tbuckley/cabot-search huggingface dataset:
SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays
Authors: Miguel A Anton, Dorleta Gorostiaga, Elizabeth Guruceaga, Victor Segura, Pedro Carmona-Saez, Alberto Pascual-Montano, Ruben Pio, Luis M Montuenga, Angel Rubio
Journal: Genome biology (2008)

Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.
An 88-Year-Old Woman Facing the End of Life
Authors: Joanne Lynn
Journal: JAMA (1997)

Dr DALEY: Mrs J is an 88-year-old widow who has had multiple recent episodes of congestive heart failure [CHF] requiring hospitalization. She lives alone in an assisted living center for senior citizens in a suburb of Boston, Mass. She has 1 daughter, Mrs V, who is very involved in her care. She has Medicare insurance and a supplemental Medigap insurance policy. Mrs J has long-standing essential hypertension, coronary artery disease with stable angina pectoris, aortic stenosis, and an elevated alkaline phosphatase suggestive of Paget disease of the bone. She has chronic CHF, paroxysmal atrial fibrillation, 2 to 3 episodes of angina per week relieved by nitroglycerin, and recurrent episodes of flash pulmonary edema, necessitating 4 hospital admissions in the previous 10 months. Within the past year, Mrs J refused needle biopsy for evaluation of a multinodular goiter. Functionally, she needs assistance only with bathing, but notes fatigue and some shortness
Postmortem Arteriographic Studies of the Human Lung in Pulmonary Embolization
Authors: George T. Smith, Gustave J. Dammin, Lewis Dexter
Journal: JAMA (1964)

PULMONARY EMBOLISM is now the most common lethal pulmonary disease in adults seen at necropsy in the general hospital population. It is the third most common nonlethal pulmonary lesion after pneumonia and emphysema. In 1960, it was the third most common cause of death in this hospital; it was the main cause of death in 15% of the patients autopsied, and it was a major contributory cause in an additional 19%. These findings promoted the study of the number, size, and distribution of pulmonary emboli, and of the pulmonary parenchymal and circulatory alterations resulting from them. Previous reports have considered particular aspects of the physiology or pathology of pulmonary embolism, but without detailed correlation of one approach with others. The methods used have not identified smaller emboli, or delineated the extent of anatomic alterations. Moreover, there has been no method for estimating the number of emboli or the reduction in
Clinical Experience with Tolbutamide
Authors: G. Walker, J. D. H. Slater, E. K. Westlake, J. D. N. Nabarro
Journal: BMJ (1957)

Abatacept is a CTLA-4-Ig fusion protein that binds to the costimulatory ligands CD80 and CD86 and blocks their interaction with the CD28 and CTLA-4 receptors expressed by T cells, therefore inhibiting T cell activation and function. Abatacept has shown clinical efficacy in treating some autoimmune diseases but has failed to show clinical benefit in other autoimmune conditions. The reasons for these disparate results are not clear and warrant further investigation of abatacept's mode of action. Longitudinal specimens from the Immune Tolerance Network9s A Cooperative Clinical Study of Abatacept in Multiple Sclerosis trial were used to examine the effects of abatacept treatment on the frequency and transcriptional profile of specific T cell populations in peripheral blood. We found that the relative abundance of CD4<sup>+</sup> T follicular helper (Tfh) cells and regulatory T cells was selectively decreased in participants following abatacept treatment. Within both cell types, abatacept reduced the proportion of activated cells expressing CD38 and ICOS and was associated with decreased expression of genes that regulate cell-cycle and chromatin dynamics during cell proliferation, thereby linking changes in costimulatory signaling to impaired activation, proliferation, and decreased abundance. All cellular and molecular changes were reversed following termination of abatacept treatment. These data expand upon the mechanism of action of abatacept reported in other autoimmune diseases and identify new transcriptional targets of CD28-mediated costimulatory signaling in human regulatory T and Tfh cells, further informing on its potential use in diseases associated with dysregulated Tfh activity.
Injuries to riders in the cross country phase of eventing: the importance of protective equipment
Authors: M R Whitlock
Journal: British Journal of Sports Medicine (1999)

To determine the distribution of injuries in the eventing discipline of equestrian sports and the effectiveness of the protective equipment worn.Data on all injuries sustained in the cross country phase over fixed obstacles were collected from 54 days of competition from 1992 to 1997. This involved 16,940 rides.Data on a total of 193 injuries were collected, which included two deaths. This represents an injury rate of 1.1%. Head and facial injuries represented the largest group (31%), with one third of these requiring treatment in hospital. All riders were wearing protective helmets and body protectors.Eventing is one of the most dangerous equestrian sports. Improved protective equipment, which is mandatory for 1999, should reduce the severity of these injuries.
A model of the development of the brain as a construct of the thyroid system.
Authors: Kembra L Howdeshell
Journal: Environmental Health Perspectives (2002)

Thyroid hormone is essential for normal brain development. However, little is known about the molecular and cellular mechanisms that mediate thyroid hormone action on the developing brain or the developmental events selectively affected. Consequently, although a large number of environmental chemicals interfere with the thyroid system, there are few neurodevelopmental end points to recruit for toxicological studies. Therefore, my goal here is to review what is known about the relative timing of normal brain construction and thyroid system development, with special focus on the period of in utero development in humans and the comparable developmental period in laboratory rats. These data are presented as a timeline to aid in the identification of thyroid-sensitive end points in brain development and to highlight important data gaps. I discuss the known influence of certain synthetic chemicals on the thyroid system and include a brief review of the effects of developmental exposure to chemicals on thyroid system function. The relationship between the thyroid hormone and retinoic acid systems, as well as the thyroid hormone sensitivity of the developing cochlea, is also discussed.
Gestation Period and Ovulation Time
Authors: Jas. D. P. Graham
Journal: BMJ (1944)

<b>Background and Purpose.</b> The purpose of this case report is to demonstrate the application of constraint-induced movement therapy with an individual with upper-extremity hemiparesis within 4 months after sustaining a cerebrovascular accident (stroke). Such patients often fail to develop full potential use of their affected upper extremity, perhaps due to a “learned nonuse phenomenon.” <b>Case Description.</b> The patient was a 61-year-old woman with right-sided hemiparesis resulting from an ischemic lacunar infarct in the posterior limb of the left internal capsule. The patient9s less-involved hand was constrained in a mitten so that she could not use the hand during waking hours, except for bathing and toileting. On each weekday of the 14-day intervention period, the patient spent 6 hours being supervised while performing tasks using the paretic upper extremity. Pretreatment, posttreatment, and 3-month follow-up outcome measures included the Wolf Motor Function Test and the Motor Activity Log (MAL). <b>Outcomes.</b> For the Wolf Motor FunctionTest, both the mean and median times to complete 16 tasks improved from pretreatment to posttreatment and from posttreatment to follow-up. Results of the MAL indicated an improved self-report of both “how well” and “how much” the patient used her affected limb in 30 specified daily tasks. These improvements persisted to the follow-up. <b>Discussion.</b> Two weeks of constraining the unaffected limb, coupled with practice of functional movements of the impaired limb, may be an effective method for restoring motor function within a few months after cerebral insult. Encouraging improvements such as these strongly suggest the need for a group design that would explore this type of intervention in more detail.
Cystatin C and Contrast-Induced Acute Kidney Injury
Authors: Carlo Briguori, Gabriella Visconti, Natalia V. Rivera, Amelia Focaccio, Bruno Golia, Rosalia Giannone, Diletta Castaldo, Francesca De Micco, Bruno Ricciardelli, Antonio Colombo
Journal: Circulation (2010)

Background— Cystatin C (CyC) is more sensitive than serum creatinine (sCr) to rapidly detect acute changes in renal function. Methods and Results— We measured CyC together with sCr in 410 consecutive patients with chronic kidney disease undergoing either coronary and/or peripheral angiography and/or angioplasty. sCr was assessed at baseline and 24 and 48 hours after contrast media exposure. CyC was assessed at baseline and at 24 hours. Major adverse events (including death of any cause and dialysis) at 12 months were assessed. At 48 hours after contrast media exposure, contrast-induced acute kidney injury (defined as a sCr increase ≥0.3 mg/dL) occurred in 34 patients (8.2%). A CyC increase concentration ≥10% at 24 hours after contrast media exposure was detected in 87 patients (21.2%). This was the best CyC cutoff for the early identification of patients at risk for contrast-induced acute kidney injury (negative predictive value=100%; positive predictive value=39.1%). According to the defined cutoffs (that is, increase in CyC ≥10% and sCr ≥0.3 mg/dL), major adverse events occurred in 16 of 297 patients (5.4%) without any cutoffs satisfied (group 1), in 9 of 49 patients (18.4%) with only a CyC increase ≥10% (group 2), and in 9 of 31 patients (29%) with both cutoffs satisfied (group 3). By logistic regression analysis, the independent predictors of major adverse events at 1 year were group 2 (odds ratio=2.52; 95% confidence interval, 1.17 to 5.41; P =0.02), group 3 (odds ratio=4.45; 95% confidence interval, 1.72 to 11.54; P =0.002), and baseline glomerular filtration rate (odds ratio=0.91; 95% confidence interval, 0.88 to 0.95; P &lt;0.001). Conclusions— In patients with chronic kidney disease, CyC seems to be a reliable marker for the early diagnosis and prognosis of contrast-induced acute kidney injury.
A Multicentre Year-long Randomised Controlled Trial of Exercise Training Targeting Physical Functioning in Men with Prostate Cancer Previously Treated with Androgen Suppression and Radiation from TROG 03.04 RADAR
Authors: Daniel A. Galvão, Nigel Spry, James Denham, Dennis R. Taaffe, Prue Cormie, David Joseph, David S. Lamb, Suzanne K. Chambers, Robert U. Newton
Journal: European Urology (2013)
The Sicilian Gambit: a response to Drs Colatsky and Harrison
Authors: M. R Rosen, M. J Janse, P. J Schwartz
Journal: Cardiovascular Research (1992)

Journal Article The Sicilian Gambit: a response to Drs Colatsky and Harrison Get access Michael R Rosen, Michael R Rosen Departments of Pharmacology and Pediatrics, College of Physicians and Surgeons, 630 W 168th Street, New York, NY 10032, USA: M R Rosen, M J Janse, P J Schwartz. Correspondence to Dr Rosen. Search for other works by this author on: Oxford Academic PubMed Google Scholar Michiel J Janse, Michiel J Janse Departments of Pharmacology and Pediatrics, College of Physicians and Surgeons, 630 W 168th Street, New York, NY 10032, USA: M R Rosen, M J Janse, P J Schwartz. Search for other works by this author on: Oxford Academic PubMed Google Scholar Peter J Schwartz Peter J Schwartz Departments of Pharmacology and Pediatrics, College of Physicians and Surgeons, 630 W 168th Street, New York, NY 10032, USA: M R Rosen, M J Janse, P J Schwartz. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 26, Issue 6, June 1992, Pages 568–570, https://doi.org/10.1093/cvr/26.6.568 Published: 01 June 1992 Article history Received: 04 March 1992 Accepted: 14 March 1992 Published: 01 June 1992
Sleep Deprivation Per Se Does Not Decrease the Hypercapnic Ventilatory Response in Humans
Authors: CHRISTINA M. SPENGLER, STEVEN A. SHEA
Journal: American Journal of Respiratory and Critical Care Medicine (2000)

Several studies have found that sleep deprivation reduces the hypercapnic ventilatory response (HCVR). Such results may have been affected by uncontrolled activities or environmental influences during the sleep deprivation period. The current study determined the “pure” effect of sleep deprivation on respiratory control under strictly controlled behavioral and environmental conditions. After 2 d of acclimation in the laboratory, 10 subjects maintained wakefulness (confirmed by EEG), a constant semirecumbent posture, ate regular small meals, had constant interaction with experimenters, and stayed in an environment with constant low light (10 lux) and constant room temperature for 41 consecutive hours. Measurements of HCVR, resting ventilation, V˙ o 2 and V˙ co 2 were performed every 2 h. Comparisons were made of six pairs of measurements, with each pair separated by 24 h of sleep deprivation. None of the respiratory variables changed significantly with 24 h of sleep deprivation. Mean HCVR increased by 17% with sleep deprivation (3.12 versus 3.54 L · min− 1 · mm Hg− 1; not significant). These results show that sleep deprivation per se does not reduce the sensitivity of central chemoreceptors nor change resting ventilation or metabolism. The reduced HCVR after sleep loss found in previous studies may have been affected by uncontrolled activities or environmental influences during sleep deprivation periods.
Recognising pseudo-seizures.
Authors: T B Hassan, T J Underhill, D Jefferson
Journal: BMJ (1990)

I would cross swords with Mr Smith in regard to "tight heel cords" as a primary condition.It is, of course, a contraction of the muscles and there seems to be clear evidence that it is secondary to the foot deformity.5There is now no good reason why children with physiological flat feet should flood orthopaedic clinics and, even worse, have ineffec- tual treatment "to reassure the parents" when the pathological flat foot can now be confidently identi- fied, the principle of treatment understood, and orthoses designed and continued for an adequate time, thus avoiding the considerable limitation of ambulation in the adult hypermobile foot.
TRAVEL NOTES. VI.FATHER DAMIEN, THE LEPER HERO.
Authors: NICHOLAS SENN
Journal: JAMA (1904)

S. S. Sierra, July 18. "Nothing is more delightful than the light of truth."—Cicero. There are heroes and heroines, men and women, who in times of danger do not hesitate to sacrifice their lives in attempts to save others. Heroism consists in acts of unselfishness and courage of the highest type, under conditions of impending danger, or calling for a degree of self-sacrifice from which the average mortal instinctively shrinks. Untimely death and self-imposed deprivation of the comforts of life for the benefit of others who are in danger or distress exact from heroes the highest and noblest qualities of man—undaunted courage, unselfish charity and unconquerable love, and boundless humanity toward mankind. Such a combination of the highest virtues is, indeed, rare, and when found entitles the hero to profound respect, highest admiration and permanent gratitude of all nations, and more especially the one benefited by
Mortality and causes of death of end-stage renal disease in children: A Dutch cohort study
Authors: Jaap W. Groothoff, Mariken P. Gruppen, Martin Offringa, Jeroen Hutten, Marc R. Lilien, Nicole J. van de Kar, Eric D. Wolff, Jean Claude Davin, Hugo S.A. Heymans
Journal: Kidney International (2002)
DNA adduct formation and mutation induction by nitropyrenes in Salmonella and Chinese hamster ovary cells: relationships with nitroreduction and acetylation.
Authors: R H Heflich, E K Fifer, Z Djuric, F A Beland
Journal: Environmental Health Perspectives (1985)

Nitrated pyrenes are environmental pollutants and potent mutagens in the Salmonella reversion assay. In this study reversion induction by 1-nitropyrene and 1,8-dinitropyrene in Salmonella typhimurium TA1538 and mutation induction by 1-nitropyrene in Chinese hamster ovary (CHO) cells were related to the extent of metabolism and DNA adduct formation. In suspension cultures of Salmonella typhimurium TA1538, 1,8-dinitropyrene was up to 40-fold more mutagenic than 1-nitropyrene, although both compounds were metabolized at similar rates with nitroreduction being the major pathway. The major metabolite formed from 1-nitropyrene after 2 hr of incubation was 1-nitrosopyrene, while 1-amino-8-nitropyrene was the major metabolite formed from 1,8-dinitropyrene. 1-Nitrosopyrene and 1-nitro-8-nitrosopyrene elicited mutation values consistent with their being intermediates in the activation pathways. However, subsequent to nitroreduction, 1,8-dinitropyrene appeared to be further activated by acetylation, while 1-nitropyrene was not. Each nitrated pyrene produced a major DNA adduct substituted at the C8-position of deoxyguanosine. Although 1,8-dinitropyrene was more mutagenic than 1-nitropyrene, both compounds induced a similar number of revertants per adduct. Incubation of 1-nitrosopyrene with CHO cells produced a rapid concentration- and time-dependent induction of mutations and the conversion of 1-nitrosopyrene to 1-aminopyrene. In contrast, 1-nitropyrene did not induce mutations and was not converted to 1-aminopyrene. Both compounds produced the same major adduct, but adduct formation by 1-nitropyrene was much lower than by 1-nitrosopyrene.(ABSTRACT TRUNCATED AT 250 WORDS)
Pentablock copolymers of poly(ethylene glycol), poly((2-dimethyl amino)ethyl methacrylate) and poly(2-hydroxyethyl methacrylate) from consecutive atom transfer radical polymerizations for non-viral gene delivery
Authors: Fu-Jian Xu, Hongzhe Li, Jun Li, Zhongxing Zhang, En-Tang Kang, Koon-Gee Neoh
Journal: Biomaterials (2008)
The Clinical Use of THAM-Reply
Authors: Felice Manfredi
Journal: JAMA (1961)

<h3>To the Editor:—</h3> All of our patients with severe respiratory acidosis treated with THAM were simultaneously assisted with artificial devices. Our results concur with Dr. Nahas' and other authors' experience that THAM infusions may depress minute ventilation in the normal, as well as in patients with respiratory acidosis. In the abstract of our paper, we did<i>not</i>state that THAM<i>absorbs</i>CO<sub>2</sub>in the gas phase.
Anatomically Oriented Right Ventricular Volume Measurements With Dynamic Three-Dimensional Echocardiography Validated by 3-Tesla Magnetic Resonance Imaging
Authors: Petra S. Niemann, Luiz Pinho, Thomas Balbach, Christian Galuschky, Michael Blankenhagen, Michael Silberbach, Craig Broberg, Michael Jerosch-Herold, David J. Sahn
Journal: Journal of the American College of Cardiology (2007)
Anoxia-induced changes in composition and permeability of sarcolemmal membranes in rat heart cell cultures
Authors: J C ALTONA, A VAN DER LAARSE
Journal: Cardiovascular Research (1982)

The effects of energy-deprivation on composition and permeability of the sarcolemmal membrane of cardiac cells was studied using monolayer cultures of neonatal rat heart cells incubated in the absence of oxygen and metabolic substrates for 0 to 10 h at 37°C. In the course of anoxia the cells were analysed for cholesterol content, a sarcolemmal sterol, and L-leucyl-naphthylamidase (LNA) activity, a sarcolemmal protein. In addition, sarcolemmal permeability was studied by measuring the efflux of α-hydroxybutyrate dehydrogenase (HBDH) activity from the incubated cells. To test whether cholesterol and LNA are indeed markers of sarcolemmal membrane of the heart cells used, sarcolemmal preparations were obtained using an isolation method with cation-coated beads. The results of this study indicate that during anoxia and substrate depletion, changes in sarcolemmal cholesterol content precede sarcolemmal LNA liberation and cytoplasmic HBDH release. It is concluded that energy-deprivation in cardiac cells destroys sarcolemmal structure and function, secondary to the loss of cholesterol.
An energetic tale of AMPK-independent effects of metformin
Authors: Russell A. Miller, Morris J. Birnbaum
Journal: Journal of Clinical Investigation (2010)

Metformin has become a mainstay in the modest therapeutic armamentarium for the treatment of the insulin resistance of type 2 diabetes mellitus. Although metformin functions primarily by reducing hepatic glucose output, the molecular mechanism mediating this effect had remained elusive until recently. Metformin impairs ATP production, activating the conserved sensor of nutritional stress AMP-activated protein kinase (AMPK), thus providing a plausible and generally accepted model for suppression of gluconeogenic gene expression and glucose output. In this issue of the JCI, Foretz et al. refute this hypothesis by showing that AMPK is dispensable for the effects of metformin on hepatic glucose output in primary hepatocytes; rather, their data suggest that the antidiabetic effects of metformin in the liver are mediated directly by reducing energy charge.
A new method to calculate aortic valve area without left heart catheterization.
Authors: D C Warth, W J Stewart, P C Block, A E Weyman
Journal: Circulation (1984)

Assessment of the severity of aortic stenosis remains a commonly encountered clinical problem. Noninvasive evaluation has to date not proven sufficiently accurate in most cases to permit clinical decision making in the individual patient. Therefore, cardiac catheterization and measurement of the valve area with use of the Gorlin equation remains the standard approach in patients with suspected aortic stenosis. Doppler ultrasound allows direct measurement of blood velocity in cardiac chambers. This technique was used to study 16 patients with suspected aortic stenosis after cardiac catheterization. Aortic valve area (AVA) was calculated with the equation AVA = CO/(SEP X mean velocity), where CO is cardiac output measured by thermodilution and SEP is the systolic ejection period derived from the Doppler tracings. The resulting value was compared with valve area calculated from cardiac catheterization data and an excellent correlation was noted (r = .99). This study demonstrates that Doppler ultrasound can be used to accurately measure aortic valve area without the need for left heart catheterization.