psychiatrist's involvement with aged patients
Authors: F K Garetz
Journal: American Journal of Psychiatry (1975)

The author studied via questionnaire psychiatrists' involvement with older patients in relation to their own ages and the nature of their practices. Older psychiatrists see a higher proportion of older patients, advocate more comprehensive treatment, and find older patients more interesting and gratifying. Psychiatrists in general psychiatry and those who have a primarily inpatient practice see the largest proportion of older patients.
Neoplasms Occurring in Aged Fischer Rats, With Special Reference to Testicular, Uterine, and Thyroid Tumors&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: B B Jacobs, R A Huseby
Journal: JNCI Journal of the National Cancer Institute (1967)

Inbred Fischer rats were set aside as nonbreeders specifically to obtain tumors of endocrine organs and endocrine-responsive tissues that might be used in studies of hormone responsivity. The average age at death or autopsy was 675 days for 102 females, and 725 days for 92 males. The tumor data are recorded for those animals that were autopsied (91%). Sixty-eight percent of the males developed testicular interstitial (Leydig) cell tumors and in three fourths these were bilateral. One half of the 20 tumors transplanted into isologous hosts grew to a palpable size. In all instances where growth occurred it was more rapid in castrate than in intact male recipients. At least four of these transplanted tumors produced androgen. Twenty-one percent of the females had macroscopically evident uterine polypoid tumors that were endometrial in origin. Nine of these were transplanted into isologous hosts; 4 grew as sarcomas and 5 maintained their original benign, polyp-like microscopic appearance. Three of these latter tumors grew more rapidly in intact females than in intact males or castrate hosts of either sex. Nine of the aged rats developed grossly evident tumors of the thyroid that morphologically were typical type-gamma nodules. A papillary adenocarcinoma was found in the contralateral lobe of the thyroid of 1 of these rats. Only 1 type-gamma nodule was transplanted, and after 1 year it has grown to approximately 1 cm in diameter in 1 of the 2 untreated male recipients. The incidence of breast, adrenal medullary, and pituitary tumors, as well as of other miscellaneous tumors, was not notably different from that reported by several investigators observing aged rats of different genetic background.
Divorce and child custody resolution: conflicting legal and psychological paradigms
Authors: J W Jacobs
Journal: American Journal of Psychiatry (1986)

The resolution of divorce conflict, especially the determination of child custody, is a major social policy concern of both the legal and mental health professions. The differences between the adversarial and mediation legal approaches parallel the phenomenological/psychoanalytic and the family therapy models of the mental health field. A philosophical and practical relationship exists uniting the adversarial and phenomenological/psychoanalytic traditions, while mediation is strongly aligned with family systems theory and therapy. Each paradigm offers American families alternative methods of resolving disputes. A greater synthesis of paradigms is required to give effective help to divorcing couples and their children.
THU0477 Effect of Recent Spinal Cord Injury on The OPG/RANKL System and Its Relationship with Bone Loss and Antiosteoporotic Response To Denosumab Therapy. Preliminary Results
Authors: L. Gifre, J. Vidal, S. Ruiz-Gaspà, E. Portell, A. Monegal, A. Muxi, N. Guañabens, P. Peris
Journal: Annals of the Rheumatic Diseases (2016)

<h3>Background</h3> Spinal cord injury (SCI) has been associated with a marked increase in bone loss and bone remodeling, especially short-term after injury. However, the pathogenesis and clinical management of this process remain unclear, as well as the role of the key regulators of bone remodeling, the OPG/RANKL system. <h3>Objectives</h3> To analyze the role of the regulators of bone remodeling, OPG and RANKL, in the bone loss associated with recent SCI as well as the effect of antiosteoporotic therapy with denosumab in these bone regulators in a prospective study. <h3>Methods</h3> Twenty-three male patients (aged 18 - 67 years [mean 36 ± 16 years]) with recent (&lt;6 months) complete SCI were prospectively included (43.5% paraplegic, 56.5% tetraplegic). Patients were followed every 6 months. All patients received calcium and vitamin D supplementation. Antiosteoporotic therapy with denosumab was recommended when patients developed densitometric osteoporosis during follow-up. Serum levels of OPG and RANKL (Biomedica, Vienna, Austria), bone turnover markers (PINP, bone ALP, sCTX) and bone mineral density (BMD) at the lumbar spine and total hip were assessed at baseline (99±30 days after SCI), prior to initiating antiosteoporotic treatment (14±4 months post-SCI) and during antiosteoporotic therapy with denosumab (6 months after initiating treatment). The results were compared with a healthy control group. <h3>Results</h3> At baseline, SCI patients showed a significant increase in RANKL serum levels compared to controls (3.4±1.7 vs. 2.3±1.6 pg/mL, p=0.022) which correlated with days-since-SCI (r=0.589, p=0.005) and became undetectable after denosumab treatment in 67% of the patients (p=0.001). OPG serum levels were similar to controls at baseline (87.7±38.7 vs. 71.7±25.4, p=0.1) and did not change with denosumab treatment. No differences were observed in RANKL and OPG levels on comparing tetraplegic vs. paraplegic patients. Neither were RANKL or OPG levels related to the increase in bone loss and bone turnover markers after SCI. Patients with undetectable RANKL serum levels after denosumab treatment did not present further sublesional bone loss but increased total hip BMD (+2.5±1.3%, p=0.005), and bone markers markedly decreased (PINP: -53%, p=0.007; sCTX: -68%, p=0.005). <h3>Conclusions</h3> This study shows that short-term after SCI there is an increase in RANKL serum levels which become undetectable after denosumab treatment. The preventive effect of denosumab on sublesional bone loss further suggests a contributory role of RANKL in this clinical process. <h3>Acknowledgement</h3> Work funded by a Grant from the SEIOMM (Spanish Society for Bone and Mineral Research). <h3>Disclosure of Interest</h3> None declared
Association of Circulating MicroRNA-124-3p Levels With Outcomes After Out-of-Hospital Cardiac Arrest
Authors: Yvan Devaux, Josef Dankiewicz, Antonio Salgado-Somoza, Pascal Stammet, Olivier Collignon, Patrik Gilje, Olof Gidlöf, Lu Zhang, Mélanie Vausort, Christian Hassager, Matthew P. Wise, Michael Kuiper, Hans Friberg, Tobias Cronberg, David Erlinge, Niklas Nielsen
Journal: JAMA Cardiology (2016)

The value of microRNAs (miRNAs) as biomarkers has been investigated in various clinical contexts. Initial small-scale studies suggested that miRNAs might be useful indicators of outcome after cardiac arrest.To address the prognostic value of circulating miRNAs in a large cohort of comatose patients with out-of-hospital cardiac arrest.This substudy of the Target Temperature Management After Cardiac Arrest (TTM) trial, a multicenter randomized, parallel-group, assessor-blinded clinical trial, compared the 6-month neurologic outcomes and survival of patients with cardiac arrest after targeted temperature management at 33°C or 36°C. Five hundred seventy-nine patients who survived the first 24 hours after the return of spontaneous circulation and who had blood samples available for miRNA assessment were enrolled from 29 intensive care units in 9 countries from November 11, 2010, to January 10, 2013. Final follow-up was completed on July 3, 2013, and data were assessed from February 1, 2014, to February 1, 2016.Blood sampling at 48 hours after the return of spontaneous circulation.The primary end point was poor neurologic outcome at 6 months (cerebral performance category score, 3 [severe neurologic sequelae], 4 [coma], or 5 [death]). The secondary end point was survival until the end of the trial. Circulating levels of miRNAs were measured by sequencing and polymerase chain reaction.Of the 579 patients (265 men [80.3%]; mean [SD] age, 63 [12] years), 304 patients (52.5%) had a poor neurologic outcome at 6 months. In the discovery phase with short RNA sequencing in 50 patients, the brain-enriched miR-124-3p level was identified as a candidate prognostic variable for neurologic outcomes. In the validation cohort of 529 patients, mean (SD) levels of miR-124-3p were higher in patients with a poor outcome (8408 [12 465] copies/µL) compared with patients with a good outcome (1842 [3025] copies/μL; P < .001). The miR-124-3p level was significantly associated with neurologic outcomes in the univariable analysis (odds ratio, 6.72; 95% CI, 4.53-9.97). In multivariable analyses using logistic regression, miR-124-3p levels were independently associated with neurologic outcomes (odds ratio, 1.62; 95% CI, 1.13-2.32). In Cox proportional hazards models, higher levels of miR-124-3p were significantly associated with lower survival (hazard ratio, 1.63; 95% CI, 1.37-1.93).Levels of miR-124-3p can be used as prognostication tools for neurologic outcome and survival after out-of-hospital cardiac arrest. Thus, miRNA levels may aid in tailoring health care for patients with cardiac arrest.clinicaltrials.gov Identifier: NCT01020916.
Abstract B1-06: Tumor genotyping using full cloud based pipeline
Authors: Hiroki Ueda, Shogo Yamamoto, Hiroyuki Aburatani
Journal: Cancer Research (2015)

Abstract With emergence of Next Generation Sequencer (NGS), data processing using cloud computing and parallel computation becomes necessary. To process huge NGS data, especially yielded from illumina Hiseq2000 sequencer, we have developed a Hadoop/Spark based mapping soft “Volt” which used spaced hash index and Smith-Waterman algorithm with comparable speed and accuracy to existing NGS mapping software. This software can run both on standalone environment and Hadoop/Spark environment, and in later case, the software is directory integrated using Hadoop API and can read and write data to Hadoop Distributed File System (HDFS), and mapping process is distributed using MapReduce framework. To speedup mapping speed, the software uses two seeds match for near perfect hit, and uses full length seed hit for mismatched hit. Also, we have developed tumor genotyper “karkinos” which detects single nucleotide variation (SNV), copy number variation (CNV), calculate tumor cellularity simultaneously. In this genotyper, we proposed “Open genotyper format”, by using that, each heuristic filtering algorithm can be implemented by add on style development. We integrated software into one analysis pipeline and tested on large cohort of liver cancer data. Detailed algorithm and performance data will be shown at the meeting. Citation Format: Hiroki Ueda, Shogo Yamamoto, Hiroyuki Aburatani. Tumor genotyping using full cloud based pipeline. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-06.
FDA Electronic Bulletin Board
Authors: Stuart L. Nightingale
Journal: JAMA (1995)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
PROGNOSIS FOR ACUTE GLOMERULONEPHRITIS
Authors: P VALLERY-RADOT, P MILLIEZ, C LAROCHE, S HARFOUCHE, P SAMARCQ
Journal: JAMA (1965)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
BCL-2 Family Of Genes Is a Key Regulator In The Pathogenesis Of SF3B1 Mutant and Wild Type MDS With Ring Sideroblasts and Represents a Novel Drug Target In This Disease
Authors: Valeria Visconte, Reda Z Mahfouz, Ali Tabarroki, Edy Hasrouni, Heesun J. Rogers, Yogen Saunthararajah, Brian T. Hill, Matt Kalaycio, Mikkael A. Sekeres, John Barnard, Ramon V. Tiu
Journal: Blood (2013)