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Publication
Journal: Journal of biomolecular NMR
January/24/1996
Abstract
The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
Publication
Journal: Nucleic acids research
September/26/2010
Abstract
The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.
Publication
Journal: Cancer research
June/14/1988
Abstract
A case-control study of oral and pharyngeal cancer conducted in four areas of the United States provided information on the tobacco and alcohol use of 1114 patients and 1268 population-based controls. Because of the large study size, it could be shown that the risks of these cancers among nondrinkers increased with amount smoked, and conversely that the risks among nonsmokers increased with the level of alcohol intake. Among consumers of both products, risks of oropharyngeal cancer tended to combine more in a multiplicative than additive fashion and were increased more than 35-fold among those who consumed two or more packs of cigarettes and more than four alcoholic drinks/day. Cigarette, cigar, and pipe smoking were separately implicated, although it was shown for the first time that risk was not as high among male lifelong filter cigarette smokers. Cessation of smoking was associated with a sharply reduced risk of this cancer, with no excess detected among those having quit for 10 or more years, suggesting that smoking affects primarily a late stage in the process of oropharyngeal carcinogenesis. The risks varied by type of alcoholic beverage, being higher among those consuming hard liquor or beer than wine. The relative risk patterns were generally similar among whites and blacks, and among males and females, and showed little difference when oral and pharyngeal cancers were analyzed separately. From calculations of attributable risk, we estimate that tobacco smoking and alcohol drinking combine to account for approximately three-fourths of all oral and pharyngeal cancers in the United States.
Publication
Journal: Methods in enzymology
October/18/1992
Abstract
This chapter describes corrections that have to be applied to measured membrane potentials in patch clamp experiments. Some of them [Eqs. (1)-(3)] are required regardless of the nature of the reference electrode (in the Ringer's solution bath) whenever the pipette-filling solution is different from the bath solution. They represent the liquid junction potentials that are present at the pipette tip before patch formation. In addition, corrections have to be applied when the bath solution is being changed during a measurement (i.e., after seal formation). In that case the following rules apply. (1) The new solution should never get into contact with the bare silver/silver chloride wire of the reference electrode. This requirement is best met by using a salt bridge. (2) The "best" salt bridge is a 3 M KCl bridge with an abrupt KCl-bath fluid boundary at its tip (see above). This bridge does not require any additional potential corrections, but it may lead to KCl poisoning of the bath or become contaminated by solutions used previously. (3) Local solution changes (microperfusion by puffer pipette, U tool or sewer pipe arrangements) as well as recessed KCl bridges require additional corrections, which (together with the simple liquid junction potential correction) are approximately given by Eqs. (6)-(8). It should be stressed that all equations given here represent approximate corrections, since liquid junction potentials are thermodynamically ill-defined. This is particularly relevant for Eqs. (6) and (7) where the sum of two liquid junction potentials appears.
Authors
Publication
Journal: International journal of cancer
January/17/2005
Abstract
Esophageal cancer incidence and mortality rates in Linxian, China are among the highest in the world. We examined risk factors for esophageal squamous cell carcinoma (ESCC), gastric cardia cancer (GCC), and gastric noncardia cancer (GNCC) in a population-based, prospective study of 29,584 adults who participated in the Linxian General Population Trial. All study participants completed a baseline questionnaire that included questions on demographic characteristics, personal and family history of disease, and lifestyle factors. After 15 years of follow-up, a total of 3,410 incident upper gastrointestinal cancers were identified, including 1,958 ESCC, 1,089 GCC and 363 GNCC. Cox proportional hazard models were used to estimate risks. Increased age and a positive family history of esophageal cancer (including ESCC or GCC) were significantly associated with risk at all 3 cancer sites. Additional risk factors for ESCC included being born in Linxian, increased height, cigarette smoking and pipe smoking; for GCC, male gender, consumption of moldy breads and pipe smoking; and for GNCC, male gender and cigarette smoking. Protective factors for ESCC included formal education, water piped into the home, increased consumption of meat, eggs and fresh fruits and increased BMI; for GCC, formal education, water piped into the home, increased consumption of eggs and fresh fruits and alcohol consumption; and for GNCC, increased weight and BMI. General socioeconomic status (SES) is a common denominator in many of these factors and improving SES is a promising approach for reducing the tremendous burden of upper gastrointestinal cancers in Linxian.
Publication
Journal: JAMA
May/8/1996
Abstract
OBJECTIVE
To determine the impact of tobacco- and alcohol-related deaths on overall mortality following inpatient treatment for alcoholism and other nonnicotine drugs of dependence.
METHODS
Population-based retrospective cohort study.
METHODS
Olmsted County, Minnesota (the Rochester Epidemiology Project), and the Inpatient Addiction Program (IAP) at Mayo Clinic, Rochester.
METHODS
All 845 Olmsted County residents admitted to an inpatient addiction program for treatment of alcoholism and other nonnicotine drugs of dependence during the period 1972 through 1983.
METHODS
Patients were followed up through the medical record linkage system of the Rochester Epidemiology Project through December 1994 to obtain vital status, and death certificates were obtained for those who died. The underlying cause of death was classified as alcohol related, tobacco related, both, or neither based on the classification from the Centers for Disease Control and Prevention. The observed number of deaths by underlying cause were compared with the expected number using cause-specific 1987 death rates for the white population of the United States. All-cause mortality was also compared with that expected for persons in the West North Central Region of the United States of like age, sex, and year of birth. Univariate and multivariate assessments were made to identify predictors of all-cause mortality from baseline demographic information.
RESULTS
At admission, the mean (SD) age of the 845 patients was 41.4 (14.5) years, and 35% were women. Altogether, 78% had alcohol as their only nonnicotine drug of dependence and 18% had alcohol and other nonnicotine drugs of dependence, while 4% were classified as having a nonalcohol, nonnicotine drug dependence alone. At admission, 75% were current and 8% former cigarette smokers, 3% were current cigar or pipe smokers, and 2% were current users of smokeless tobacco. Follow-up after the index IAP admission totaled 8913 person-years (mean [SD] of 10.5 [5.6] years per patient). Death certificates were obtained for 96% (214) of the 222 patients who died. Of these 214 deaths, 50.9% (109) had a tobacco-related and 34.1% (73) had an alcohol-related underlying cause (P<.001). The cumulative mortality significantly exceeded that expected (P<.001); at 20 years, the observed mortality was 48.1% vs an expected 18.5%. Multivariate predictors of mortality, even after adjusting for expected mortality, were older age at admission (P<.001) and male sex (P<.001).
CONCLUSIONS
Patients previously treated for alcoholism and/or other nonnicotine drug dependence had an increased cumulative mortality that was due more to tobacco-related than to alcohol-related causes. Nicotine dependence treatment is imperative in such high-risk patients.
Publication
Journal: MMWR. Morbidity and mortality weekly report
June/9/2015
Abstract
Tobacco use and addiction most often begin during youth and young adulthood. Youth use of tobacco in any form is unsafe. To determine the prevalence and trends of current (past 30-day) use of nine tobacco products (cigarettes, cigars, smokeless tobacco, e-cigarettes, hookahs, tobacco <em>pipes</em>, snus, dissolvable tobacco, and bidis) among U.S. middle (grades 6-8) and high school (grades 9-12) students, CDC and the Food and Drug Administration (FDA) analyzed data from the 2011-2014 National Youth Tobacco Surveys (NYTS). In 2014, e-cigarettes were the most commonly used tobacco product among middle (3.9%) and high (13.4%) school students. Between 2011 and 2014, statistically significant increases were observed among these students for current use of both e-cigarettes and hookahs (p<0.05), while decreases were observed for current use of more traditional products, such as cigarettes and cigars, resulting in no change in overall tobacco use. Consequently, 4.6 million middle and high school students continue to be exposed to harmful tobacco product constituents, including nicotine. Nicotine exposure during adolescence, a critical window for brain development, might have lasting adverse consequences for brain development, causes addiction, and might lead to sustained tobacco use. For this reason, comprehensive and sustained strategies are needed to prevent and reduce the use of all tobacco products among youths in the United States.
Publication
Journal: American journal of epidemiology
August/15/1979
Abstract
An excess of electrical wiring configurations suggestive of high current-flow was noted in Colorado in 1976--1977 near the homes of children who developed cancer, as compared to the homes of control children. The finding was strongest for children who had spent their entire lives at the same address, and it appeared to be dose-related. It did not seem to be an artifact of neighborhood, street congestion, social class, or family structure. The reason for the correlation is uncertain; possible effects of current in the water pipes or of AC magnetic fields are suggested.
Publication
Journal: Archives of internal medicine
June/20/2000
Abstract
BACKGROUND
Obstructive lung disease (OLD) is an important cause of morbidity and mortality in the US adult population. Potentially treatable mild cases of OLD often go undetected. This analysis determines the national estimates of reported OLD and low lung function in the US adult population.
METHODS
We examined data from the Third National Health and Nutrition Examination Survey (NHANES III), a multistage probability representative sample of the US population. A total of 20,050 US adults participated in NHANES III from 1988 to 1994. Our main outcome measures were low lung function (a condition determined to be present if the forced expiratory volume in 1 second-forced vital capacity ratio was less than 0.7 and the forced expiratory volume in 1 second was less than 80% of the predicted value), a physician diagnosis of OLD (chronic bronchitis, asthma, or emphysema), and respiratory symptoms.
RESULTS
Overall a mean (SE) of 6.8% (0.3%) of the population had low lung function, and 8.5% (0.3%) of the population reported OLD. Obstructive lung disease (age-adjusted to study population) was currently reported among 12.5% (0.7%) of current smokers, 9.4% (0.6%) of former smokers, 3.1% (1.1%) of pipe or cigar smokers, and 5.8% (0.4%) of never smokers. Surprisingly, 63.3% (0.2%) of the subjects with documented low lung function had no prior or current reported diagnosis of any OLD.
CONCLUSIONS
This study demonstrates that OLD is present in a substantive number of US adults. In addition, many US adults have low lung function but no reported OLD diagnosis, which may indicate the presence of undiagnosed lung disease.
Publication
Journal: Proteins
May/1/2008
Abstract
Successful protein expression, purification, and crystallization for challenging targets typically requires evaluation of a multitude of expression constructs. Often many iterations of truncations and point mutations are required to identify a suitable derivative for recombinant expression. Making and characterizing these variants is a significant barrier to success. We have developed a rapid and efficient cloning process and combined it with a protein microscreening approach to characterize protein suitability for structural studies. The Polymerase Incomplete Primer Extension (PIPE) cloning method was used to rapidly clone 448 protein targets and then to generate 2143 truncations from 96 targets with minimal effort. Proteins were expressed, purified, and characterized via a microscreening protocol, which incorporates protein quantification, liquid chromatography mass spectrometry and analytical size exclusion chromatography (AnSEC) to evaluate suitability of the protein products for X-ray crystallography. The results suggest that selecting expression constructs for crystal trials based primarily on expression solubility is insufficient. Instead, AnSEC scoring as a measure of protein polydispersity was found to be predictive of ultimate structure determination success and essential for identifying appropriate boundaries for truncation series. Overall structure determination success was increased by at least 38% by applying this combined PIPE cloning and microscreening approach to recalcitrant targets.
Publication
Journal: Protein expression and purification
June/29/2004
Abstract
Microtubules can be assembled in vitro from purified alpha/beta tubulin heterodimers in the presence of GTP. Tubulin is routinely obtained from animal brain tissue through repetitive cycles of polymerization-depolymerization, followed by ion-exchange chromatography to remove any contaminating microtubule-associated proteins and motors. Here, we show that only two cycles of polymerization-depolymerization of pig brain tubulin in the presence of a high-molarity PIPES buffer allow the efficient removal of contaminating proteins and production of a high-concentration tubulin solution. The proposed protocol is rapid and yields more active tubulin than the traditional ion-exchange chromatography-based procedures.
Publication
Journal: JAMA
August/16/2000
Abstract
BACKGROUND
Adults aged 18 to 24 years, many of whom are in college, represent the youngest legal targets for tobacco industry marketing. Cigarette smoking has been described among college students, but little is known about non-cigarette tobacco use by college students or cigar use by adults of any age.
OBJECTIVE
To assess the prevalence of all forms of tobacco use (cigarettes, cigars, pipes, and smokeless tobacco) among US college students and to identify student- and college-level factors associated with use of each product.
METHODS
The Harvard College Alcohol Survey, a self-administered survey conducted in 1999.
METHODS
One hundred nineteen nationally representative US 4-year colleges.
METHODS
A total of 14,138 randomly selected students (60% response rate).
METHODS
Self-report of current (in the past 30 days), past-year, and lifetime use of cigarettes, cigars, pipes, smokeless tobacco, and all tobacco products.
RESULTS
Nearly half (45.7%) of respondents had used a tobacco product in the past year and one third (32.9%) currently used tobacco. Cigarettes accounted for most of the tobacco use (28.5% current prevalence), but cigar use was also substantial (37.1% lifetime prevalence, 23.0% past-year prevalence, and 8.5% current prevalence) and combinations of the 2 were common. Total tobacco use was higher in men than in women (37. 9% vs 29.7%; P<.001), despite nearly identical current cigarette smoking rates between the sexes (28.5% for women vs 28.4% for men), because of greater use of cigars (current prevalence, 15.7% vs 3.9%; P<.001) and smokeless tobacco (current prevalence, 8.7% vs 0.4%; P<. 001) by men. Tobacco use was significantly higher among white students (P<.001), users of other substances (alcohol and marijuana) (P<.001), and students whose priorities were social rather than educational or athletic (P<.05). Among students who had used both cigars and cigarettes, only 8.9% smoked cigars at an earlier age than they had smoked cigarettes.
CONCLUSIONS
Our study indicates that tobacco use is common among college students and is not limited to cigarettes. College appears to be a time when many students are trying a range of tobacco products and are in danger of developing lifelong nicotine dependence. National efforts to monitor and reduce tobacco use of all types should expand to focus on college students and other young adults. JAMA. 2000;284:699-705
Publication
Journal: Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association
April/24/2005
Abstract
A smoking machine protocol and yields for "tar", nicotine, PAH, and CO are presented for the standard 171-puff steady periodic smoking regimen proposed by Shihadeh et al. [Shihadeh, A., Azar, S., Antonios, C., Haddad, A., 2004b. Towards a topographical model of narghile water-pipe cafe smoking: A pilot study in a high socioeconomic status neighborhood of Beirut, Lebanon. Pharmacology Biochemistry and Behavior 79(1), 75]. Results show that smokers are likely exposed to more "tar" and nicotine than previously thought, and that pyronsynthesized PAH are present in the "tar" despite the low temperatures characteristic of the tobacco in narghile smoking. With a smoking regimen consisting of 171 puffs each of 0.53l volume and 2.6s duration with a 17 s interpuff interval, the following results were obtained for a single smoking session of 10 g of mo'assel tobacco paste with 1.5 quick-lighting charcoal disks applied to the narghile head: 2.94 mg nicotine, 802 mg "tar", 145 mg CO, and relative to the smoke of a single cigarette, greater quantities of chrysene, phenanthrene, and fluoranthene. Anthracene and pyrene were also identified but not quantified. The results indicate that narghile smoke likely contains an abundance of several of the chemicals thought to be causal factors in the elevated incidence of cancer, cardiovascular disease and addiction in cigarette smokers.
Publication
Journal: Nature
October/17/2005
Abstract
Rich circumstantial evidence suggests that the extensive behavioural diversity recorded in wild great apes reflects a complexity of cultural variation unmatched by species other than our own. However, the capacity for cultural transmission assumed by this interpretation has remained difficult to test rigorously in the field, where the scope for controlled experimentation is limited. Here we show that experimentally introduced technologies will spread within different ape communities. Unobserved by group mates, we first trained a high-ranking female from each of two groups of captive chimpanzees to adopt one of two different tool-use techniques for obtaining food from the same 'Pan-pipe' apparatus, then re-introduced each female to her respective group. All but two of 32 chimpanzees mastered the new technique under the influence of their local expert, whereas none did so in a third population lacking an expert. Most chimpanzees adopted the method seeded in their group, and these traditions continued to diverge over time. A subset of chimpanzees that discovered the alternative method nevertheless went on to match the predominant approach of their companions, showing a conformity bias that is regarded as a hallmark of human culture.
Publication
Journal: Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association
January/12/2003
Abstract
A first-generation smoking machine and protocol have been developed in order to study the mainstream smoke aerosol and elucidate thermal-fluid processes of the argileh water pipe. Results using a common mo'assel tobacco mixture show that, contrary to popular perceptions, the mainstream smoke contains significant amounts of nicotine, "tar" and heavy metals. With a standard smoking protocol of 100 puffs of 3 s duration spaced at 30-s intervals, the following results were obtained in a single smoking session: 2.25 mg nicotine, 242 mg nicotine-free dry particulate matter (NFDPM), and relative to the smoke of a single cigarette, high levels of arsenic, chromium and lead. It was found that increasing puff frequency increased the NFDPM but had little effect on nicotine delivery, while removing the water from the bowl increased by several-fold the nicotine, but had little effect on NFDPM. It was also found that the charcoal disk heat source contributed less than 2% of total particulate matter (TPM), and that characteristic temperatures of the tobacco varied from 450 degrees C nearest the heat source to 50 degrees C furthest away, indicating that the NFDPM is likely a result of devolatilization rather than chemical reaction, and will thus differ significantly in composition from that of cigarette smoke.
Authors
Publication
Journal: Journal of the National Cancer Institute
April/27/1977
Abstract
From personal interviews obtained for 7,518 incident cases of invasive cancer from the population-based Third National Cancer Survey, the quantitative lifetime use of cigarettes, cigars, pipes, unsmoked tobacco, wine, beer, hard liquor, and combined alcohol were recorded, as well as education and family income level. In an initial screening analysis of these data, Mantel-Haenszel 2 X 2 contingency tabulations and multiple regression analyses were used to compare each specific cancer site with controls from other sites to test for associations with the "exposure variables." Significant positive associations with cigarette smoking were found for cancers of the lung, larynx, oral cavity, esophagus, stomach, pancreas, bladder, kidney, and uterine cervix. Other forms of tobacco were associated with cancers of the oral cavity, larynx, lung, and cervix. Consumption of wine, beer, hard liquor, and all combined showed positive associations with neoplasms of the oral cavity larynx, esophagus, colon, rectum, breast, and thyroid gland. College educaton and high income both showed positive associations with cancers of the breast, thyroid gland, uterine corpus, and melanomas in males. These same indicators of high socioeconomic status showed inverse associations with invasive neoplasms of the uterine cervix, lung, lip-tongue, and colon in females. College attendance (but not income) showed an inverse association with stomach cancer and positive association with pancreatic cancer in males. Still other tumor sties showed "suggestive" associations with each of these exposure variables. In the analyses producing these results, age, race, sex, smoking, drinking, education, income, parity, foreign birth, marital status, and geographic location were used as stratification variables separately or in combination when appropriate to assess and control for their potentially confounding affects and to examine results in different strata to assess interaction.
Publication
Journal: The Journal of biological chemistry
November/12/1997
Abstract
The observation that the nematode cell death effector gene product Ced-3 is homologous to human interleukin-1beta-converting enzyme (caspase-1) has led to the discovery of at least nine other human caspases, many of which are implicated as mediators of apoptosis. Significant interest has been given to aspects of the cell biology and substrate specificity of this family of proteases; however, quantitative descriptions of their biochemical characteristics have lagged behind. We describe the influence of a number of environmental parameters, including pH, ionic strength, detergent, and specific ion concentrations, on the activity and stability of four caspases involved in death receptor-mediated apoptosis. Based on these observations, we recommend the following buffer as optimal for investigation of their characteristics in vitro: 20 mM piperazine-N,N'-bis(2-ethanesulfonic acid) (PIPES), 100 mM NaCl, 10 mM dithiothreitol, 1 mM EDTA, 0.1% 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonic acid (CHAPS), 10% sucrose, pH 7.2. Caspase activity is not affected by concentrations of Ca2+ below 100 mM, but is abolished by Zn2+ in the submicromolar range, a common characteristic of cysteine proteases. Optimal pH values vary from 6.8 for caspase-8 to 7.4 for caspase-3, and activity of all is relatively stable between 0 and 150 mM NaCl. Consequently, changes in the physiologic pH and ionic strength would not significantly alter the activity of the enzymes, inasmuch as all four caspases are optimally active within the range of these parameters found in the cytosol of living and dying human cells.
Publication