THEORETICAL STUDIES ON THE METHODS OF RECONSTRUCTING PHYLOGENETIC TREES FROM DNA SEQUENCE DATA (MOLECULAR EVOLUTION, HOMINOID EVOLUTION, COMPUTER SIMULATION)

(1) A mathematical theory for computing the probabilities of various nucleotide configurations is developed, and the probability of obtaining the correct phylogenetic tree (model tree) from sequence data is evaluated for six phylogenetic tree-making methods (UPGMA, distance Wagner method, transformed distance method, Fitch-Margoliash's method, maximum parsimony method, and compatibility method). The number of nucleotides (m*) necessary to obtain the correct tree with a probability of 95% is estimated with special reference to the human, chimpanzee, and gorilla divergence. m* is at least 4,200, but the availability of outgroup species greatly reduces m* for all methods except UPGMA. m* increases if transitions occur more frequently than transversions as in the case of mitochondrial DNA. (2) A new tree-making method called the neighbor-joining method is proposed. This method is applicable either for distance data or character state data. Computer simulation has shown that the neighbor-joining method is generally better than UPGMA, Farris' method, Li's method, and modified Farris method on recovering the true topology when distance data are used. A related method, the simultaneous partitioning method, is also discussed. (3) The maximum likelihood (ML) method for phylogeny reconstruction under the assumption of both constant and varying evolutionary rates is studied, and a new algorithm for obtaining the ML tree is presented. This method gives a tree similar to that obtained by UPGMA when constant evolutionary rate is assumed, whereas it gives a tree similar to that obtained by the maximum parsimony tree and the neighbor-joining method when varying evolutionary rate is assumed. ^

Acute and chronic pain in calves after different methods of rubber-ring castration

The goal of the present study was to evaluate the effect of different methods of rubber-ring castration on acute and chronic pain in calves. Sixty-three 4-6 week-old calves were randomly and sequentially allocated to one of five groups: Group RR (traditional rubber ring castration); group BRR (combination of one rubber ring with Burdizzo); group Rcut (one rubber ring applied with the scrotal tissue and rubber ring removed on day 9); group 3RR (three rubber rings placed one above the other around the scrotal neck); and group CO (controls; sham-castrated). All calves received 0.2 mL/kg bodyweight lidocaine 2%, injected into the spermatic cords and around the scrotal neck 15 min before castration. The presence of acute and chronic pain was assessed using plasma cortisol concentrations, response to palpation of scrotal area, time from castration until complete wound healing, and behavioural signs. Calves of group 3RR showed severe swelling and inflammation, and licking of the scrotal area occurred significantly more often than in groups Rcut and CO. Technique 3RR was discontinued for welfare reasons before the end of the study. All castration groups had significantly more pain upon palpation than calves of group CO, but palpation elicited markedly less pain in group Rcut than in the other castration groups. The most rapid healing time and shortest duration of chronic pain after castration was achieved in group Rcut. For welfare reasons, the Rcut technique should be considered as a valuable alternative to traditional rubber ring castration of calves at 4-6 weeks of age.

Speech outcome in complete unilateral cleft lip and palate - a comparison of three methods of the hard palate closure.

The aim of this study was to compare the speech in subjects with cleft lip and palate, in whom three methods of the hard palate closure were used. One hundred and thirty-seven children (96 boys, 41 girls; mean age = 12 years, SD = 1·2) with complete unilateral cleft lip and palate (CUCLP) operated by a single surgeon with a one-stage method were evaluated. The management of the cleft lip and soft palate was comparable in all subjects; for hard palate repair, three different methods were used: bilateral von Langenbeck closure (b-vL group, n = 39), unilateral von Langenbeck closure (u-vL group, n = 56) and vomerplasty (v-p group, n = 42). Speech was assessed: (i) perceptually for the presence of a) hypernasality, b) compensatory articulations (CAs), c) audible nasal air emissions (ANE) and d) speech intelligibility; (ii) for the presence of compensatory facial grimacing, (iii) with clinical intra-oral evaluation and (iv) with videonasendoscopy. A total rate of hypernasality requiring pharyngoplasty was 5·1%; total incidence post-oral compensatory articulations (CAs) was 2·2%. The overall speech intelligibility was good in 84·7% of cases. Oronasal fistulas (ONFs) occurred in 15·7% b-vL subjects, 7·1% u-vL subjects and 50% v-p subjects (P < 0·001). No statistically significant intergroup differences for hypernasality, CAs and intelligibility were found (P > 0·1). In conclusion, the speech after early one-stage repair of CUCLP was satisfactory. The method of hard palate repair affected the incidence of ONFs, which, however, caused relatively mild and inconsistent speech errors.

Jewish Philanthropy : an exposition of principles and methods of Jewish social service in the United States

by Boris D. Bogen

Comparison of alternative methods of contact tracing in a syphilis control program

The purpose of this study was to compare the relative effectiveness of alternative methods of tracing named contacts of syphilis patients. A total of 236 contacts, identified by patients in two City of Houston Department of Health and Human Services clinics during the period April 1 through July 31, 1987, were studied. After contacts were grouped by sex and age, the proportion brought to examination by each of three methods, and by a combination of methods, was determined for each subgroup.^ The study found that 78.4% of all the 236 named sex contacts reported were located and brought to examination by the various methods of contact tracing and that 21.6% were missed. Of the 185 contacts examined, a combination of methods identified 47.7% of the cases, telephone contact, 28.6%, field contact, 16.9%, and patient referral, 11.8%.^ Of the 236 contacts reported, males made up 56.8% and females 43.2%. Contact tracing was more successful among females, with 81.4% of the 102 named female contacts, as compared to 76.1% of the 134 named male contacts being brought to examination. It is not known whether equal efforts were exerted in the follow-up of both male and female contacts. In both female and male subgroups, a combination of methods brought over 40% of sex contacts to examination. Telephone contact among females yielded 27.7% of the cases and field contact 18.1%, whereas in males, telephone contact identified 29.4% of the cases and field contact 15.7%. Patient referral was the least productive method in both sex groups, locating 12.8% in males as compared to 10.8% in females.^ On an age specific basis, a combination of methods was the most effective method in the 15-39 age group, whereas telephone contact was most effective in the 40-44 age group, and field contact in the 50-54 age group. Of all the methods of contact tracing, patient referral was the least productive in most age groups.^ Future studies of contact tracing should incorporate several important variables which were not examined in this study. ^

The Need for Balanced Methods of Measuring Performance

Michelle Rhee weighs in on measuring success in pubic education.

Placement Methods of Phosphorus and Potassium for Corn and Soybean Managed with No-till and Chisel-plow/Disk Tillage

No-till management limits the incorporation of crop residue and fertilizer with soil resulting in wetter, colder soils and the accumulation of organic matter, phosphorus (P), and potassium (K) near the soil surface. Banding of P and K could be more effective than broadcast fertilization by counteracting stratification, applying nutrients in the root zone (starter effect), and minimizing reactions with the soil that may reduce their availability to plants. Therefore, this long-term study was established in 1994 to evaluate P and K fertilizer placement methods and grain yield of corn-soybean rotations managed with notill and chisel-plow/disk tillage.

Concentration of trace elements in samples of sea water determined by use of two methods of concentrating

A device and a specific procedure for simultaneous concentration of trace ele¬ments from sea water by co-precipitating them in precipitate of magnesium hydroxide obtained by electrolytic alkalization of samples in a two-chamber electrolyzer are described. Analyses of sea water samples for zinc, iron, copper, nickel and lead demonstrate that the method produces a thousand-fold concentration and gives results that agree well with those obtained by extractive concentration using diethyldithiocarbamate and 8-hydroxyquinoline in chloroform. Extracts were analyzed by flame atomic absorption. Correlation coefficients of results obtained with use of these two methods of concentration were 0.76-0.87 for zinc, iron, and copper at confidence levels of 0.05-0.07. Average zinc and iron concentrations determined by the method differed by less than 10%.

Adjustment methods of national input-output tables for harmonized and consistent multi-regional input-output databases

Despite the fact that input–output (IO) tables form a central part of the System of National Accounts, each individual country's national IO table exhibits more or less different features and characteristics, reflecting the country's socioeconomic idiosyncrasies. Consequently, the compilers of a multi-regional input–output table (MRIOT) are advised to thoroughly examine the conceptual as well as methodological differences among countries in the estimation of basic statistics for national IO tables and, if necessary, to carry out pre-adjustment of these tables into a common format prior to the MRIOT compilation. The objective of this study is to provide a practical guide for harmonizing national IO tables to construct a consistent MRIOT, referring to the adjustment practices used by the Institute of Developing Economies, JETRO (IDE-JETRO) in compiling the Asian International Input–Output Table.

A new way of teaching different subjects in a foreign language in the Building Engineering Degree at the Universidad Politécnica.

The European Union has been promoting linguistic diversity for many years as one of its main educational goals. This is an element that facilitates student mobility and student exchanges between different universities and countries and enriches the education of young undergraduates. In particular, a higher degree of competence in the English language is becoming essential for engineers, architects and researchers in general, as English has become the lingua franca that opens up horizons to internationalisation and the transfer of knowledge in today’s world. Many experts point to the Integrated Approach to Contents and Foreign Languages System as being an option that has certain benefits over the traditional method of teaching a second language that is exclusively based on specific subjects. This system advocates teaching the different subjects in the syllabus in a language other than one’s mother tongue, without prioritising knowledge of the language over the subject. This was the idea that in the 2009/10 academic year gave rise to the Second Language Integration Programme (SLI Programme) at the Escuela Arquitectura Técnica in the Universidad Politécnica Madrid (EUATM-UPM), just at the beginning of the tuition of the new Building Engineering Degree, which had been adapted to the European Higher Education Area (EHEA) model. This programme is an interdisciplinary initiative for the set of subjects taught during the semester and is coordinated through the Assistant Director Office for Educational Innovation. The SLI Programme has a dual goal; to familiarise students with the specific English terminology of the subject being taught, and at the same time improve their communication skills in English. A total of thirty lecturers are taking part in the teaching of eleven first year subjects and twelve in the second year, with around 120 students who have voluntarily enrolled in a special group in each semester. During the 2010/2011 academic year the degree of acceptance and the results of the SLI Programme have been monitored. Tools have been designed to aid interdisciplinary coordination and to analyse satisfaction, such as coordination records and surveys. The results currently available refer to the first and second year and are divided into specific aspects of the different subjects involved and into general aspects of the ongoing experience.

Multidisciplinary Learning, Another way of Teaching Maths in Engineering

Multidisciplinary training is widely appreciated in industry and business, and nevertheless usually is not addressed in the early stages of most undergraduate programs. We outline here a multidisciplinary course for undergraduates studying engineering in which mathematics would be the common language, the transverse tool. The goal is motivating students to learn more mathematics and as a result, improve the quality of engineering education. The course would be structured around projects in four branches in engineering: mechanical, electrical, civil and bio-tech. The projects would be chosen among a wide variety of topics in engineering practice selected with the guidance of professional engineers. In these projects mathematics should interact with at least two other basic areas of knowledge in engineering: chemistry, computers science, economics, design or physics.