Defining the structure of irregular nucleic acids: conventions and principles

The algorithm "Curves", that we have recently presented in this journal (J. Biolmol. Str. Dynam. 6, 63-91 (1988], is updated to take into account the conventions developed at the Cambridge meeting on DNA curvature (September 1988) and extended to the calculation of local parameters. In addition, the principles which govern the choices made in establishing the Curves algorithm are compared with the approaches adopted by other authors.     

‘Seeing’ Atomic Radiations

Miller, Christina G., and Louise A. Berry. Coastal Rescue: Preserving Our Seashores. New York: Atheneum (Macmillan), 1989. 120 pp. $12.95 hardcover. Reviewed by Wayne Hanley.

Marschall, Laurence A. The Supernova Story. New York: Plenum Press, 1988. 296 pp. $22.95 hardcover. Reviewed by Julian R. Brandou.

Young, Steven B. To the Arctic: An Introduction to the Far Northern World. New York: John Wiley &; Sons, 1989. 354 pp. $24.95 hardcover. Reviewed by Emanuel D. Rudolph.

Eldredge, Niles. Life Pulse: Episodes from the Story of the Fossil Record. New York: Facts On File Publications, 1987. 246 pp. $10.95 paperback. Reviewed by Robert G. Hoehn.

Langhorne, M. J., J. O. Donham, J. F. Gross, and D. Rehmke. Teaching with Computers: A New Menu for the 90's. Phoenix, Ariz.: The Oryx Press, 1988. 218 pp. 822.50 paperback. Reviewed by John M. Newell.

VanCleave, Janice Pratt. Chemistry for Every Kid: 101 Easy Experiments That Really Work. New York: John Wiley &; Sons, 1989. 232 pp. $10.95 paperback. Reviewed by Edward L. Shaw, Jr.

Smithsonian Family Learning Project. Science Activity Book: 20 Exciting Experiments for Parents and Kids To Do, (More Science Activities: 20 Exciting Experiments To Do, Still More Science Activities: 20 Exciting Experiments To Do). New York: Galison Books, 1987, (1988, 1989). 96 pp. $9.95. Reviewed by Susan McCarthy.

Summerlin, Lee R., and James L. Ealy, Jr. Chemical Demonstrations: A Source Book for Teachers, Vol. 1 (2d Ed.). 1988. Reviewed by Ann C. Howe and Alice D. Anderson.

Summerlin, Lee R., Christie L. Borgford, Julie B. Ealy. Chemical Demonstrations: A Source Book for Teachers, Vol. 2 (2d Ed.). 1988. Washington, D.C.: American Chemical Society. 197 pp., 233 pp. each $19.95 paperback. Reviewed by Ann C. Howe and Alice D. Anderson.

Berger, Melvin. Atoms, Molecules and Quarks. New York: G. P. Putnam's Sons, 1986. 79 pp. $9.99 hardcover. Reviewed by Harold H. Jaus.

Hersey, Robert L. How to Think with Numbers. Providence, R.I.: Janson Publications, 1982. 133 pp. $795 paperback. Reviewed by C. Bruce Hunter.

Treffert, Darold A. Extraordinary People: Understanding “Idiot Savants.” New York: Harper &; Row, 1989. 291 pp. $17.95 hardcover Reviewed by Elissa Malcohn.     

An Automatic Search for Similar Spatial Arrangements of α-Helices and β-Strands in Globular Proteins

Abstract

A fast search algorithm to reveal similar polypeptide backbone structural motifs in proteins is proposed. It is based on the vector representation of a polypeptide chain fold in which the elements of regular secondary structures are approximated by linear segments (Abagyan and Maiorov, J. Biomol. Struct. Dyn. 5, 1267–1279 (1988)). The algorithm permits insertions and deletions in the polypeptide chain fragments to be compared. The fast search algorithm implemented in FASEAR program is used for collecting βαβ supersecondary structure units in a number of α/β proteins of Brookhaven Data Bank. Variation of geometrical parameters specifying backbone chain fold is estimated. It appears that the conformation of the majority of the fragments, although almost all of them are right-handed, is quite different from that of standard βαβ units. Apart from searching for specific type of secondary structure motif, the algorithm allows automatically to identify new recurrent folding patterns in proteins. It may be of particular interest for the development of tertiary template approach for prediction of protein three-dimensional structure as well for constructing artificial polypeptides with goal-oriented conformation.     

Field Investigations

Lockhart, Gary. The Weather Companion: An Album of Meteorological History, Science, Legend, and Folklore. New York: John Wiley &; Sons, 1988. 230 pp. $12.95 paperback Reviewed by Albert C. Jensen

Davidovits, Joseph, and Margic Morris. The Pyramids: An Enigma Solved . New York: Hippocrene Books, 1988. 263 pp. $16.95 hardcover Reviewed by Clarence J. Murphy     

Stimulating the Need to Know…

Nations, James D. Tropical Rainforest: Endangered Environment . New York: Franklin Watts, 1988. 143 pp. $12.90 hardcover. Reviewed by Jorge Zamacona Evenes.

Sharp, D.W.A., ed. The Penguin Dictionary of Chemistry , 2d ed. New York: Penguin, 1990. 434 pp. $9.95 paperback. Reviewed by Wayne Hanley.

Hale, W.G., and J.P. Margham. The HarperCollins Dictionary of Biology. New York: Harper Collins, 1991. 569 pp. $12.95 paperback; $25.00 hardcover. Reviewed by Wayne Hanley.

Sparks, John, and Tony Soper. Penguins. New York: Fact On File, 1987. 246 pp. $1995 hardcover. Reviewed by Wayne Hanley.

Mountfort, Guy. Rare Birds of the World . A Collins/ICBP Handbook. New York: Penguin (The Stephen Greene Press), 1988. 256 pp. $2995 hardcover. Reviewed by John W. McLure.

Woodcock, Martin. Collins Handguide to the Birds of the Indian Subcontinent . New York: Penguin (The Stephen Greene Press), 1989. 176 pp. $11.95 paperback. Reviewed by James Scheib.

Harris, Michael. The Collins Field Guide to the Birds of Galapagos . New York: Penguin (The Stephen Greene Press), 1989. 160 pp. $1995 hardcover. Reviewed by Jim Fuller.

Brudenell-Bruce, P. G. C. The Collins Guide to the Birds of New Providence and the Babama Islands. New York: Penguin (The Stephen Greene Press), 1989. 142 pp. $14.95 paperback. Reviewed by Carol A. Thompson.     

Description of a new species of Alboglossiphonia Lukin, 1976 (Hirudinea: Glossiphoniidae) from Egypt

Abstract

Alboglossiphonia disugi n.sp. was collected from the Nile and freshwater channels in the delta region of Egypt during 1988. The morphology, anatomy and taxonomy of the leech are dealt with.     

Hétéroptères Miridae de Guyane française: Liste préliminaire,descriptions de taxa nouveaux et données additionnelles

Deux nouveaux genres et six espèces nouvelles sont décrits de Guyane française, à savoir: Diplozona emboíiata n. sp., Guianocoris unicolor n. g., n. sp., Lundioides couturíerin. gen, n. sp., Neella guiana n. sp., Phytocorís guianus n. sp. et Phytocorís jugatus n. sp. La nouvelle combinaison Guianocoris ruber (Carvalho & Carpintero 1991a) n. comb, est proposée. Deux espèces sont redécrites et illustrées: Sthenaridea carvalhoi Schuh & Schwartz 1988 et Proboscidotyius nigrosquamis (Maldonado 1969). Les genitalias femelles d’lridopeplus pellucidipennis Bergroth 1910 sont décrits pour la premiere fois, ainsi que le mâle d’Henicocnemis luctuosa (Stål 1860). La variabilité de Monalonion annulipes Signoret 1858 est mise en évidence. Quatorze espèces sont signalées comme nouvelles pour la faune de Guyane: Fuivius bisbistiilatus (Stål 1860), F. satipoensis Carvalho & Costa 1994 Henicocnemis Iuctuosa (Stål 1860), Horcisoides punctatus (Carvalho 1976), Maxacalinus cuiabanus Carvalho 1976, Notholopus coreoides Carvalho 1975, N. cuiabanus Carvalho 1975, Proboscidotyius nigrosquamis (Maldonado 1969), Sthenaridea carvalhoi Schuh & Schwartz 1988, Taedia bananaiensis Carvalho & Costa 1994, T. cajabiana Carvalho 1976, T. coimbrai Carvalho 1975, T. compactoides Carvalho 1975 et T. xinguana Carvalho 1975, ce qui porte la liste provisoire des Miridae du Dèpartement à 46 espèces.     

A pilot randomized controlled trial of a commercial diet and exercise weight loss program in minority breast cancer survivors

Objective:

Obesity is associated with poorer breast cancer outcomes and losing weight postdiagnosis may improve survival. As Hispanic and black women have poorer breast cancer prognosis than non‐Hispanic whites diagnosed at similar age and stage, and have higher rates of obesity, effective weight loss strategies are needed. We piloted a randomized, waitlist‐controlled, crossover study to examine the effects and feasibility of the commercial Curves weight loss program among Hispanic, African American and Afro‐Caribbean breast cancer survivors.

Design and Methods:

Women with stage 0–IIIa breast cancer ≥6 months posttreatment, sedentary, and BMI ≥25 kg/m² were randomized to the immediate arm (IA): 6 months of the Curves program followed by 6 months of observation; or the waitlist control arm (WCA): 6 months of observation followed by 6 months of the Curves program. The Curves program uses a 30‐min exercise circuit and a high‐vegetable/low‐fat/calorie‐restricted diet.

Results:

A total of 42 women enrolled (79% Hispanic, 21% black), mean age 51 (range 32–69) and mean BMI 33.2(±5.9) kg/m²; 91% were retained at month 12. At month 6, women in the IA lost an average 3.3% (±3.5%) of body weight (range: 1.7% gain to 10.6% loss), as compared with 1.8% (±2.9%) weight loss in the WCA (P = 0.04). At month 12, on average women in the IA regained some but not all of the weight lost during the first 6 months (P = 0.02).

Conclusions:

Minority breast cancer survivors were recruited and retained in a weight loss study. Six months of the Curves program resulted in moderate weight loss, but weight loss was not maintained postintervention. Future interventions should identify methods to increase uptake and maintenance of weight loss behaviors.     

Use of the Cadzow procedure in 2D NMR for the reduction of t1 noise

Summary A data processing approach is proposed for reducing the t₁ noise observed in multidimensional NMR spectra. This method is based on the use of the Cadzow procedure [Cadzow, J.A. (1988) IEEE Trans. Acous. Speech Signal Proc., 36, 49–62], and is demonstrated to be efficient for simulated cases as well as real experiments.     

An algorithm to equiprobably generate all directed trees withk labeled terminal nodes and unlabeled interior nodes

A computer algorithm is presented which equiprobably generates any member of the set of all directed trees withk labeled terminal nodes and unlabeled interior nodes. The algorithm requires roughlyk ² /2 storage locations. The one-time initialization requiresO(k ² ) time, while generating each tree requiresO(k) time. Contribution No. 477 in Ecology and Evolution, State University of New York at Stony Brook. This research was supported by Grant No. DEB8003508 from the National Science Foundation to Robert R. Sokal.     

Big-game,small-game,and gamebird hunting in New Zealand: Hunting effort,harvest, and expenditure in 1988

Abstract

A postal survey of 8639 licensed firearm owners in 1989 indicated that an estimated 117 200 ± 6300 New Zealanders (3.5% of the total population) did some hunting in 1988. An estimated 33 100 former hunters did not hunt in 1988 but thought it likely that they would hunt again in future. The survey provided useful estimates of 1988 national totals for hunting effort (4.4 million hunter days), gross expenditure ($NZ100 million), and harvest (6.5 million animals).

Small-game hunting dominated, involving 81% of hunters, 59% of total hunting effort, and 86% of total numerical harvest: rabbits (Oryctolagus cuniculus) and possums (Trichosurus vulpecula) each comprised 40% of the national bag. Gamebird hunting involved 48% of hunters, 19% of effort, and 11% of total harvest: ducks comprised 73% of the gamebird harvest. Although big-game hunting attracted the fewest hunters (42%) it ranked second for hunting effort (21%). Big game formed 3% of the total numerical harvest: pigs (Sus scrofa), goats (Capra hircus), and red deer (Cervus elaphus scoticus) were the most commonly taken. Big-game were estimated to comprise 49% of total harvest biomass, followed by small-game (47%), and gamebirds (4%). Most deer (nearly 60%) were taken for recreation, with helicopter-based hunting accounting for only one-third the total deer harvest.

A quarter of those people hunting in 1988 hunted on five or fewer days that year, and a relatively small group of mainly professional hunters accounted for a disproportionately large share of the overall harvest Hunters reported spending an average of $851 each on hunting in 1988. Expenditure on big-game comprised 44% of the total, small-game 23%, and gamebirds 33%. Expenditure per animal harvested or per day hunted was greater for big-game animals (other than goats) than for gamebirds, which were more expensive to hunt than small-game. Total hunting effort was inversely related to the average expenditure per animal harvested, regardless of the type of game.     

Assessing augmentative releases of parasitoids using the «Recruitment method», with reference toEdovum puttleri,a parasitoid of the colorado potato beetle [Coleoptera: chrysomelidae]

Release of approximately 17,700 experienced adult femaleEdovum puttleri Grissell against 1^st generation Colorado potato beetle eggs in 1987 in a 0.4 ha potato field in S. Deerfield, Massachusetts resulted in only 3.6% parasitism as assessed by direct measurement of host and parasitoid recruitment. Levels of non-viability indicated an additional 2.8% of hosts killed by parasitoid hostfeeding, for an overall impact of 6.4%. Release in 1988 of 126,300 parasitoid against 1^st generation hosts in a 0.4 ha potato (Solanum tuberosum L.) field at the same site produced only slightly higher levels of parasitism (10.6%) and host feeding (2.0%). Release in 1987 of 32,800 wasps against 2^nd generation eggs resulted in only 0.7% parasitism and 0.3% host feeding due to the toxicity of fenvalerate (Pydrin^R) residues from a single application applied for control of the potato leafhopper,Empoasca fabae (Harris). Release in 1988 of 47,400 wasps against the 2^nd host generation in the absence of any pesticide applications resulted in 34.4% parasitism and 16.1% host feeding, for a total impact of 50.5%. Difference in parasitization levels between host generations supports the idea thatE. puttleri adults require an in-field carbohydrate source such as aphid honeydew to reproduce. In Massachusetts, aphid populations in potato typically do not develop until the end of the 1^st larval generation. The recruitment method ofVan Driesche & Bellows (1988) proved to be a satisfactory approach for determining results of augmentative parasitoid releases.      

Finding Hamiltonian paths in tournaments on clusters

This paper presents a general methodology for the communication-efficient parallelization of graph algorithms using the divide-and-conquer approach and shows that this class of problems can be solved in cluster environments with good communication efficiency. Specifically, the first practical parallel algorithm, based on a general coarse-grained model, for finding Hamiltonian paths in tournaments is presented. On any such parallel machines, this algorithm uses only (3log p+1), where p is the number of processors, communication rounds, which is independent of the tournament size, and can reuse the existing linear-time algorithm in the sequential setting. For theoretical completeness, the algorithm is revised for fine-grained models, where the ratio of computation and communication throughputs is low or the local memory size, , of each individual processor is extremely limited for any , solving the problem with O(log p) communication rounds, while the hidden constant grows with the scalability factor 1/∊. Experiments have been carried out on a Linux cluster of 32 Sun Ultra5 computers and an SGI Origin 2000 with 32 R10000 processors. The algorithm performance on the Linux Cluster reaches 75% of the performance on the SGI Origin 2000 when the tournament size is about one million. Computational resources and technical support are provided by the Center for Computational Research (CCR) at the State University of New York at Buffalo. Chun-Hsi Huang received his Ph.D. degree in Computer Science from the State University of New York at Buffalo in 2001. His is currently an Assistant Professor of Computer Science and Engineering at the University of Connecticut. His interests include High Performance Parallel Computing, Cluster and Grid Computing, Biomedical and Health Informatics, Algorithm Design and Analysis, Experimental Algorithms and Computational Biology. Sanguthevar Rajasekaran received his Ph.D. degree in Computer Science from Harvard University in 1988. Currently he is the UTC Chair Professor of Computer Science and Engineering at the University of Connecticut and the Director of Booth Engineering Center for Advanced Technologies (BECAT). His research interests include Parallel Algorithms, Bioinformatics, Data Mining, Randomized Computing, Computer Simulations, and Combinatorial Optimization. Laurence Tianruo Yang received is Ph.D. degree in Computer Science from the Oxford University. He is currently a professor of Computer Science of the St. Francis Xavier University in Canada. His research interests include high-performance computing, embedded systems, computer archtecture and high-speed networking. Xin He received his Ph.D. degree in Computer Science from the Ohio State University in 1987. He is currently Professor of Computer Science and Engineering at the State University of New York at Buffalo. His research interests include Algorithms, Data Structures, Combinatorics and Computational Geometry.     

Changes in the plant community of a Brazilian grassland savannah after 22 years of invasion by Pinus elliottii Engelm

Abstract

Background: The invasion by Pinus elliottii is one of the most serious threats to the remaining native cerrado vegetation in São Paulo State, Brazil, causing biodiversity losses yet to be evaluated. We conducted a study in an area where P. elliottii began establishing in 1988.

Aims: To estimate diversity losses in the plant community and to understand the floristic and structural changes resulting from pine tree invasion of grassland savannah.

Methods: All plants taller than 50 cm were sampled in 35 plots (64 m² each) within an area densely invaded by P. elliottii and in 10 plots in non-invaded grassland savannah. Density, species richness, diversity, ground cover and spatial distribution were compared by Wilcoxon tests, non-metric multidimensional scaling and Payandeh indices.

Results: Twenty-two years after the arrival of the first invasive trees (founders), the grassland savannah has become a dense pine forest with 12,455 individuals ha^?1, a basal area of 26.44 m² ha^?1, a sparse native woody understory comprised of 16 species (H'?=?0.44), density of 1210 individuals ha^?1 and the herbaceous layer totally absent.

Conclusions: Invasion by Pinus elliottii has completely changed the structure of the grassland savannah and caused severe plant diversity losses. Native species surviving the invasion in the understory do not typically represent the previous composition and functional traits of the native vegetation.     

Adattamenti fisiologici alla vita « aerea » nel genere Tillandsia

Abstract

Physiological adaptations to « aerial » life in the genus Tillandsia.—Ten « atmospheric » Tillandsia species, with different degree of adaptation to drought, were investigated to verify the occurrence of CAM and to determine their daily transpiration pattern.

Most of the species were collected during the Botanical Expeditions of the Accademia dei Lincei in Latin America in 1969 and 1971. All species had been maintained in the greenhouse of the Naples Botanical Garden during the winter months and in the open air during the warmer months, previous to experiments. The diurnal cycle of transpiration, the malic acid content and cell sap pH of the leaves were studied under outdoor conditions. Curves of malic acid and pH variations typical of CAM have been obtained for all the examined species. Moreover, the transpiration data indicate that stomata are open at night. The rates of transpiration appear to be extremely low. The highest transpiration rates refer to the species of the relatively moister habitats, the lowest to the more xeric species. Results indicate that CAM and low rates of transpiration are ecological adaptations to extremely dry habitats.     

An evolution of pulse speed in arteries

In this work, treating the artery as a thick-walled cylindrical shell made of an incompressible, isotropic and elastic solid, utilizing the large deformation theory and the stress-strain relation proposed by Demiray (1976b,Trans. ASME Ser. E, J. Appl. Mech.,98, 194–197), an explicit expression for the pulse speed is obtained and the effect of lumen pressure and the axial stretch on wave speed is discussed. Numerical results indicate that the wave speed increases with lumen pressure but decreases with the axial stretch. The results of the present model are compared with our previous work (Demiray, 1988,J. Biomech. 21, 55–58) on the same subject.     

Mumps, measles, and rubella vaccine and the incidence of autism recorded by general practitioners: a time trend analysis

ObjectiveTo estimate changes in the risk of autism and assess the relation of autism to the mumps, measles, and rubella (MMR) vaccine. DesignTime trend analysis of data from the UK general practice research database (GPRD).SettingGeneral practices in the United Kingdom.SubjectsChildren aged 12 years or younger diagnosed with autism 1988-99, with further analysis of boys aged 2 to 5 years born 1988-93.ResultsThe incidence of newly diagnosed autism increased sevenfold, from 0.3 per 10 000 person years in 1988 to 2.1 per 10 000 person years in 1999. The peak incidence was among 3 and 4 year olds, and 83% (254/305) of cases were boys. In an annual birth cohort analysis of 114 boys born in 1988-93, the risk of autism in 2 to 5 year old boys increased nearly fourfold over time, from 8 (95% confidence interval 4 to 14) per 10 000 for boys born in 1988 to 29 (20 to 43) per 10 000 for boys born in 1993. For the same annual birth cohorts the prevalence of MMR vaccination was over 95%.ConclusionsBecause the incidence of autism among 2 to 5 year olds increased markedly among boys born in each year separately from 1988 to 1993 while MMR vaccine coverage was over 95% for successive annual birth cohorts, the data provide evidence that no correlation exists between the prevalence of MMR vaccination and the rapid increase in the risk of autism over time. The explanation for the marked increase in risk of the diagnosis of autism in the past decade remains uncertain.     

Anceaux's Glasses

The Kayapó (Disappearing World Series) Producer: Michael Beckham; Director: Michael Beckham; Camera: Michael Blakeley; Sound: David Woods; Editor: Paul Griffiths‐Davies; Consultant Anthropologist: Terence Turner; Distributor: Enquiries to Granada Television International, 1221 6th Avenue, Suite 3468, New York, NY 10020 USA, (212) 809–8480. 1987, 52 min., color. Original: 16mm, only available for distribution on video. Language: Original Kayapo, Narration English, Subtitles English.

Independent Films and Videos from Latin America: Producers’ Obstacles, National Diversity, and the Cultural Woes of Their Foreign Audiences Review of Democracy in Communication: Popular Film and Video in Latin America. A catalogue compilation of various videotapes. 1988, color. Original language: Spanish, English subtitles. Distributed by: Karen Ranucci, 124 Washington Place, New York, NY, tele. 212–463–9198.     

Breeding ecology of a suburban population of Woodpigeons Columba palumbus in northwest England

Capsule Between 1981 and 2008 population size was stable, but there were negative trends in breeding parameters.

Aims To determine the current status and long‐term population trend of an isolated breeding population of Bearded Vultures Gypaetus barbatus (Corsica, Mediterranean).

Methods The total Bearded Vulture population was monitored between 1981 and 2008.

Results The current effective breeding population size of Bearded Vultures in Corsica is ten pairs/trios with a slight increase of one to two pairs since 1983. The population is currently estimated at 25 individuals. Breeding parameters (laying rate, breeding success and productivity) have decreased significantly over the full 28‐year study period, although the decrease was not significant when the data set was restricted to 1988–2008. A mean of 60.3% (n = 204) of pairs have laid, but this proportion is highly variable between years. Productivity has been very low (0.16 young/pair/year, n = 233). Breeding parameters of the Corsican population of Bearded Vultures are very low compared with those of other western European populations in the Pyrenees.

Conclusions This isolated insular population is of small size (eight to ten pairs/trios) but shows a stability of distribution and numbers, but low (and decreasing) breeding rates, making this insular population one the most threatened in Europe.