tbuckley/cabot-search huggingface dataset:
Reconciling the Numbers: ESTs Versus Protein-Coding Genes
Authors: Anton Nekrutenko
Journal: Molecular Biology and Evolution (2004)

The number of expressed sequences greatly surpasses the estimated number of protein-coding genes in mammalian genomes. An evolutionary approach reveals that only 9% to 14% of human-expressed and mouse-expressed sequences are able to code for proteins. Clustering of these sequences using cross-species relationships suggests that millions of expressed sequences may correspond to only approximately 20,000 distinct protein-coding transcripts.
Quantitative effects of Nf1 inactivation on in vivo hematopoiesis
Authors: Youyan Zhang, Brigit R. Taylor, Kevin Shannon, D. Wade Clapp
Journal: Journal of Clinical Investigation (2001)

The NF1 tumor-suppressor gene is frequently inactivated in juvenile myelomonocytic leukemia, and Nf1 mutant mice model this myeloproliferative disorder (MPD). Competitive repopulation assays were performed to quantify the proliferative advantage of Nf1–/– hematopoietic cells in vivo. Nf1 mutant stem cells demonstrated a growth advantage that was greatest in myeloid lineage cells and least pronounced in T lymphocytes. Surprisingly, although low numbers of Nf1-deficient cells consistently outcompeted wild-type cells, levels of chimerism were stable over months of observation, and MPD was not observed unless threshold numbers of mutant cells were injected. These data showing that normal competitor cells can strongly modulate the growth of mutant populations in vivo have general implications for modeling cancer in the mouse. In particular, strains in which cancer-associated mutations are expressed in fields of target cells may not accurately model early events in tumorigenesis because they eliminate the requirement for a mutant clone to outcompete resident normal cells.
Pegylated interferon for chronic hepatitis C in children affects growth and body composition: Results from the pediatric study of hepatitis C (PEDS-C) trial
Authors: Maureen M. Jonas, William Balistreri, Regino P. Gonzalez-Peralta, Barbara Haber, Steven Lobritto, Parvathi Mohan, Jean P. Molleston, Karen F. Murray, Michael R. Narkewicz, Philip Rosenthal, Kathleen B. Schwarz, Bruce A. Barton, John A. Shepherd, Paul D. Mitchell, Christopher Duggan
Journal: Hepatology (2012)

Weight loss and changes in growth are noted in children treated with interferon alpha (IFN-α). The aim of this study was to prospectively determine changes in weight, height, body mass index (BMI), and body composition during and after treatment of children with hepatitis C virus (HCV). Children treated with pegylated interferon alpha-2a (Peg-IFN-α2a) ± ribavirin in the Pediatric Study of Hepatitis C (PEDS-C) trial underwent anthropometric measurements, dual-energy X-ray absorptiometry scan, as well as dietary and activity assessments during and after treatment. One hundred and fourteen (55% male) children, with a mean age of 11 ± 3 years, were randomized, and 107 received treatment for at least 24 weeks. Subjects were divided into three groups according to duration of treatment: 24 (N = 14), 48 (N = 82), or 72 (N = 11) weeks. Decrements of up to 0.50 z score were observed for weight, height, and BMI while on therapy among all groups (P ≤ 0.01, compared to baseline). In the group treated for 48 weeks, 29 (33%) subjects had greater than 0.5-unit decrement in height-for-age z (HAZ) score. Though weight-for-age and BMI z scores returned to baseline after cessation of therapy, mean HAZ score was slower to rebound, still lower than baseline at 96 weeks post-therapy for the long-treatment duration group (P = 0.03) and lower than baseline in most children treated for 48 weeks. Percent body fat, fat-free mass z scores, and triceps skinfold z scores decreased with therapy. Dietary energy intake and levels of physical activity did not change during treatment.Peg-IFN-α2a was associated with significant changes in body weight, linear growth, BMI, and body composition in children. These effects were generally reversible with cessation of therapy, although HAZ scores had not returned to baseline after 2 years of observation in many. Longer term growth data are needed among children treated for chronic HCV.
Rebuilding Afghanistan's health service is hampered by insecurity and lack of funds
Authors: Klaus Morales
Journal: BMJ (2005)

A basic package of health services, including some antenatal and neonatal care, family planning services, and immunisation programmes, is being rolled out in Afghanistan, a London conference was told last week.

“About half of the population and 70% of all districts are now receiving this basic package,” said Dr Ahmad Jan Naeem, of the Ministry of Public Health in Kabul. However, extending the package, which also includes the provision of some essential drugs, was being hampered by the difficulty of reaching remote areas, continuing insecurity, and a lack of funding, he added.

“Distribution of the work force is a major problem in Afghanistan. Eighty per cent of doctors are in …
[130] ADENOVIRAL GENE DELIVERY OF INTERLEUKIN-10 REDUCES HEPATIC ISCHEMIA-REPERFUSION INJURY IN RATS THRU INHIBITION OF KUPFFER CELL ACTIVATION
Authors: M. Froh, P. Walbrun, S. Netter, R. Wiest, J. Schoelmerich, C. Hellerbrand
Journal: Journal of Hepatology (2007)
892 URSODEOXYCHOLIC ACID (UDCA) IN THE TREATMENT OF INTRAHEPATIC CHOLESTASIS OF PREGNANCY (ICP): A SYSTEMATIC REVIEW AND META-ANALYSES WITH SPECIFIC ASSESSMENT OF FETAL OUTCOME
Authors: V. Di Martirio, L. Sentilhes, H.M. Reyes, A. Glantz, J. Kondrackiene, T. Binder, P.L. Nicastri, A. Locatelli, A. Floreani, I. Hernandez, Y. Bacq
Journal: Journal of Hepatology (2011)
Toward a Science of Consciousness: Journey to the Centers of the Mind
Authors: S. W G Derbyshire
Journal: BMJ (1996)

Susan A Greenfield W H Freeman, £17.95, pp 221 ISBN 0 7167 2723 4

Materialist interpretations of personality and human behaviour are becoming increasingly popular as the trend towards biological psychiatry continues. Within this framework discussion of the materialist basis of human consciousness has been revived, spawning several publications. Among the most recent is Greenfield's Journey to the Centers of the Mind. Books on human consciousness largely follow a similar pattern: all tend to exaggerate the problem, speculate wildly around their claims for a solution, and then collapse in failure a few pages before the end. Greenfield's journey, while enjoyable and readable, is sadly no …
Feasibility of Adjustment of Insulin Dose by Insulin-Requiring Type II Diabetic Patients
Authors: John C Floyd, Martha M Funnell, Imtiaz Kazi, Carolyn Templeton
Journal: Diabetes Care (1990)

Type II (non-insulin-dependent) diabetes accounts for most of the diabetes morbidity and expense, yet no systematic study of the effects of intensification of treatment by such patients who require insulin treatment has been conducted. Therefore, patients were recruited from our diabetes clinics, and by random assignment, experimental and control groups were created (n = 26 and 27, respectively) that were not different at 0 mo regarding 20 demographic, physiological, and treatment variables. Experimental patients practiced an algorithm for adjustment of insulin dosage based on daily prebreakfast capillary blood glucose (CBG) measurements and any symptomatic hypoglycemia. At 2-, 4-, and 6-mo visits, records of CBG measurements were available to the physicians (n = 7), who changed insulin dosages of both groups ad libitum. Feasibility of the experimental treatment is evidenced by study completion by 87% of enrollers, monitoring on 88% of days, accuracy of CBG recording (recorded as percentage of memory meter value, 100.8), weight gain not exceeding that of control subjects, practice of treatment algorithm to effect changes in insulin dosage, modest increase in frequency of mild insulin reactions, and a decrease of glycosylated hemoglobin into the normal range.
946 SHOTGUN PROTEOMICS IDENTIFIES SPECIFIC PROTEIN PROFILES IN APOPTOTIC BODIES FROM BILIARY EPITHELIAL CELLS
Authors: A. Lleo, W. Zhang, W.H. McDonald, D. Friedman, E.H. Seeley, P.S. Leung, P. Invernizzi, M.E. Gershwin
Journal: Journal of Hepatology (2013)
A patient with thalassaemia major and back pain
Authors: D. A Tsitsikas, F. A Barroso, P. Telfer, B. Kaya, J. Evanson, A. Provan
Journal: BMJ (2008)

A 37 year old man with β thalassaemia major presented to the haematology day unit with a three week history of increasing back pain. The pain was aggravated by movement and the patient found it increasingly difficult to walk. He said he felt “wobbly” on his feet. He had no history to indicate sphincter dysfunction. He was regularly transfused and his haemoglobin at presentation was 11.3 g/dl.

On neurological examination, his tone was normal, and he had normal power (5/5) in all muscle groups of his lower limbs. He had brisk knee jerks and, to a lesser extent, ankle jerks bilaterally, with an upgoing plantar response on the right side and an equivocal reaction on the left. He had hypoaesthesia of his legs and torso with a sensory level at T5. He showed no signs of cerebellar dysfunction. His gait was not assessed. The rest of the examination was unremarkable. An urgent MRI scan of the whole spine was performed the same day.⇓



Figure 1 Magnetic resonance image of the patient’s spine



1 What is the clinical diagnosis?

2 What does the magnetic resonance image show?

3 How would you manage this patient immediately and in the long term?

### Short answers 

1 Acute spinal cord compression with a sensory level at T5 caused by extramedullary haematopoiesis.

2 The magnetic resonance image shows spinal cord compression, maximal at T5 and T8, caused by masses of extramedullary haematopoiesis behind the spinal canal compressing the cord.⇓



Figure 2 The magnetic resonance image of the …
Clinical Use of the New Beta-Lactam Antimicrobial Drugs
Authors: GEO. F. BROOKS
Journal: Annals of Internal Medicine (1983)

New beta-lactam antimicrobial agents with extended antibacterial activity for gram-negative bacilli are being developed and marketed. These drugs provide major advances, especially for treatment of serious infections caused by multiresistant organisms. Several of the drugs have been marketed and many more will be available. Some of these drugs are considerably more costly than the older beta-lactams. The large number of new antimicrobial drugs coupled with their high costs pose complex problems for physicians, microbiology laboratories, and pharmacists. Community hospitals, large general hospitals, and tertiary care hospitals have different needs for patient care and will need different formats for unbiased education, susceptibility testing, pharmacy stocking, and controlling or monitoring for inappropriate use.
Estimating Prognosis with the Aid of a Conversational-Mode Computer Program
Authors: Alvan R. Feinstein, Joel F. Rubinstein, Walter A. Ramshaw
Journal: Annals of Internal Medicine (1972)

A "conversational-mode" computer program can search a stored "library" of clinical experience for prognostic information. The library contains coded data for details of the clinical course of a "base population" of 678 patients with primary lung cancer. In estimating prognosis, the clinician at the computer terminal enters data to describe the new patient. The computer determines how many base-population members are identical in the cited characteristics. This first search seldom yields enough identical patients for prognosis. The clinician can reduce the specificity of resemblance by eliminating properties and by converting others into ranges and clusters. After each such modification, the computer indicates the number of library patients with the specified similarities. When the "resemblance group" is large enough, the computer lists the treatment of those patients and the results. All of the critical decisions are made by the clinician, who must choose the properties for a resemblance group and who decides when the group characteristics and size are adequate for prognostic extrapolations. The computer is merely a device for storage, retrieval, quantification, and display of the data needed for decisions.
Foot Infections in Diabetic Patients
Authors: Mark H. Eckman
Journal: JAMA (1995)

To examine the cost-effectiveness of approaches to the diagnosis and treatment of patients with type II (non-insulin-dependent) diabetes mellitus (NIDDM) who have foot infections and suspected osteomyelitis.Decision and cost-effectiveness analyses were performed using a Markov model. We examined the prevalence of osteomyelitis, the major complications and efficacies of long-term antibiotic therapy and surgery, and the performance characteristics of four diagnostic tests (roentgenography, technetium Tc 99m bone scanning, indium in 111-labeled white blood cell scanning, and magnetic resonance imaging). Data were drawn from the English-language literature using MEDLINE searches and bibliographies from selected articles.Primary care.Patients with NIDDM who had foot infections and suspected osteomyelitis but no signs of systemic toxicity.Following hospitalization for surgical débridement and intravenous antibiotic therapy: (1) treatment for presumed soft-tissue infection, (2) culture-guided empiric treatment for presumed osteomyelitis, (3) 71 combinations of diagnostic tests preceding antibiotic therapy for osteomyelitis, (4) 71 combinations of tests preceding amputation, and (5) immediate amputation.Quality-adjusted life expectancy, average costs.Culture-guided empiric treatment for osteomyelitis with 10 weeks of oral antibiotic therapy has similar effectiveness to testing followed by a long course of antibiotic therapy if any test result is positive. However, empiric treatment is the least expensive strategy.Noninvasive testing adds significant expense to the treatment of patients with NIDDM in whom pedal osteomyelitis is suspected, and such testing may result in little improvement in health outcomes. In patients without systemic toxicity, a 10-week course of culture-guided oral antibiotic therapy following surgical débridement may be as effective as and less costly than other approaches.
MicroRNA Signature Obtained From the Comparison of Aggressive With Indolent Non-Hodgkin Lymphomas: Potential Prognostic Value in Mantle-Cell Lymphoma
Authors: Rashmi S. Goswami, Eshetu G. Atenafu, Yali Xuan, Levi Waldron, Patricia P. Reis, Thomas Sun, Alessandro Datti, Wei Xu, John Kuruvilla, David J. Good, Raymond Lai, Alanna J. Church, Wilson S. Lam, Tara Baetz, David P. LeBrun, Laurie H. Sehn, Pedro Farinha, Igor Jurisica, Denis J. Bailey, Randy D. Gascoyne, Michael Crump, Suzanne Kamel-Reid
Journal: Journal of Clinical Oncology (2013)

Mantle-cell lymphoma (MCL) has a variable natural history but is incurable with current therapies. MicroRNAs (miRs) are useful in prognostic assessment of cancer. We determined an miR signature defining aggressiveness in B-cell non-Hodgkin lymphomas (NHL) and assessed whether this signature aids in MCL prognosis.We assessed miR expression in a training set of 43 NHL cases. The miR signature was validated in 44 additional cases and examined on a training set of 119 MCL cases from four institutions in Canada. miRs significantly associated with overall survival were examined in an independent cohort of 114 MCL cases to determine association with patient outcome. miR expression was combined with current clinical prognostic factors to develop an enhanced prognostic model in patients with MCL.Fourteen miRs were differentially expressed between aggressive and indolent NHL; 11 of 14 were validated in an independent set of NHL (excluding MCL). miR-127-3p and miR-615-3p were significantly associated with overall survival in the MCL training set. Their expression was validated in an independent MCL patient set. In comparison with Ki-67, expression of these miRs was more significantly associated with overall survival among patients with MCL. miR-127-3p was combined with Ki-67 to create a new prognostic model for MCL. A similar model was created with miR-615-3p and Mantle Cell Lymphoma International Prognostic Index scores.Eleven miRs are differentially expressed between aggressive and indolent NHL. Two novel miRs were associated with overall survival in MCL and were combined with clinical prognostic models to generate novel prognostic data for patients with MCL.
PHOTOGRAPHING THE EYE-GROUND.
Authors: SHIRLS JACKSON
Journal: JAMA (1901)

The illustration shows a photograph of the eye-ground and the instrument with which it was taken. As the drawing indicates, the instrument is essentially a self-illuminating ophthalmoscope, where a little camera-practically an artificial eye—is substituted for the observer's eye. The patient's head is fixed immovably in the operating-chair, to which the movable arm of the camera is attached. The camera is swung in front of the patient's eye, and is rested firmly upon the cheek with an intervening pad for thermal insulation. The cap at the back of the plate-holder is removed, and with the pupil dilated and the unobstructed eye fixed upon a remote object, a faint inverted image of the fundus may be focused upon the ground glass. The movable collar is fixed by the screw to mark this point upon the scale of diopters, from which a rough estimate of the refraction may be had—a rough optometer
Homeostatic Scaling Requires Group I mGluR Activation Mediated by Homer1a
Authors: Jia-Hua Hu, Joo Min Park, Sungjin Park, Bo Xiao, Marlin H. Dehoff, Sangmok Kim, Takashi Hayashi, Martin K. Schwarz, Richard L. Huganir, Peter H. Seeburg, David J. Linden, Paul F. Worley
Journal: Neuron (2010)
Linear IgA disease in a patient with bladder carcinoma
Authors: J.M. RÓDENAS, M.T. HERRANZ, J. TERCEDOR, A. CONCHA
Journal: British Journal of Dermatology (1997)

Journal Article Linear IgA disease in a patient with bladder carcinoma Get access J.M. RÓDENAS, J.M. RÓDENAS Departments of Dermatology, Hospital General Universitario Morales Meseguer, Av. Marqueés de los Vélez, 30008 Murcia, Spain. Search for other works by this author on: Oxford Academic Google Scholar M.T. HERRANZ, M.T. HERRANZ Departments of Internal Medicine. Hospital General Universitario Morales Meseguer, Av. Marqueés de los Vélez, 30008 Murcia, Spain. Search for other works by this author on: Oxford Academic Google Scholar J. TERCEDOR, J. TERCEDOR Departments of Dermatology, Hospital Virgen de las Nieves, 18014 Granada, Spain Search for other works by this author on: Oxford Academic Google Scholar A. CONCHA A. CONCHA Departments of Pathology, Hospital Virgen de las Nieves, 18014 Granada, Spain Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 136, Issue 2, 1 February 1997, Pages 257–259, https://doi.org/10.1046/j.1365-2133.1997.d01-1182.x Published: 01 February 1997 Article history Accepted: 08 July 1996 Published: 01 February 1997
SPONTANEOUS RUPTURE OF THE INTESTINE IN THE NEW-BORN
Authors: THOMAS H. RUSSELL
Journal: JAMA (1928)

March 22, 1921, I saw in consultation with Dr. Platt Rogers of West Haven, Conn., and operated on a new-born baby who presented a very interesting and unusual picture, namely, a spontaneous rupture of the cecum. The case seemed to merit reporting, so I had the literature searched and have succeeded in finding records of twenty-three cases of spontaneously ruptured intestine in the new-born. <h3>REPORT OF CASE</h3> The history of my case is as follows: The parents were of English stock and were both in good health, neither having had any serious illness. The father was 23 and the mother 20. The mother had one other child 2 years old, alive and well; labor had lasted eleven hours, and it was a vertex presentation. One year later the mother had a miscarriage at four months. The baby in question was a girl, born three days and fourteen hours before admission
MHC-Restricted T-cell Recognition
Authors: Rolf M. Zinkernagel
Journal: JAMA (1995)

IN 1973, immunology was preoccupied with graft rejection and immune responses against model antigens. The biological function of transplantation antigens coded by the major histocompatibility gene complex (MHC) was unknown; clearly its function was not to render organ transplantation difficult. This changed when MHC restriction of T-cell recognition was discovered by two young immunologists. The historical background to this effort is discussed in the accompanying article by Peter Doherty.<sup>1</sup>This article describes the experiments that were done at that time, summarizes subsequent advances that led to our current understanding of how T cells work, and discusses some of the consequences for clinical medicine. <h3>EXPERIMENTAL CHANCE AND DISCOVERY</h3> After an internship in Basel and studies in Lausanne with H. Isliber, I obtained a Swiss fellowship to work with R. V. Blanden and Peter Doherty in G. Ada's department in Canberra. Peter Doherty and I joined forces to analyze the nature
In-Hospital Cardiopulmonary Resuscitation
Authors: Howard Brody, Tom Tomlinson
Journal: JAMA (1989)

<h3>To the Editor.—</h3> Although our article<sup>1</sup>was cited by all four authors who discussed do-not-resuscitate (DNR) orders in a recent issue of<i>JAMA</i>,<sup>2-5</sup>a critical distinction was missed that might have clarified the apparent disagreement between Murphy<sup>2</sup>and Youngner.<sup>3</sup>The former called for unilateral DNR decisions by the physician when resuscitation is demonstrably futile; the latter accused the former of unacceptable paternalism in excluding patient or family participation in DNR discussions. The distinction missing from this debate is that between the physician's decision whether resuscitation should be offered and the decision whether resuscitation should be discussed. As we explained in our article, when resuscitation is futile and offers nothing of benefit to the patient, it need not be offered as a matter of choice since it serves neither the patient's interests nor his rights. In this case, the decision against resuscitation is a matter of the
Diisocyanate antigen–enhanced production of monocyte chemoattractant protein-1, IL-8, and tumor necrosis factor-α by peripheral mononuclear cells of workers with occupational asthma
Authors: Zana L. Lummus, Rafeul Alam, Jonathan A. Bernstein, David I. Bernstein
Journal: Journal of Allergy and Clinical Immunology (1998)
Detection of a new heparin-dependent inhibitor of thrombin in human plasma.
Authors: D M Tollefsen, M K Blank
Journal: Journal of Clinical Investigation (1981)

We have demonstrated that human plasma contains a heparin-dependent inhibitor of thrombin that is distinguishable from antithrombin III (AT III). When a 1:50 dilution of plasma was incubated with greater than or equal to 0.01 U/ml heparin and 1 U/ml 125I-thrombin, the labeled thrombin B-chains became incorporated into two complexes of Mr-96,000 and Mr-85,000 that were separated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and beta-mercaptoethanol. Neither complex was detectable at heparin concentrations less than 0.01 U/ml. When a limiting amount of 125I-thrombin was present, the proportion of radioactivity incorporated into each of the two complexes varied with the heparin concentration. Thus, the Mr-85,000 complex predominated at 0.01-5 U/ml heparin, whereas the Mr-96,000 complex predominated at 5-100 U/ml heparin. The Mr-85,000 complex reacted with antibodies to human AT III and comigrated with the purified thrombin-AT III complex. The Mr-96,000 complex did not react with antibodies to AT III or to alpha 1-antitrypsin, and it was detected in normal quantities after incubating 125I-thrombin with plasma immunodepleted of AT III, alpha 2-antiplasmin, alpha 2-macroglobulin, C1 inactivator, alpha 1-antichymotrypsin, or inter-alpha-trypsin inhibitor. The protein that combines with thrombin to form the Mr-96,000 complex was estimated to be present at a minimum concentration of 90 +/- 26 micrograms/ml (mean +/- SD) in identical to any of the known plasma protease inhibitors and that at relatively high heparin concentrations in vitro it reacts with thrombin more rapidly than does AT III.