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Smith RF, Kinder LL, Walker DG, Buckley LA, Hammond JM. Amidrazones. 4. Ylide syntheses. J Org Chem 2002. [DOI: 10.1021/jo00431a008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Smith RF, Johnson DS, Abgott RA, Madden MJ. Amidrazones. II. Tautomerism and alkylation studies. J Org Chem 2002. [DOI: 10.1021/jo00947a020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Smith RF, Blondell RD, Abgott RA, Lipkowitz KB, Richmond JA, Fountain KA. Stevens rearrangement of carbamoylaminimides. J Org Chem 2002. [DOI: 10.1021/jo00928a012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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104
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Koike ST, Smith RF. First Report of Rust Caused by Puccinia allii on Wild Garlic in California. PLANT DISEASE 2001; 85:1290. [PMID: 30831813 DOI: 10.1094/pdis.2001.85.12.1290d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wild garlic (Allium vineale) is a bulbous perennial weed that was introduced from Europe and is now established throughout the eastern and much of the western United States. In 2001, wild garlic plants growing in Monterey County, CA were infected with a rust fungus. Uredinia and telia were present on leaves, resulting in small (2 to 5 mm long) lesions; however, leaf dieback and other symptoms were not observed. The orange urediniospores were spherical to ellipsoidal, echinulate, and mea-sured 26 to 30 × 25 to 28 μm. Telia were black in mass and divided into locules by fused paraphyses. Teliospores were located within the locules and were brown, smooth-walled, two-celled, and measured 40 to 50 × 17 to 20 μm. Teliospore pedicels were hyaline, usually fractured, and measured 3 to 15 μm. One-celled mesospores were not observed. Based on these morphological characteristics, the pathogen was identified as Puccinia allii (1,2). To our knowledge, this is the first report of rust caused by P. allii on wild garlic in California. Because of this finding, an experiment was designed to determine whether wild garlic could be a source of rust inoculum for commercial allium crops. Wild garlic bulbs were planted in 4-in. pots (10 cm square) and grown in a greenhouse. At the 4- to 5-leaf stage the plants were transplanted in a garlic (Allium sativum) cultivar trial that had been inoculated with an isolate of P. allii from garlic. When plants were evaluated 2 months later, uredinia and telia were observed on the wild garlic plants, and the fungus was confirmed to be P. allii. Wild garlic, therefore, could be a source of overwintered inocula for the rust disease that occurs on commercial garlic and onion (A. cepa) in California (2). References: (1) D. M. Jennings et al. Mycol. Res. 94:83, 1990. (2) S. T. Koike et al. Plant Dis. 85:585, 2001.
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Abstract
Long-Evans hooded rats were given 5% alcohol (EtOH), 10% EtOH or tap water as sole fluid from postnatal day 21 (P21) to P70. The 10% EtOH group drank 26% less and 10% EtOH males gained 7.6% less weight than the tap water control group. There were no significant consumption or weight differences between 5% EtOH and control subjects. At P105, 35 days after the conclusion of alcohol dosing, we conducted several behavioral tests. Males in the 10% group drank 67.8% more alcohol than controls in a two-bottle preference test. On a DRL-20-s operant reinforcement schedule, a difficult timing task dependent upon limbic structures, subjects in the 10% group had higher barpress rates, while those in the 5% group had lower barpress rates than controls. On this task, 10% females received fewer reinforcements, while both 5% and 10% males earned more reinforcements than controls. Efficiency ratios were lowest for 10% females and highest for 5% males. Males in the 5% group had shorter latencies than controls to find the platform in a Morris water maze and were significantly more likely than controls to initially find the platform. These data suggest that EtOH consumption during periadolescent development may have long-lasting neurobehavioral effects.
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Guy CS, Kelly DF, McGarry JW, Guy F, Björkman C, Smith RF, Trees AJ. Neospora caninum in persistently infected, pregnant cows: spontaneous transplacental infection is associated with an acute increase in maternal antibody. Vet Rec 2001; 149:443-9. [PMID: 11688746 DOI: 10.1136/vr.149.15.443] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Nine cows which were naturally and persistently infected with Neospora caninum were housed and observed intensively throughout pregnancy. No recrudescence of a latent infection was detected by PCR tests on maternal blood but fetal infection, implying a recrudescence of maternal parasitosis, was associated with a marked increase in maternal antibody. The increase occurred in the second half of pregnancy in five cows which infected their calves, and before mid-pregnancy in one cow which aborted. There was no change in the avidity of the antibody, which remained high and characteristic of long-term infection. In three infected cows that gave birth to uninfected calves there was no marked increase in maternal antibody. Antigen-specific interferon gamma responses of peripheral blood mononuclear cells were observed in all the infected cattle but they did not vary significantly either during pregnancy, or whether the cows did or did not infect their calves, although the responses were consistently higher in the latter. There was no change in the plasma concentrations of cortisol or acute phase proteins associated with the recrudescence of the parasite. Three uninfected cows housed with the infected cows remained uninfected throughout the experiment. No immunosuppressive event was detected which might have provoked parasite recrudescence but the acute antibody rise associated with transplacental infection provides a valuable, non-invasive marker for further studies to investigate the cause and consequences of parasite recrudescence in N caninum infection in cattle.
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Fiedorowicz H, Bartnik A, Dunn J, Smith RF, Hunter J, Nilsen J, Osterheld AL, Shlyaptsev VN. Demonstration of a neonlike argon soft-x-ray laser with a picosecond-laser-irradiated gas puff target. OPTICS LETTERS 2001; 26:1403-1405. [PMID: 18049619 DOI: 10.1364/ol.26.001403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We demonstrate a neonlike argon-ion x-ray laser, using a short-pulse laser-irradiated gas puff target. The gas puff target was formed by pulsed injection of gas from a high-pressure solenoid valve through a nozzle in the form of a narrow slit and irradiated with a combination of long, 600-ps and short, 6-ps high-power laser pulses with a total of 10 J of energy in a traveling-wave excitation scheme. Lasing was observed on the 3p (1)S(0)?3s (1)P(1) transition at 46.9 nm and the 3d (1)P(1)?3p (1)P(1) transition at 45.1 nm. A gain of 11 cm(-1) was measured on these transitions for targets up to 0.9 cm long.
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Chambers KL, Ellard GA, Hewson AT, Smith RF. Urine test for the assessment of smoking status. Br J Biomed Sci 2001; 58:61-5. [PMID: 11440208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
A simple, quick and inexpensive test for smoking status would be useful in a variety of settings. The non-polar barbituric acid derivative 1,3-dibutyl-2-thiobarbituric acid (DBTB) is described as a novel derivatisation reagent for nicotine and its metabolites in the König reaction to assess smoking status. The relative performance of qualitative methods for assessing smoking status using DBTB and the previously employed derivatisation reagent 1,3-diethyl-2-thiobarbituric acid (DETB), as well as quantitatively-based methods for determining 'total nicotine metabolites' (TNMs) using these two reagents, were evaluated against a cotinine-based radioimmunoassay (RIA) as the 'gold standard'. Clinical sensitivity and specificity for all the approaches studied were in excess of 94%. Simple qualitative assessment by eye was superior to quantitatively-based measures of smoking status. Correlation between estimation of nicotine metabolites using DBTB, DETB and RIA were good. The most efficient and convenient method to distinguish between smokers and non-smokers was the simple qualitative method using the more lipophilic reagent DBTB.
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Koike ST, Smith RF, Davis RM, Nunez JJ, Voss RE. Characterization and Control of Garlic Rust in California. PLANT DISEASE 2001; 85:585-591. [PMID: 30823022 DOI: 10.1094/pdis.2001.85.6.585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 1998, a devastating outbreak of rust disease severely damaged the garlic crop in California, resulting in yield losses of 51% and an economic loss of 27% to the industry. The disease also occurred in 1999 and 2000, indicating that rust may have become an annual problem in some parts of the state. The presence of urediniospores, two-celled teliospores, and telial paraphyses indicated that the pathogen was Puccinia allii. Isolates from garlic infected onion and chives, but not leek, elephant garlic, or shallot in inoculation experiments. Garlic cloves obtained from diseased plants were planted under controlled conditions, but the resulting plants did not develop rust. Fungicide trials were conducted for 3 years and showed that none of the currently registered materials gave satisfactory control. However, tebuconazole and azoxystrobin provided good protection against rust if sprayed at 10-day intervals. A variety trial of 34 garlic cultivars and selections was planted, inoculated, and evaluated for resistance to rust. Although there was variability in rust severity among the selections, acceptable levels of resistance were not observed in any cultivar.
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Nagy KK, Krosner SM, Roberts RR, Joseph KT, Smith RF, Barrett J. Determining which patients require evaluation for blunt cardiac injury following blunt chest trauma. World J Surg 2001; 25:108-11. [PMID: 11213149 DOI: 10.1007/s002680020372] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The objective of this study was to determine prospectively which risk factors require cardiac monitoring for blunt cardiac injury (BCI) following blunt chest trauma. All patients who sustained blunt chest trauma had an electrocardiogram (ECG) on admission to our urban level I trauma center. Those with ST segment changes, dysrhythmias, hemodynamic instability, history of cardiac disease, age > 55 years, or a need for general anesthesia within 24 hours (group 1) were admitted to the intensive care unit (ICU) for 24 hours where they were subjected to serial ECGs, creatinine phosphokinase (CPK) assays, and echocardiography (ECHO). Those with only mechanism for BCI, i.e., none of the above risk factors (group 2), were admitted to a nonmonitored bed and had a follow-up ECG 24 hours later. A series of 315 patients were admitted with blunt chest trauma during a 17-month period; 144 patients were in group 1 and 171 in group 2. Overall, 22 patients were diagnosed as BCI (+BCI), defined as evolving ST segment changes, dysrhythmias, a CPK-MB index of > 2.5, or hemodynamic instability. Of the 18 +BCI patients in group 1, all were symptomatic (i.e., none was included solely for a cardiac history, age, or need for general anesthesia). Six of these patients required treatment for dysrhythmias, hypotension, or pulmonary edema; one of whom died. Four patients with +BCI were in group 2 and had ECG changes at 24 hours; none of these four had any sequelae from their +BCI. None of the ECHOs demonstrated abnormal wall motion. Patients who sustain blunt chest trauma with a normal ECG, normal blood pressure, and no dysrhythmias on admission require no further intervention for BCI. Patients with ST segment changes, dysrhythmias, or hypotension following blunt chest trauma should be monitored for 24 hours, as this subgroup occasionally requires further treatment for complications of BCI. ECHO adds nothing as a screening test.
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Abstract
There is growing concern in many parts of the world that fertility of dairy cattle is reducing as milk yields increase. Stress could be one important cause. As an example, fertility is lower after caesarian operations. Delayed uterine involution after dystocia is associated with abnormal ovarian cyclicity and prolonged intervals to the next pregnancy. There is a greater reduction in fertility as the clinical conditions of lameness, milk fever or mastitis worsen. Changes in social groupings greatly increase the number of inseminations required per pregnancy. Transport reduces the number of CL after superovulation, and can interfere with pregnancy rates after estrous synchronization. Embryos collected from heat-stressed donors are less viable and have delayed trophoblast function. Human-animal interactions influence stress-responses in cattle--the behavior of stockman and embryo transfer personnel could affect success. Putting aside financial aspects, exposure of an animal to avoidable stress compromises welfare, whether application of biotechnology is involved or not. The fact that stressors can be deleterious to such an important function as reproduction, emphasizes that stress is very important and should be minimized whenever possible.
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Palmer ME, Smith RF, Chambers K, Tetler LW. Separation of nicotine metabolites by capillary zone electrophoresis and capillary zone electrophoresis/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2001; 15:224-231. [PMID: 11180554 DOI: 10.1002/1097-0231(20010215)15:3<224::aid-rcm213>3.0.co;2-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The use of capillary zone electrophoresis (CZE) and capillary zone electrophoresis/mass spectrometry (CZE/MS) has been demonstrated, in principle, for the separation of nicotine and nicotine metabolites. The buffer system developed for separation and detection by CZE/UV was modified for use in CZE/MS analysis. Several of the metabolites are isobaric and tandem mass spectrometric (MS/MS) techniques have been used to differentiate such analytes.
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Williams DJ, Guy CS, McGarry JW, Guy F, Tasker L, Smith RF, MacEachern K, Cripps PJ, Kelly DF, Trees AJ. Neospora caninum-associated abortion in cattle: the time of experimentally-induced parasitaemia during gestation determines foetal survival. Parasitology 2000; 121 ( Pt 4):347-58. [PMID: 11072897 DOI: 10.1017/s0031182099006587] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The parasite, Neospora caninum is an important cause of abortion in cattle. It is transmitted vertically or horizontally and infection may result in abortion or the birth of a live, healthy but infected calf at full-term. Only a proportion of infected cattle abort and the pathogenesis of abortion is not understood. Groups of cattle were infected with 10(7) N. caninum tachyzoites intravenously at different times relative to gestation. Intravenous inoculation was chosen to reproduce the putative haematogenous spread of N. caninum following either recrudescence of endogenous infection or de novo infection. In all cattle, infection was accompanied by high gamma-interferon and lymphoproliferative responses, and a biased IgG2 response indicating that N. caninum infection is accompanied by a profound Th1 helper T cell-like response. Infection at 10 weeks gestation resulted in foetopathy and resorption of foetal tissues 3 weeks after infection in 5 out of 6 cows. Infection at 30 weeks gestation resulted in the birth of asymptomatic, congenitally-infected calves at full term in all 6 cows, whereas the 6 cows infected before artificial insemination gave birth to live, uninfected calves. These results suggest that the reason some cows abort is related to the time during gestation when they become infected or an existing infection recrudesces.
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Raap DK, Morin B, Medici CN, Smith RF. Adolescent cocaine and injection stress effects on the estrous cycle. Physiol Behav 2000; 70:417-24. [PMID: 11110994 DOI: 10.1016/s0031-9384(00)00287-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chronic cocaine exposure during critical periods of development induces short- and long-term effects. During the pubertal period, the hypothalamic-pituitary-gonadal (HPG) axis undergoes many dynamic changes. The present study investigated whether chronic periadolescent cocaine alters reproductive maturity in the rat. Sixty female Long-Evans hooded rats were randomly assigned to one of three conditions (20 mg cocaine/kg/day, saline injected and uninjected), for dosing from postnatal day 21 (P21) through P60. Several indicators of reproductive maturation and functioning were assessed during and following treatment. Cocaine exposure had no effect on the onset of puberty or on the date of first ovulation. The number of proestrus-estrus transitions was significantly lower in cocaine-exposed females compared to uninjected females, but not compared to saline-injected controls. This reduction was observed during exposure to cocaine, as well as after the cessation of injections. During the dosing period, cocaine-exposed rats also exhibited a greater number of cycles that had no clear P-E transition than did UN subjects; this effect disappeared once injections stopped. These alterations suggest immediate, and possibly persisting, alterations in the control of ovulation after chronic cocaine exposure throughout adolescence. Interestingly, during the injection period, the saline-injected females had a significantly greater number of diestrus days compared to uninjected and cocaine-injected animals, as well as a lower proportion of regular 4- and 5-day cycles. These differences disappeared once injections stopped. These results suggest a stress-induced irregularity of the estrous cycle, possibly attenuated by cocaine and recoverable after exposure. The present findings indicate that the HPG axis is susceptible to short-term, and possibly to long-term, alterations induced by cocaine exposure throughout the adolescent period.
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Nagy KK, Roberts RR, Joseph KT, Smith RF, An GC, Bokhari F, Barrett J. Experience with over 2500 diagnostic peritoneal lavages. Injury 2000; 31:479-82. [PMID: 10908739 DOI: 10.1016/s0020-1383(00)00010-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This study was undertaken to confirm the safety and efficacy of diagnostic peritoneal lavage (DPL) for trauma patients. A prospectively maintained database of all DPLs performed in the past 75 months was analyzed. A red blood cell count of 100,000/mm(3) was considered positive for injury in blunt trauma; 10,000/mm(3) was considered positive for peritoneal penetration in penetrating trauma. Information relative to type of injury, DPL result, laparotomy result and complications, was analysed to determine if DPL was more or less suited to any specific indication or type of patient. Over a 75 month period, 2501 DPLs were performed at our urban level I trauma center. The overall sensitivity, specificity and accuracy for the above thresholds were 95, 99 and 98%. The majority (2409, 96%) were performed using percutaneous or "closed" seldinger technique. Ninety-two (4%) were performed using open technique because of pelvic fractures, previous scars and pregnancy. Open DPL was less sensitive than closed DPL in patients who sustained blunt trauma (90 vs 95%) but slightly more sensitive in determining penetration (100 vs 96%). Overall, there were 21 complications (0.8%). There was no difference in complication rate between open and closed DPL. In conclusion, DPL remains a highly accurate, sensitive and specific test with an extremely low complication rate. It can be performed either open or closed with comparable results. We recommend its use in the evaluation of both blunt and penetrating trauma.
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Friesinger GC, Smith RF. Old age, left bundle branch block and acute myocardial infarction: a vexing and lethal combination. J Am Coll Cardiol 2000; 36:713-6. [PMID: 10987589 DOI: 10.1016/s0735-1097(00)00801-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nagy KK, Smith RF, Roberts RR, Joseph KT, An GC, Bokhari F, Barrett J. Prognosis of penetrating trauma in elderly patients: a comparison with younger patients. THE JOURNAL OF TRAUMA 2000; 49:190-3; discussion 193-4. [PMID: 10963528 DOI: 10.1097/00005373-200008000-00003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND It has previously been shown that elderly patients have a worse prognosis than their younger counterparts after sustaining blunt trauma. This is due in part to a higher incidence of comorbid conditions as well as less physiologic reserve in an elderly population sustaining largely blunt trauma. We compared the outcome after penetrating trauma in elderly patients to matched "younger" patients to determine whether they had a similarly poor prognosis. METHODS Elderly patients (> or = 65 years) were identified from our trauma registry. Sex, mechanism of injury, and Abbreviated Injury Score/Injury Severity Score were determined from the registry. Patients presenting with traumatic arrest were excluded. The registry was then searched for patients aged 15 to 40 years with the same sex, mechanism of injury, and Abbreviated Injury Score in each region. A chart review was then performed to determine additional details of their hospital stay. The two groups were then compared using Student's t test and Fisher's exact chi2 test, as appropriate. RESULTS Eighty-five elderly patients (OLD group) were admitted with penetrating trauma between 1983 and 1998. They were compared with 85 matched young patients (YOUNG group). Each group included 66 male and 19 female patients. In each group, gunshot wounds occurred in 45.9%, stab wounds in 52.9%, and shotgun wounds in 1.2% of patients. The average Injury Severity Score in each group was 5.5 +/- 5.6 (range, 1-29) and the regional Abbreviated Injury Scores were likewise equal in both groups. The OLD patients had an average hospital stay of 6.9 +/- 9.1 days compared with 4.3 +/- 5.7 days in the YOUNG patients (p < 0.05). Twenty-seven OLD patients spent 7.3 +/- 9.2 days in the intensive care unit compared with 19 YOUNG patients who stayed 3.4 +/- 3.2 days (p < .05). A total of 91 comorbidities were identified in 58 OLD patients compared with 18 in 15 YOUNG patients (p < .0001). Eighty-six invasive procedures were performed in the OLD group compared with 96 in the YOUNG group (p = not significant). Nineteen OLD patients (22.3%) and 15 YOUNG patients (17.6%) suffered one or more complications, including death (p = not significant). A total of 91% of surviving OLD patients were discharged to home compared with 100% of surviving YOUNG patients (p < .01). CONCLUSION Elderly patients who sustain penetrating trauma have more comorbidities than their younger counterparts. This may account for their longer hospital stay and lesser ability to be discharged home. These patients do not have an increased complication rate and should continue to be managed aggressively.
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Abstract
Stress is revealed by the inability of an animal to cope with its environment, a phenomenon that is often reflected in a failure to achieve genetic potential. Field data from dairy cows show that stressors such as milk fever or lameness increase the calving to conception interval by 13-14 days, and an extra 0.5 inseminations are required per conception. We suggest that a variety of endocrine regulatory points exist whereby stress limits the efficiency of reproduction. Transport produces an immediate constant increase in arginine vasopressin (AVP) and corticotrophin-releasing hormone (CRH) secretion in ewes, but adrenocorticotrophic hormone (ACTH) reaches a maximum in the first hour while cortisol is highest during the second hour. In contrast, after an insulin injection, the hypothalamo-pituitary-adrenal (HPA) response is delayed occurring only after glucose decreases below a threshold. Changes in AVP, CRH and ACTH each follow a similar time course, but eventually the secretion of AVP and CRH decreases while glucose is still at a nadir. Negative feedback effects appear to operate mainly at the pituitary level during transport but at the hypothalamus during hypoglycaemia. We also have endocrine evidence to show that stressors interfere with precise timings of reproductive hormone release within the follicular phase. Transport, or insulin, reduce the frequency and amplitude of gonadotrophin-releasing hormone and LH pulses, suggesting that these stressors exert effects at the hypothalamus or higher centres in the brain. Both stressors also delay the onset of the luteinising hormone (LH) surge. Preliminary results suggest that opioids mediate these effects but progesterone/glucocorticoid receptors are not involved because the antagonist, RU486, is unable to reverse insulin-induced delays in the LH surge. There is also evidence to support effects at pituitary level because exogenous ACTH, or transport, reduce the amount of LH released by challenges with GnRH. The reduction in endogenous GnRH/LH secretion ultimately deprives the ovarian follicle of adequate gonadotrophin support leading to reduced oestradiol production by slower growing follicles. Thus, there is a level of interference by stressors at the ovary. Reproduction is such an important physiological system that animals have to ensure that they can respond to their surroundings; thus, it is advantageous to have several protein mechanisms, i.e. at higher brain, hypothalamus, pituitary and target gland levels. However, when pushed too far, subfertility occurs.
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Smith RF, Germanson T, Judd D, Wong M, Ziesche S, Anand IS, Taylor WR, Cohn JN. Plasma norepinephrine and atrial natriuretic peptide in heart failure: influence of felodipine in the third Vasodilator Heart Failure Trial. V-HeFT III investigators. J Card Fail 2000; 6:97-107. [PMID: 10908083 DOI: 10.1016/s1071-9164(00)90011-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Reflex activation of the sympathetic nervous system by short-acting dihydropyridine calcium channel antagonists has been reported to harm hypertensive patients. Different neurohormonal profiles and their response to treatment may influence the effectiveness of dihydropyridine vasodilator treatment of heart failure. METHODS Four hundred fifty men with left ventricular (LV) systolic dysfunction were administered standard heart failure treatment and felodipine extended release (ER) or placebo in the Vasodilator Heart Failure Trial III (V-HeFT III). Plasma norepinephrine (PNE) levels, atrial natriuretic peptide (ANP) levels, exercise capacity, LV ejection fraction (EF), cardiac dimensions and function, and arrhythmia frequency were measured. Hospital-free survival for baseline neurohormonal classes was assessed. RESULTS Distributions of ANP and PNE levels at baseline in patients with heart failure of ischemic and nonischemic causes were virtually identical. ANP levels at baseline were inversely related to LVEF (r = -0.39; P = .0001), exercise duration (r = -0.19; P = .0001), and peak oxygen consumption (r = -0.27; P = .008) and directly related to LV (r = 0.23; P = .0006) and right ventricular dilatation (r = 0.23; P = .0008). The increase in ANP levels between baseline and 3 months (P = .02) and 1 year (P = .03) was significantly less in the felodipine-ER group than in the placebo group, but PNE levels did not differ between treatment groups. Hospital-free survival was directly related to baseline ANP (P = .0002) and PNE levels (P = .004). All-cause mortality was related to baseline PNE levels (P = .02) but not baseline ANP levels. CONCLUSION Levels of ANP and PNE hormones are related to LV dysfunction, exercise performance, and hospital-free survival in heart failure and PNE levels are related to all-cause mortality. Treatment with felodipine ER did not adversely affect survival in any neurohormone subclass.
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Mathews F, Yudkin P, Smith RF, Neil A. Nutrient intakes during pregnancy: the influence of smoking status and age. J Epidemiol Community Health 2000; 54:17-23. [PMID: 10692957 PMCID: PMC1731547 DOI: 10.1136/jech.54.1.17] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
STUDY OBJECTIVE To examine the relation of antioxidant and other nutrient intakes in pregnancy to smoking and sociodemographic variables. DESIGN Cohort study. SETTING St Mary's Maternity Hospital, Portsmouth. PARTICIPANTS Pregnant nulliparous women, with no existing complications of pregnancy, were recruited from antenatal booking clinics. A total of 774 women completed seven day food diaries, and supplied detailed data on their use of nutrient supplements. MAIN RESULTS Smokers had lower intakes of most micronutrients. After adjustment for the confounding effects of maternal age, height, and education, only vitamin C and carotenoid intakes remained significantly depressed. Age was strongly and significantly associated with the intake of most nutrients, including antioxidants, and this association was independent of other maternal factors. Antioxidant intake was therefore lowest in young women who smoked: for example smokers under 24 years had a mean vitamin C intake of 57 mg (SD 35) compared with 106 mg (SD 52) for non-smokers aged 28 and over (difference 49 mg, 95% CI 39, 59). The corresponding intakes of carotenoid equivalents were 1335 micrograms (SD 982) and 2093 micrograms (SD 1283) (difference 758 micrograms, 95% CI 496, 1020). CONCLUSIONS The study has identified, for the first time, young pregnant women as a group at particular risk of low micronutrient intake. The health implications of poor nutrition now need to be evaluated, particularly for those women who smoke.
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Dobson H, Tebble JE, Ozturk M, Smith RF. Effect of transport on pulsatile LH release in ovariectomized ewes with or without prior steroid exposure at different times of year. JOURNAL OF REPRODUCTION AND FERTILITY 1999; 117:213-22. [PMID: 10690188 DOI: 10.1530/jrf.0.1170213] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The initial aim of the present study was to test whether the stress of transport suppresses LH pulsatile secretion in ewes. In a pilot experiment in the late breeding season, transport resulted in an unexpected response in three out of five transported, ovariectomized ewes pretreated with oestradiol and progesterone. Before transport, seasonal suppression of LH pulses had occurred earlier than anticipated, but LH pulsatility suddenly restarted for the period of transport. This finding was reminiscent of unexplained results obtained in ovariectomized ewes infused centrally with high doses of corticotrophin-releasing hormone after pretreatment with low doses of oestradiol with or without progesterone. Hence, an additional aim of the present study was to examine whether these latter results with corticotrophin-releasing hormone could be reproduced by increasing endogenous corticotrophin-releasing hormone secretion by transport. Subsequent experiments used groups of at least eight ovariectomized ewes at different times of the year with or without prior exposure to steroids to assess whether these unexpected observations were associated with season or the prevailing endocrine milieu. In the mid-breeding season, transport for 4 h in the absence of steroid pretreatment for 8 months reduced LH pulse frequency from 7.5 +/- 0.3 to 6.3 +/- 0.4 pulses per 4 h (P < 0.05) and LH pulse amplitude from 2.6 +/- 0.5 to 1.8 +/- 0.3 ng ml-1 (P < 0.05). Similarly, in the mid-breeding season, 34 h after the cessation of pretreatment with oestradiol and progesterone, transport suppressed LH pulse frequency from 6.1 +/- 0.4 to 5.5 +/- 0.3 pulses per 4 h (P < 0.05) with a tendency of effect on amplitude (6.2 +/- 2.7 to 2.61 +/- 0.6 ng ml-1; P = 0.07; note the large variance in the pretransport data). During mid-anoestrus, evidence of a suppressive effect of transport was only observed on LH pulse amplitude (4.7 +/- 0.6 versus 3.0 +/- 0.5 pulses per 4 h; P < 0.05) in ovariectomized ewes that had not been exposed to ovarian steroids for 4 months. Repetition of the pilot experiment with 12 ewes during the transition into anoestrus resulted in one ewe with LH pulses seasonally suppressed but increased by transport; 11 ewes had a distinct pulsatile LH pattern which was decreased by transport in six ewes. In anoestrus, there was no effect of transport on LH pulse frequency or amplitude in intact ewes, or those ovariectomized 2-3 weeks previously, with or without prior oestradiol and progesterone treatment. However, basal concentrations of cortisol were greater in anoestrus than in the breeding season, and the increment in cortisol during transport was similar in anoestrus and the breeding season but greater during the transition into anoestrus (P < 0.05). Progesterone concentrations increased from 0.31 +/- 0.02 ng ml-1 before transport to 0.48 +/- 0.05 ng ml-1 during the second hour of transport (P < 0.05). In conclusion, transport reduced LH pulse frequency and amplitude in ovariectomized ewes that had not been exposed to exogenous steroids for at least 4 months. In most animals, the previously observed increase in LH pulsatility induced by exogenous CRH was not reproduced by increasing endogenous CRH secretion by transport. However, in four ewes, transport did increase LH pulsatility, but only during the transition into anoestrus in ewes with seasonally suppressed LH profiles after withdrawal of steroid pretreatment.
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Abstract
Anthropomorphic carotid bifurcation flow phantoms that incorporate different stenotic geometries within the internal carotid artery have been developed. This technique produces high-fidelity, life-size vascular flow models that are compatible with magnetic resonance techniques. The models, in conjunction with a computer-controlled flow pump, address the need for a complex vascular geometry that can be used to verify magnetic resonance angiography (MRA) techniques that quantify stenosis severity and blood flow. Stenotic geometries, with up to 80% diameter reduction, have been fabricated in two different phantom materials. Plastic phantoms provide a durable, rigid geometry where the absolute dimensions of the model are well known. Agar gel phantoms provide tissue-like signal (T1, T2) up to the lumen boundary and are also compatible with ultrasound techniques. In this paper the technique to produce vascular flow phantoms is outlined and the compatibility of these phantoms with MRA techniques is demonstrated. J. Magn. Reson. Imaging 1999;10:533-544.
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Quinton ND, Laird SM, Okon MA, Li TC, Smith RF, Ross RJ, Blakemore AI. Serum leptin levels during the menstrual cycle of healthy fertile women. Br J Biomed Sci 1999; 56:16-9. [PMID: 10492910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Leptin is a protein, produced by adipose tissue, which has cytokine and hormonal properties. Serum leptin levels can be considered as a measure of body fat mass, and are involved in regulation of body weight. Previous studies suggest that leptin may have an additional role in reproduction, and there is also evidence for involvement in the hypothalamic-pituitary-gonadal axis. In this study, we investigate the possible changes in serum leptin concentration throughout the menstrual cycle. Samples were collected from apparently healthy, fertile women at different stages in their menstrual cycle, timed precisely according to the luteinising hormone (LH) surge. Mean serum leptin levels were significantly higher in the luteal phase (median 11.4 ng/mL) than in the follicular phase (median 10.0 ng/mL) (P < 0.001). In addition, mean serum leptin levels correlated with body mass index (r = 0.54, P < 0.05), but showed no correlation with luteal-phase progesterone levels. Results showed that levels of serum leptin vary during the menstrual cycle, and add to the mounting evidence that leptin has a role in reproduction. These fluctuations should be taken into account whenever studies are performed using female subjects.
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Quinton ND, Smith RF, Clayton PE, Gill MS, Shalet S, Justice SK, Simon SA, Walters S, Postel-Vinay MC, Blakemore AI, Ross RJ. Leptin binding activity changes with age: the link between leptin and puberty. J Clin Endocrinol Metab 1999. [PMID: 10404799 DOI: 10.1210/jc.84.7.2336] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The timing of the physical transition from child to adult is determined by a biological clock that switches off the pituitary gonadal axis during infancy until puberty. Body composition (and in particular, fat mass), through leptin, are critical signals to this clock. However, no direct relationship between leptin and puberty has been demonstrated. Leptin is bound in the circulation by a high-affinity binding protein, which has been identified as a soluble leptin receptor. We found circulating levels of leptin binding activity (LBA) to be low at birth, to be high in the prepubertal years, to fall through puberty, and then to remain stable during adult life. LBA correlated with pubertal status in both boys and girls. We postulate that the fall in LBA, associated with increasing age and puberty, reflects a reduction in expression of truncated leptin receptors, and leptin is then available to the full-length receptor, which transmits the biological signal for leptin. The high levels of LBA occur during the years when the pituitary gonadal axis is quiescent. Thus, the change in LBA could explain how leptin regulates puberty.
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Crow FW, Duholke WK, Martin GE, Smith RF, Thamann TJ, Cooper AM, Hallberg JW, Blinn JR, Chidestere CG. Structural identification of a novel degradant of the antibiotic pirlimycin formed under thermal stress conditions. J Heterocycl Chem 1999. [DOI: 10.1002/jhet.5570360436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Quinton ND, Smith RF, Clayton PE, Gill MS, Shalet S, Justice SK, Simon SA, Walters S, Postel-Vinay MC, Blakemore AI, Ross RJ. Leptin binding activity changes with age: the link between leptin and puberty. J Clin Endocrinol Metab 1999; 84:2336-41. [PMID: 10404799 DOI: 10.1210/jcem.84.7.5834] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The timing of the physical transition from child to adult is determined by a biological clock that switches off the pituitary gonadal axis during infancy until puberty. Body composition (and in particular, fat mass), through leptin, are critical signals to this clock. However, no direct relationship between leptin and puberty has been demonstrated. Leptin is bound in the circulation by a high-affinity binding protein, which has been identified as a soluble leptin receptor. We found circulating levels of leptin binding activity (LBA) to be low at birth, to be high in the prepubertal years, to fall through puberty, and then to remain stable during adult life. LBA correlated with pubertal status in both boys and girls. We postulate that the fall in LBA, associated with increasing age and puberty, reflects a reduction in expression of truncated leptin receptors, and leptin is then available to the full-length receptor, which transmits the biological signal for leptin. The high levels of LBA occur during the years when the pituitary gonadal axis is quiescent. Thus, the change in LBA could explain how leptin regulates puberty.
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Phogat JB, Smith RF, Dobson H. Effect of transport on pituitary responsiveness to exogenous pulsatile GnRH and oestradiol-induced LH release in intact ewes. JOURNAL OF REPRODUCTION AND FERTILITY 1999; 116:9-18. [PMID: 10505051 DOI: 10.1530/jrf.0.1160009] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study examined the effect of transport on GnRH self-priming in vivo as well as the consequential effects on the oestradiol-induced LH surge. The follicular phases of ewes (eight per group) were synchronized with progestin sponges, and 50 micrograms oestradiol benzoate was injected 24 h (time zero) after sponge removal to improve precision in the timing of the LH surge. Beginning 8 h after oestradiol, saline or GnRH (500 ng, i.v.) was given at 2 h intervals with or without 8 h transport beginning 0.5 h before the first GnRH injection (late transport) and effects were compared with those observed during early transport, that is, starting 2.5 h before the first GnRH injection. In all ewes, GnRH alone induced a maximum LH response of 1.9 +/- 0.4 ng ml-1 after the first challenge. The response was enhanced (P < 0.01) after the second and third GnRH injections (7.4 +/- 1.4 ng ml-1 and 7.6 +/- 1.7 ng ml-1, respectively). This self-priming effect after the second GnRH was reduced by late transport (7.4 +/- 1.4 versus 4.2 +/- 0.8 ng ml-1; P < 0.05) but not early transport, that is, transport initiated closer to the time of GnRH administration had greater suppressive effects on LH secretion. Throughout transport, spontaneous LH pulse frequency was lower in treated than it was in control ewes (2.38 +/- 0.53 versus 4.50 +/- 0.53 pulses per 8 h; P < 0.01), with marked effects in the first 4 h of transport (1.0 +/- 0.19 versus 2.63 +/- 0.38 pulses per 4 h; P < 0.02). Spontaneous pulse amplitude also tended to decrease during transport (0.13 +/- 0.02 versus 0.20 +/- 0.03 ng ml-1; P = 0.07). When LH turnover was stimulated by exogenous GnRH, the onset of the LH surge was delayed (controls: 20.5 +/- 2.0 h versus GnRH alone: 25.3 +/- 1.5 h; P < 0.05) and the duration was reduced (8.5 +/- 0.9 versus 6.5 +/- 0.4 h; P < 0.05). Transport tended to delay the LH surge in saline-treated ewes (20.5 +/- 2.0 versus 22.9 +/- 1.9 h; P = 0.08), with a further delay imposed by late transport plus GnRH (27.5 +/- 1.6 h; P < 0.05) but not by early transport plus GnRH (27.8 +/- 2.5 versus 26.4 +/- 2.4 h; P > 0.05), that is, effects mediated by increasing LH turnover were only manifest if transport occurred near the LH surge, when there was insufficient time to replenish stores of releasable LH. In all transported ewes, plasma cortisol increased from 4.5 +/- 1.0 ng ml-1 to 29.2 +/- 5.5 ng ml-1 (P < 0.001) within 15 min of the start of transport and was significantly lower (P < 0.01) by 6.5 h. Plasma progesterone also increased from 0.30 +/- 0.04 to 0.38 +/- 0.04 ng ml-1 (P < 0.05). In conclusion, transport affected the oestradiol-induced LH surge by causing a 50% reduction in the self-priming effect of exogenous GnRH, but hypothalamic effects were also revealed by a two-fold decrease in spontaneous LH pulse frequency in saline-treated ewes.
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Dobson H, Tebble JE, Phogat JB, Smith RF. Effect of transport on pulsatile and surge secretion of LH in ewes in the breeding season. JOURNAL OF REPRODUCTION AND FERTILITY 1999; 116:1-8. [PMID: 10505050 DOI: 10.1530/jrf.0.1160001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The aim of this study was to elucidate the mechanism(s) involved in stress-induced subfertility by examining the effect of 4 h transport on surge and pulsatile LH secretion in intact ewes and ovariectomized ewes treated with steroids to induce an artificial follicular phase (model ewes). Transport caused a greater delay in the onset of the LH surge in nine intact ewes than it did in ten ovariectomized ewes (intact: 41.0 +/- 0.9 h versus 48.3 +/- 0.8 h, P < 0.02; ovariectomized model: 40.8 +/- 0.6 h versus 42.6 +/- 0.5 h, P < 0.02). Disruption of the hypothalamus-pituitary endocrine balance in intact ewes may have reduced gonadotrophin stimulation of follicular oestradiol production which had an additional effect on the LH surge mechanism. In the ovariectomized model ewes, this effect was masked by the exogenous supply of oestradiol. However, in these model ewes, there was a greater suppression of maximum LH surge concentrations (intact controls: 29 +/- 4 ng ml-1 versus intact transported 22 +/- 5 ng ml-1, P < 0.02; ovariectomized model controls: 35 +/- 7 ng ml-1 versus model transported 15 +/- 2 ng ml-1, P < 0.02). Subsequent exposure to progesterone for 12 days resulted in the resumption of a normal LH profile in the next follicular phase, indicating that acute stress leads to a temporary endocrine lesion. In four intact ewes transported in the mid-follicular phase, there was a suppression of LH pulse amplitude (0.9 +/- 0.3 versus 0.3 +/- 0.02 ng ml-1, P < 0.05) but a statistically significant effect on pulse frequency was not observed (2.0 +/- 0.4 versus 1.7 +/- 0.6 pulses per 2 h). In conclusion, activation of the hypothalamus-pituitary-adrenal axis by transport in the follicular phase of intact ewes interrupts surge secretion of LH, possibly by interference with LH pulsatility and, hence, follicular oestradiol production. This disruption of gonadotrophin secretion will have a major impact on fertility.
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Phogat JB, Smith RF, Dobson H. Effect of adrenocorticotrophic hormone (ACTH1-24) on ovine pituitary gland responsiveness to exogenous pulsatile GnRH and oestradiol-induced LH release in vivo. Anim Reprod Sci 1999; 55:193-203. [PMID: 10379672 DOI: 10.1016/s0378-4320(99)00023-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The present experiment was designed to determine if and how exogenous ACTH replicates the effects of stressors to delay the preovulatory LH surge in sheep. Twenty-four hours after oestrous synchronisation with prostaglandin in the breeding season, groups of 8-9 intact ewes were injected with 50 microg oestradiol benzoate (0 h) followed 8 h later by 3 injections of saline or GnRH (500 ng each, i.v.) at 2 h intervals (controls). Two further groups received an additional 'late' injection of ACTH (0.8 mg i.m.) 7.5 h after oestradiol, i.e., 0.5 h before the first saline or GnRH challenge. To examine if the duration of prior exposure to ACTH was important, another group of ewes was given ACTH 'early', i.e. 2.5 h before the first GnRH injection. The first GnRH injection produced a maximum LH response of 1.9+/-0.4 ng/ml which was significantly (p < 0.01) enhanced after the second and third GnRH challenge (7.1+/-1.5 ng/ml and 7.0+/-1.7 ng/ml, respectively; 'self-priming'). Late ACTH did not affect the LH response after the first GnRH challenge (1.9+/-0.4 vs. 1.8+/-0.3 ng/ml; p > 0.05) but decreased maximum LH concentrations after the second GnRH to 35% (7.1+/-1.5 vs. 4.6+/-1.1 ng/ml; p = 0.07) and to 40% after the third GnRH (7.0+/-1.7 vs. 4.0+/-0.8 ng/ml; p = 0.05). When ACTH was given early, 4.5 h before the second GnRH, there was no effect on this LH response suggesting that the effect decreases with time after ACTH administration. Concerning the oestradiol-induced LH surge, exogenous GnRH alone delayed the onset time (20.5+/-2.0 vs. 27.8+/-2.1 h; p > 0.05) and reduced the duration of the surge (8.5+/-0.9 vs. 6.7+/-0.6 h; p > 0.05). The onset of the LH surge was observed within 40 h after oestradiol on 29 out of 34 occasions in the saline +/- GnRH treated ewes compared to 11 out of 34 occasions (p < 0.05) when ACTH was also given, either late or early. In those ewes that did not have an LH surge by the end of sampling, plasma progesterone concentrations during the following oestrous cycle increased 2 days later suggesting a delay, not a complete blockade of the LH surge. In conclusion, we have revealed for the first time that ACTH reduces the GnRH self-priming effect in vivo and delays the LH surge, at least partially by direct effects at the pituitary gland.
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Crow FW, Duholke WK, Hadden CE, Smith RF, Thamann TJ, Kaluzny BD, Hahn DA, Mallory CS, Farley KA, Martin GE. Complete spectroscopic structural characterization of novobiocin, isonovobiocin, decarbamylnovobiocin, 2″-(o-Carbamyl)novobiocin, and novobiocin-2″,3″-carbonate. J Heterocycl Chem 1999. [DOI: 10.1002/jhet.5570360206] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
UNLABELLED BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. AVAILABILITY BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). SUPPLEMENTARY INFORMATION Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html CONTACT (kworley,culpep)@bcm.tmc.edu
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Nagy KK, Joseph KT, Krosner SM, Roberts RR, Leslie CL, Dufty K, Smith RF, Barrett J. The utility of head computed tomography after minimal head injury. THE JOURNAL OF TRAUMA 1999; 46:268-70. [PMID: 10029032 DOI: 10.1097/00005373-199902000-00012] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To determine if patients who present with a history of loss of consciousness who are neurologically intact (minimal head injury) should be managed with head computed tomography (CT), observation, or both. METHODS We prospectively studied patients who presented to our urban Level I trauma center with a history of loss of consciousness after blunt trauma and a Glasgow Coma Scale score of 15. All patients underwent CT of the head and were subsequently admitted for 24 hours of observation. RESULTS A total of 1,170 patients with minimal head injury were studied during a 35-month period. All patients had Glasgow Coma Scale scores of 15 on arrival and had a history of either loss of consciousness or amnesia to the event. Two hundred forty-seven patients (21.1%) were intoxicated with drugs or alcohol on admission; 39 patients (3.3%) had abnormalities detected by CT, including 18 intracranial bleeds; 21 patients (1.8%) had changes in therapy as a direct result of their CT results, including 4 operative procedures. No patient with negative CT results deteriorated during the subsequent observation period. CONCLUSION CT is a useful test in patients with minimal head injury because it may lead to a change in therapy in a small but significant number of patients. Subsequent hospital observation adds nothing to the CT results and is not necessary in patients with isolated minimal head injury.
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Ozturk M, Smith RF, Dobson H. Effect of prolonged exposure to oestradiol on subsequent LH secretion in ewes. JOURNAL OF REPRODUCTION AND FERTILITY 1998; 114:1-9. [PMID: 9875149 DOI: 10.1530/jrf.0.1140001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abnormal follicles can produce oestradiol continuously for up to 20 days and this inhibits the hypothalamic-pituitary axis. The present experimental series was designed to determine the minimum exposure to high or low follicular phase concentrations of oestradiol that were required to exert inhibitory effects on LH surge secretion induced by additional oestradiol administered at the end of continuous exposure to oestradiol. Experiments were also included to establish whether the inhibitory effects of prolonged oestradiol were mediated at the pituitary, and whether the failure of response to the oestradiol challenge could be corrected by exposure to normal luteal phase patterns of progesterone. Treatment of ewes between 2 and 12 days with 1, 2 or 4 oestradiol implants (3 cm) totally blocked the subsequent normal LH surge in response to an oestradiol challenge in 45 of 52 ewes pretreated with oestradiol. In the seven ewes that did have an increase in LH, the response occurred at the expected time but was greatly reduced (14 versus 40 ng ml-1), and occurred only in ewes pretreated with oestradiol implants for 2 or 4 days. We were unable to establish a robust linear time-dose relationship, i.e., when ewes were treated with lower doses of oestradiol (one or two implants) for a reduced time (2, 4 or 8 days), there was random distribution of the 7 of 32 animals that had a reduced LH surge after oestradiol challenge (with four implants or 50 micrograms injection). The present study is the first to show that exposure for only 2-4 days to continuous oestradiol at late follicular phase concentrations can disrupt LH surge release. However, in oestradiol-treated ewes, LH secretion was provoked by high or low doses (0.5 mg or 0.5 microgram) of GnRH, although it was reduced by 50%, and a GnRH self-priming effect was still evident. All of these results suggest that inhibitory effects occur at the pituitary and hypothalamus. It remains to be confirmed whether the major effect is at the pituitary by reducing GnRH receptor or LH synthesis, or at the hypothalamus via inhibition of GnRH secretion.
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Koike ST, Smith RF. First Report of Powdery Mildew Caused by Sphaerotheca fusca on Tomatillo in California. PLANT DISEASE 1998; 82:711. [PMID: 30857033 DOI: 10.1094/pdis.1998.82.6.711c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tomatillo or husk tomato (Physalis ixocarpa Brot.) is an annual Solanaceous bush grown for its fruit, which are harvested when the fruit fill the enlarged calyx and are used primarily in Hispanic cooking. In the summer of 1997, commercial field-grown tomatillo in the Salinas Valley (Monterey County) was severely affected by a powdery mildew disease. Fungal growth was found on leaves, petioles, and calyces and resulted in twisting, desiccation, and premature senescence of the tissues. The mycelium was white to gray, ectophytic, amphigenous, and effuse. Mycelial appressoria were indistinct. Conidiophore foot cells were straight, cylindric, measured 36.1 to 61.1 µm (mean 47.0) × 11.1 to 13.9 µm (mean 11.7), and were followed by 1 to 3 shorter cells. Doliform conidia were formed in chains and measured 25.0 to 50.0 µm (mean 32.5) × 11.1 to 22.2 µm (mean 17.7). The length-to-width ratios of conidia generally were less than 2.0, and fibrosin bodies were present. Germ tubes usually were laterally inserted, lacked conspicuous appressoria, and were of the pannosa-type. Cleistothecia were not observed. Based on these characters, the fungus was identified as Sphaerotheca fusca (Fr.) Blumer, Beitr. Krypt.-Fl. Schweiz (1). Pathogenicity was confirmed by gently pressing infected leaves onto leaves of potted tomatillo. Inoculated plants were kept in a chamber at 100% humidity for 48 h, and then maintained in a greenhouse. Powdery mildew developed on inoculated plants after 12 to 14 days, while uninoculated plants did not develop disease. The experiment was conducted a second time and the results were the same. This is the first report of a powdery mildew disease of tomatillo in California. Reference: (1) U. Braun. Nova Hedwigia 89:1, 1987.
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Smith RF, Mather HM, Ellard GA. Assessment of simple colorimetric procedures to determine smoking status of diabetic subjects. Clin Chem 1998; 44:275-80. [PMID: 9474024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The performance of a simple colorimetric assay for urinary nicotine metabolites to assess smoking status in diabetic subjects (n = 251) was investigated. Several variations of the colorimetric assay and a qualitative extraction procedure were evaluated in comparison with a cotinine immunoassay as the "gold standard." Among these, the best overall performance was achieved with the qualitative test (sensitivity 95%; specificity 100%). The quantitative measurement of total nicotine metabolites performed less well (sensitivity 92%; specificity 97%) but could be improved by incorporating a blank extraction (sensitivity 98%; specificity 98%). Allowance for diuresis appeared to offer no advantage over the other methods. These results support previous findings regarding the use of these colorimetric procedures in nondiabetic subjects and, contrary to other recent observations, their performance was not impaired in diabetic patients.
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Nagy KK, Brenneman FD, Krosner SM, Fildes JJ, Roberts RR, Joseph KT, Smith RF, Barrett J. Routine preoperative "one-shot" intravenous pyelography is not indicated in all patients with penetrating abdominal trauma. J Am Coll Surg 1997; 185:530-3. [PMID: 9404875 DOI: 10.1016/s1072-7515(97)00111-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND To determine which patients need a "one-shot" intravenous pyelogram (IVP) before laparotomy for penetrating abdominal trauma. STUDY DESIGN Over a 15-month period, 240 laparotomies were performed for penetrating trauma at our urban level I trauma center. Prospectively collected data included clinical suspicion of genitourinary injury, results of preoperative IVP, intraoperative findings, and operative decisions influenced by the IVP. RESULTS Preoperative IVP was performed in 175 patients (73%). Of these, 71 (41%) had suspicion of a renal injury based on the presence of a flank wound or gross hematuria. The IVP was believed to influence operative decisions in six patients, all in this group. Each of these six patients had either a shattered kidney or a renovascular injury and had a nephrectomy performed with the knowledge that a normal functioning kidney was present on the contralateral side. No patient without a flank wound or gross hematuria had an IVP that was judged to be helpful intraoperatively. Preoperative IVP was helpful only in patients with flank wounds or gross hematuria. Nephrectomy was performed in two additional patients who did not undergo IVP, both of whom presented in shock. CONCLUSIONS Routine preoperative IVP is not necessary in all patients undergoing laparotomy for penetrating trauma. The number of IVPs can be safely reduced by 60% if the indications are narrowed to include only those stable patients with a flank wound or gross hematuria.
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Nagy KK, Krosner SM, Joseph KT, Roberts RR, Smith RF, Barrett J. A method of determining peritoneal penetration in gunshot wounds to the abdomen. THE JOURNAL OF TRAUMA 1997; 43:242-5; discussion 245-6. [PMID: 9291367 DOI: 10.1097/00005373-199708000-00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND It has previously been shown that 98% of gunshot wounds that penetrate the peritoneal cavity cause injuries that require surgical repair. Many gunshot wounds in the vicinity of the abdomen (GSWA) may actually be tangential and not penetrate the peritoneal cavity at all. Patients with such wounds may not require laparotomy. It is important to determine which patients with a potential tangential GSWA actually have penetration of the peritoneal cavity to minimize negative laparotomies. This study was undertaken to determine the sensitivity, specificity, and accuracy of diagnostic peritoneal lavage (DPL) in the determination of peritoneal penetration for patients who sustain GSWA. METHODS DPL was performed for all patients who had sustained a GSWA in whom peritoneal penetration was unclear, i.e., patients whose GSWA appeared to be tangential, thoracoabdominal, or transpelvic and for whom a clear indication for laparotomy (shock, peritonitis, etc.) did not exist. Our threshold for a positive DPL was 10,000 red blood cells (RBC)/mm3. A prospective data base was kept with information on the location of the wound, DPL result, findings at laparotomy, and outcome. RESULTS During a 4-year period, 429 consecutive DPLs were performed for GSWA at our urban Level I trauma center. One hundred fifty DPLs were positive, with more than 10,000 RBC/mm3. Six of these patients were found to have no peritoneal penetration at laparotomy (false-positive). The remaining 144 patients with positive DPLs were found to have operative injuries (true-positive). Of the 279 patients with DPL counts less than 10,000 RBC/mm3, 2 developed indications for laparotomy and were found to have intraperitoneal injuries (false-negative). The remaining 277 patients had no peritoneal injuries (true-negative). This was demonstrated either by laparotomy done for another indication (n = 7) or by uneventful inpatient observation for 24 hours (n = 270). The sensitivity, specificity, and accuracy of DPL in determining peritoneal penetration in GSWA is therefore 99, 98, and 98%, respectively. CONCLUSION For patients who sustain GSWA for whom peritoneal penetration is unclear, DPL is a sensitive, specific, and accurate test to determine the need for laparotomy. It remains our test of choice when confronted with these patients.
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Phogat JB, Smith RF, Dobson H. Effect of adrenocorticotrophic hormone on gonadotrophin releasing hormone-induced luteinizing hormone secretion in vitro. Anim Reprod Sci 1997; 48:53-65. [PMID: 9412733 DOI: 10.1016/s0378-4320(97)00030-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An in vitro perifusion study investigated the effect of different forms of adrenocorticotrophic hormone (ACTH) on gonadotrophin releasing hormone (GnRH)-induced luteinizing hormone (LH) secretion, particularly GnRH self-priming, and oestradiol sensitisation of the ovine pituitary. Fragments of pituitaries were obtained from mixed-breed adult nonpregnant female sheep (without corpora lutea, unless otherwise stated). The amount of LH released by different doses of GnRH (2.5 x 10(-10) M (n = 9 chambers), 1 x 10(-10) M (n = 9), or 5 x 10(-11) M (n = 6)) was evaluated by giving two GnRH pulses (5 min each) 2 h apart. In a duplicate set of chambers, ACTH1-24 (5 x 10(-7) M) was included in the perifusate 0.5 h before the first GnRH challenge. Potassium chloride (KCl; 100 mM) was administered 2 h after the second GnRH challenge to assess the viability of the tissue and the size of the releasable LH pool. Results were expressed as percentage of LH secretion. The influence of ACTH1-24 on oestradiol sensitisation was also examined using pituitaries obtained during the luteal phase. Pituitary tissues were perifused throughout with 1 x 10(-9) M or 6 x 10(-11) M oestradiol in the medium. The LH response to the second GnRH challenge (GnRH 2) was significantly greater (p < 0.01) than after the first (GnRH 1) at the highest dose of GnRH (2.5 x 10(-10) M; 2547 +/- 804 vs. 4547 +/- 1013%), but at the lower doses (1 x 10(-10) M or 5 x 10(-11) M), the self-priming effect of GnRH was not evident (3016 +/- 550 vs. 2932 +/- 490% and 841 +/- 205 vs. 711 +/- 87%). Treatment with ACTH1-24 (5 x 10(-7) M) did not affect tonic LH secretion nor the LH response to the first or second GnRH challenge at any of the GnRH doses tested. The LH released in response to KCl was also similar from control and ACTH1-24-treated tissue at all GnRH doses. Both lower doses of GnRH (1 x 10(-10) M or 5 x 10(-11) M) produced the self-priming effect when the pituitary tissue was sensitised with the higher dose of oestradiol (1 x 10(-9) M; 1711 +/- 239 vs. 5085 +/- 1307%, and 1502 +/- 376 vs. 2619 +/- 629%). In the presence of lower concentrations of oestradiol (6 x 10(-11) M), self-priming was observed only after the higher dose of GnRH (1 x 10(-10) M; 1293 +/- 214 vs. 2865 +/- 436%), not the lower dose (5 x 10(-11) M; 985 +/- 203 vs. 1271 +/- 436%). In spite of these differences, ACTH1-24 treatment did not affect LH secretion (neither basal nor potassium-induced). The effect of ACTH1-39 (1 x 10(-8) M or 5 x 10(-7) M; n = 6 chambers per combination) on GnRH-induced LH secretion was examined using the higher (2.5 x 10(-10) M) or lower dose of GnRH (1 x 10(-10) M), with or without oestradiol sensitisation (1 x 10(-9) M). At the lower dose (1 x 10(-8) M), ACTH1-39 influenced neither tonic nor GnRH-induced LH secretion. The LH released by KCl was also similar to the control and ACTH-treated tissue. In contrast, the higher dose of ACTH1-39 (5 x 10(-7) M) increased tonic LH secretion immediately after inclusion in the medium (104 +/- 3 vs. 161 +/- 20%), but suppressed the GnRH self-priming effect after 2.5 x 10(-10) M, i.e., the LH responses to GnRH 1 and 2 were similar (1786 +/- 294 vs. 1553 +/- 373%). However, the LH response to KCl was not significantly different (p > 0.05) between the control and ACTH-treated tissues (2333 +/- 286 vs. 2638 +/- 431%). When the effect of this higher dose of ACTH1-39 on oestradiol-priming was investigated, ACTH increased tonic LH secretion but suppressed the self-priming effect of GnRH (1 x 10(-10) M GnRH; 945 +/- 274 vs. 922 +/- 323%; p > 0.05), and decreased (p < 0.05) the LH released in response to KCl compared to the controls (1803 +/- 409 vs. 4302 +/- 1017%). In summary, in vitro, ACTH1-24 did not affect either tonic LH secretion, the GnRH self-priming effect, or oestradiol sensitisation. The entire ACTH1-39 increased tonic LH secretion, but reduced GnRH self-priming and oestradiol sensitisation. (ABSTRACT TRUNCATED)
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Smith RF, Greenwood MS. Effects of cone-induction treatments on black spruce (Picea mariana) current-year needle development and gas exchange properties. TREE PHYSIOLOGY 1997; 17:407-414. [PMID: 14759849 DOI: 10.1093/treephys/17.6.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Both drought and root pruning (RP) increased the number of cones induced when black spruce (Picea mariana (Mill.) B.S.P.) grafts were injected with gibberellins A(4/7) (GA), but their effects on predawn shoot water potential and current-year needle development differed. Drought decreased predawn shoot water potential (Psi(pd)), but only during the period when irrigation was withheld, and it had no effect on the growth or gas exchange properties of current-year needles. Conversely, root pruning had little effect on Psi(pd), but it resulted in trees with smaller current-year needles that had lower nitrogen and chlorophyll concentrations and reduced rates of gas exchange up to the later stages of shoot elongation compared with needles of control trees. These findings are discussed in relation to potential effects on the development of induced cones in the following growth cycle.
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Ladunga I, Smith RF. Amino acid substitutions preserve protein folding by conserving steric and hydrophobicity properties. PROTEIN ENGINEERING 1997; 10:187-96. [PMID: 9153083 DOI: 10.1093/protein/10.3.187] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We present a comprehensive analysis of amino acid substitution patterns (sets of residues in a position of a multiple alignment) and conservation of physicochemical properties in alignments of protein sequences. Of the one million possible substitution patterns, only a few hundred account for the majority of aligned positions. Very similar distributions of substitution patterns are observed in all but one of the diverse databases of multiple alignments. In these substitution patterns we analyzed the conservation of 511 physicochemical and steric amino acid properties. Highest conservation was observed in those steric and transfer free energy-related properties that are crucial for folding. The best conserved steric properties include the minimal width of the side chains and their interactions with other residues. Among the hydrophobicity-related properties, charge and those properties that provide information on propensities to form secondary structures or side chain conformation, appear to be better conserved than pure hydrophobicity measures. Physicochemical sequence analysis based on the most conserved properties is expected to aid searching a protein sequence query against a database of multiple alignments, prediction of secondary and tertiary structures and protein engineering.
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Smith RF, Rutt BK, Fox AJ, Rankin RN, Holdsworth DW. Geometric characterization of stenosed human carotid arteries. Acad Radiol 1996; 3:898-911. [PMID: 8959179 DOI: 10.1016/s1076-6332(96)80297-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
RATIONALE AND OBJECTIVES The geometry of stenosed carotid bifurcations was analyzed to determine average representations for several stenosis grades. METHODS Film angiograms of 62 patients with internal carotid artery stenoses were digitized. Residual lumen boundaries were manually outlined. The outlines were processed with a computer to extract geometric measurements. The measurements were grouped according to stenosis grade and used to create average representations. RESULTS Accuracy and precision of the outlining technique were +/- 0.020 common carotid diameters (CCD) and +/- 0.025 CCD, respectively. Maximum narrowing of the internal carotid artery occurred at 0.3 CCD +/- 1.5 (mean +/- standard deviation) distal to the flow divider. The region of significant narrowing extended axially 1.2 CCD +/- 1.0. Poststenotic dilatations were observed, with enlargement of 1.3 +/- 0.7 times the normal diameter of the distal internal carotid artery. A tendency toward smaller bifurcation angles with increasing stenosis severity was observed. CONCLUSION Three-dimensional geometric models could be created for carotid bifurcations that were disease free (normal) and of arbitrary stenosis grade.
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Smith RF. Perspectives: sequence data base searching in the era of large-scale genomic sequencing. Genome Res 1996; 6:653-60. [PMID: 8858340 DOI: 10.1101/gr.6.8.653] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse effects on data base searches. Upcoming problems will include (1) greatly increased search times, (2) an increase in background noise of high-scoring but biologically irrelevant matches, (3) inaccurate coding region prediction, leading to problems in protein data base searching, and (4) limited first-pass sequence annotation, making it difficult to determine the biological relevance of data base hits. Improved data base annotation tools and construction of smaller data bases of representative and highly-annotated sequences for first-pass analyses will be essential to deal with the impending flood of new genomic sequence.
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Sheaff CM, Fildes JJ, Keogh P, Smith RF, Barrett JA. Safety of 65 degrees C intravenous fluid for the treatment of hypothermia. Am J Surg 1996; 172:52-5. [PMID: 8686803 DOI: 10.1016/s0002-9610(96)00055-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND To demonstrate the safety and efficacy of 65 degrees C (149 degrees F) centrally administered intravenous fluid (CIVF) compared to conventional 40 degrees C (104 degrees F) CIVF in the treatment of hypothermia. METHOD Ten beagles (9-13 kg) were prospectively randomized to receive 65 degrees C or 40 degrees C CIVF. They were anesthetized and data were collected at baseline, during hypothermia, and after 1 and 2 hours of rewarming. The plasma free/total hemoglobin (PFHb/THb) was measured to detect hemolysis. Each subject was cooled to 30 degrees C (86 degrees F) and then received either 65 degrees C or 40 degrees C CIVF through a specialized catheter in the superior vena cava for 2 hours in addition to conventional rewarming techniques. All subjects survived 7 days, after which they were sacrificed and a complete autopsy was performed. RESULTS The rewarming rate was 3.7 degrees C/hr in the 65 degrees C CIVF group and 1.75 degrees C/hr in the 40 degrees C CIVF group. Core temperatures were significantly different after 1 hour (33.4 degrees +/- 0.77 degrees versus 31.7 degrees +/- 0.57 degrees, P < 0.01) and 2 hours (37 degrees +/- 1.03 degrees versus 33.4 degrees +/- 0.89 degrees, P < 0.001). PFHb/THb was not different. Two intimal injuries occurred in each group but these were remote from the infusion site. Blinded examination by two pathologists could not differentiate the etiology of these injuries from mechanical trauma. CONCLUSION CIVF at 65 degrees C is a safe and effective means of treating hypothermia.
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Ladunga I, Wiese BA, Smith RF. FASTA-SWAP and FASTA-PAT: pattern database searches using combinations of aligned amino acids, and a novel scoring theory. J Mol Biol 1996; 259:840-54. [PMID: 8683587 DOI: 10.1006/jmbi.1996.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We introduce two new pattern database search tools that utilize statistical significance and information theory to improve protein function identification. Both the general pattern scoring theory with the specific matrices introduced here and the low redundancy of pattern databases increase search sensitivity and selectivity. Pattern scoring preferentially rewards matches at conserved positions in a pattern with higher scores than matches at variable positions, and assigns more negative scores to mismatches at conserved positions than to mismatches at variable positions. The theory of pattern scoring can be used to create log-odds pattern scores for patterns derived from any set of multiple alignments. This theoretical framework can be used to adapt existing sequence database search tools to pattern analysis. Our FASTA-SWAP and FASTA-PAT tools are extensions of the FASTA program that search a sequence query against a pattern database. In the first step, FASTA-SWAP searches the diagonals of the query sequence and the library pattern for high-scoring segments, while FASTA-PAT performs an extended version of hashing. In the second step, both methods refine the alignments and the scores using dynamic programming. The tools utilize an extremely compact binary representation of all possible combinations of amino acid residues in aligned positions. Our FASTA-SWAP and FASTA-PAT tools are well suited for functional identification of distant relatives that may be missed by sequence database search methods. FASTA-SWAP and FASTA-PAT searches can be performed using our World-Wide Web Server (http://dot.imgen.bcm.tmc.edu:9331/seq-search/Op tions/fastapat.html).
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Levin ML, Chatterjee A, Pragliola A, Worley KC, Wehnert M, Zhuchenko O, Smith RF, Lee CC, Herman GE. A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28. Genome Res 1996; 6:465-77. [PMID: 8828036 DOI: 10.1101/gr.6.6.465] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The X-linked developmental mouse mutations bare patches (Bpa) and striated (Str) may be homologous to human X-linked dominant chondrodysplasia punctata (CDPX2) and incontinentia pigmenti (IP2), respectively, based on their genetic mapping and clinical phenotypes. Bpa and Str have been localized to an overlapping critical region of 600 kb that demonstrates conserved gene order with loci in human Xq28 between DXS1104 and DXS52. As part of efforts to isolate the genes involved in these disorders, we have begun to develop a comparative transcription map spanning this region in both species. Using techniques of cross-species conservation and hybridization, exon trapping, and cDNA selection we have identified four known genes or members of gene families--caltractin, a member of the gamma-aminobutyric acid (GABAA) receptor gene family, a member of the melanoma antigen gene (MAGE) family, and several members of the murine-specific, X-linked lymphocyte regulated gene (Xlr3) family. Trapped exons and, in some cases, longer cDNAs have been isolated for potentially 7-9 additional genes. One cDNA demonstrates highly significant homology with members of the Krüppel family of zinc finger transcription factors. A second novel cDNA demonstrates homology at the 3' end of the predicted amino acid sequence to a LIM domain consensus. Gene order appears conserved among those cDNAs determined to be present in both human and mouse. Three of the murine transcripts appear to be present in multiple copies within the Bpa/Str critical region and could be associated with a predisposition to genomic rearrangements. Reverse transcriptase PCR (RT-PCR) and Northern analysis demonstrate that several of the transcripts are expressed in mid-gestation murine embryos and neonatal skin, making them candidates for the Bpa and Str mutations and their respective homologous human disorders.
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Smith RF, Wiese BA, Wojzynski MK, Davison DB, Worley KC. BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res 1996; 6:454-62. [PMID: 8743995 DOI: 10.1101/gr.6.5.454] [Citation(s) in RCA: 256] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.
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Smith RF, Jackson LS, Moore A. Establishing the cut-off concentration for the detection of etorphine in horse urine. Analyst 1996; 121:67-9. [PMID: 8588699 DOI: 10.1039/an9962100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
An 125I radioimmunoassay to determine the pattern of urinary excretion of etorphine (a semisynthetic opiate agonist) after its administration to horses is described. Three thoroughbred horses were each given 5, 15, 30 and 100 micrograms of etorphine intramuscularly. Urine was collected for up to 72 after administration. The maximum etorphine concentration after administration of a dose of 5 micrograms was 711 pg ml-1 (concentrations were greater than 100 pg ml-1 after 23 h in all three horses); a 15 micrograms gave 2661 pg ml-1 (levels remained above 100 pg ml-1 for more than 44 h in each horse); a 30 micrograms dose gave a maximum of 3344 pg ml-1 (levels were above 100 pg ml-1 for 24, 72 and 72 h); and 100 micrograms gave in excess of 10,000 pg ml-1 (levels were greater than 300 pg ml-1 for up to 70 h). Forty-eight urine samples from horses not given etorphine all had levels of etorphine less than 100 pg ml-1. There was no increase in apparent etorphine concentrations after hydrolysis of samples with beta-glucuronidase and aryl sulfatase. The half-lives of etorphine equivalents (calculated with a mono-exponential equation after the 100 micrograms dose) in the urine of the three horses were 569, 803 and 821 min, respectively. We conclude that radioimmunoassay can provide a useful first line screening procedure for the assessment of etorphine use in racing horses.
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Nagy KK, Fildes JJ, Sloan EP, Kim DO, Smith RF, Roberts RR, Krosner SM, Joseph K, Barrett J. Aspiration of free blood from the peritoneal cavity does not mandate immediate laparotomy. Am Surg 1995; 61:790-5. [PMID: 7661477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The objective was to establish the relationship between the aspiration of free blood (+ASP) versus diagnostic peritoneal lavage (DPL), abdominal injury severity, hemodynamic instability, and the need for immediate operative intervention. We prospectively compared the significance of +ASP to +DPL in our level I trauma center. Consecutive patients received sequential needle tap, catheter aspiration (ASP), and DPL. If gross blood was withdrawn during the tap or ASP, it was returned to the peritoneal cavity before completing the DPL. The DPL was considered positive if there were > 100,000 RBCs for blunt injuries or anterior abdominal stab wounds, or > 10,000 RBCs for other penetrating injuries. During a 12-month period, 566 patients fulfilled the study criteria; they were 50 per cent blunt and 50 per cent penetrating trauma. There were 70 patients with both +ASP/+DPL, 30 with -ASP/+DPL and 4 with +ASP but -DPL. Exploratory laparotomy was performed on these 104 patients (18.4%), 22 of which were considered nontherapeutic. The ATI was statistically higher in the +ASP patients (14.9 +/- 12.9 versus 8.5 +/- 8.2, P < 0.05) but was not clinically different. Overall injury severity and hemodynamic stability were not different in the two groups. The sensitivity of DPL at detecting intra-abdominal injury was higher than the ASP group (98% versus 72%), but the specificities were equal (98%). Because +ASP patients are not more critically injured or unstable than +DPL patients, and because DPL is more accurate in detecting the need for operative intervention, aspiration should be abandoned as part of the DPL procedure in patients with abdominal trauma.
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