Lines of descent and the coalescent

Some results of Kingman, Griffiths, and Ewens are unified in a probability distribution for the genealogical structure of a random sample of genes. The sample is partitioned into equivalence classes of two types, “old” and “new.” Old classes of genes are each descended from founder genes in a reference ancestral population without mutation, while new classes descend from more-recent mutant founders. From the probability distribution of the partition, some old and some new results are derived concerning allele frequencies in samples.     

Minimal Hodgkin–Huxley type models for different classes of cortical and thalamic neurons

We review here the development of Hodgkin–Huxley (HH) type models of cerebral cortex and thalamic neurons for network simulations. The intrinsic electrophysiological properties of cortical neurons were analyzed from several preparations, and we selected the four most prominent electrophysiological classes of neurons. These four classes are “fast spiking” “regular spiking” “intrinsically bursting” and “low-threshold spike” cells. For each class, we fit “minimal” HH type models to experimental data. The models contain the minimal set of voltage-dependent currents to account for the data. To obtain models as generic as possible, we used data from different preparations in vivo and in vitro, such as rat somatosensory cortex and thalamus, guinea-pig visual and frontal cortex, ferret visual cortex, cat visual cortex and cat association cortex. For two cell classes, we used automatic fitting procedures applied to several cells, which revealed substantial cell-to-cell variability within each class. The selection of such cellular models constitutes a necessary step towards building network simulations of the thalamocortical system with realistic cellular dynamical properties.     

A mathematical model for the batch reactor kinetics of algae growth

A mathematical model based on the Einstein law of photochemical equivalence is proposed to describe the batch growth of unicellular algae. The model was applied in an integrated form to cell concentration versus growth time data taken over an extended range of cell concentrations which include both the regions of “exponential” and “linear” growth. It is shown that a certain function of cell concentration contained in the integrated form of the model is linearly dependent on the growth time over both the “exponential” and “linear” growth regions.     

Visualization of structural similarity in proteins

Two new methods for the visualization of structural similarity in proteins with known three-dimensional structures are presented. They are based on the degree of equivalence of α-carbon pairs in two proteins. The quantitative measure for residue equivalence is the comparison score generated using the sequence and structure alignment method of Taylor and Orengo, which is based on the comparison of interatomic distances (and other properties that can be defined on a residue basis).The first method uses information on corresponding α-carbon positions to display vectors joining these structurally equivalent residues. These vectors can be defined as target constraints, and their minimization “bends” the two proteins toward a common average structure. In the average structure the corresponding residues virtually superpose, while insertions and deletions become clearly visible.The second method uses the comparison scores to perform a weighted least-squares fit of the two structures. It is further used to color code the two structures according to the score value, i.e., their similarity, on a continuous scale from red to blue. Examples of the methods for the comparison of flavodoxin, chemotaxis Y protein and L-arabinose-binding protein are given.     

CLADES: A classification‐based machine learning method for species delimitation from population genetic data

Species are considered to be the basic unit of ecological and evolutionary studies. As multilocus genomic data are increasingly available, there have been considerable interests in the use of DNA sequence data to delimit species. In this study, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes. Each pair of known populations is combined to form training samples with a label of “same species” or “different species”. We use support vector machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: “same species” or “different species”. Given multilocus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, for example with short species divergence time and gene flow.     

A Cultural History of Animals (6 Volumes)

ABSTRACT

Handling and training methods of horses, which specially emphasize the importance of understanding horse body language and the use of reinforcements, are often used in practice, yet their effects are not completely known. This study investigated whether the use of a sympathetic approach during the preparation for public auctions influenced the reactivity of young horses towards humans. Sixteen thoroughbred yearlings were prepared for the public auctions during one month: eight horses (“Control”) were handled according to conventional practices, while the others (“Treated”) were handled with two sessions of basic training based on body language. The reactivity of horses was assessed in the presence of an “unfamiliar person” and a “familiar person” inside the horse's box. The experimenter recorded the presence/absence of selected behaviors during seven observational moments: “approaching the box,” “opening the box door,” “entering the box,” and four consecutive observations every thirty seconds. Reactivity of horses was ranked during the first experience of “bit,” “grooming,” “shower,” and application of the “surcingle.” Heart rate was telemetrically recorded during this final test. At the end of the auction preparation, “Treated” horses exhibited more “contact” (p = 0.08) and “lick” (p < 0.05) behaviors in the presence of a person. “Control” horses showed higher (non-significant) percentages of negative (more nervous) rankings during “bit,” “grooming,” and “surcingle” tests. Two “Control” horses showed aggressive behavior during the application of the surcingle and the test was interrupted to guarantee person and animal safety. In this pilot study, horses handled with a sympathetic approach showed less reactive behaviors compared with “Control” horses. It would be interesting to enlarge the sample size and assess if the use of non-coercive handling during the whole training period influences their welfare positively and for a long time.     

Relationship between extreme pathways and structurally minimal pathways

The determination of reaction pathways is one of the most important functions that should be performed in exploring the kinetics of catalyzed chemical reactions or biochemical reactions, the latter being generally catalyzed by enzymes. It is proven that the terms, “type-I extreme pathway” and “structurally minimal pathway”, both introduced to characterize the kinetics of a catalyzed reaction are equivalent. These two terms are based on two distinct methodologies, one mainly rooted in convex analysis and the other in graph theory. The equivalence promises further even more effective methods for reaction-pathway identification by synergistic integration of existing ones.     

Owner Attachment and Problem Behaviors Related to Relinquishment and Training Techniques of Dogs

Problematic behaviors are a significant reason for relinquishment, and relinquished dogs are more likely to have problem behaviors. This study utilized standardized surveys of owners (companion animal guardians) relinquishing their dogs to shelters and dog owners visiting vaccination clinics. “Relinquishing” and “continuing” owners were asked questions in the following categories: demographic information, training methods and tools, frequencies in which their dogs engaged in problematic behaviors, and attachment to their dogs. “Relinquishers” were also asked to provide their reasons for relinquishment. The results of 129 surveys (80 relinquishing and 49 continuing) showed that relinquishers scored lower on companion animal attachment than continuing owners. Pit bull-type dogs were represented more in the relinquishing group. Relinquished dogs were no less likely to have attended training classes than continuing dogs. In both groups, owners who used punishment-based collars reported less satisfaction with their dogs' overall and leash-walking behaviors. Pit bull-type dogs were reported to be no less well behaved compared with all other breeds combined. Sixty-five percent of relinquishers reported some behavioral reason for relinquishment. Forty-eight percent of relinquishers indicated that at least 1 problem behavior was a strong influence on their decision to relinquish.     

Rice production in Afghanistan

Rice, Afghanistan’s third most important crop, is produced in every province. Although about thirteen varieties occur in the country, for marketing purposes two main classes are recognized. These two, “Loke” and “Mai-een”, are differentiated on the basis of grain size, color, consistency, and distribution.     

Variation in the Trajectories of Depressive Symptoms: Results from the Americans' Changing Lives Study

This study examines the association between race and depressive symptoms over a 16‐year study period. The analysis is based on the responses of 3,485 African-American and White respondents from four waves of the Americans' Changing Lives Panel Study. Growth mixture modeling was used to identify latent trajectory classes based on the reported levels of depressive symptoms over 16 years. Four latent trajectory classes were identified: two “high-risk” groups and two “low-risk” groups. Findings show the heterogeneity among and within racial groups in their trajectories of depressive symptoms and the distinct demographic and social relationship predictors for symptom trajectories.     

The parameters of cardiac-muscle repolarization: The measurement and information value

We performed a comparative analysis of different classes of algorithms for computer-assisted cardiological diagnostics. The concepts of an “internal” and “external” image of myocardial ischemia were formulated. We also discussed the biophysical aspects for the basic indices of spatial heterogeneity of the repolarization process in the myocardium, as well as the problems of measurement of the corresponding parameters. The experimental part was performed on two groups of patients. Both experimental and control groups included two sets of 12-lead electrocardiograms of real patients: “Normal” and “Ischemia” (with lateral localization). The experimental group consisted of 202 and 143 electrocardiograms, while the control group consisted of 200 and 91 electrocardiograms, respectively. The electrocardiograms were verified according to the Minnesota Code criteria.     

论植物医学的学科与专业

我国大多数农林高校都开设了植物保护专业,但长期以来,“植物保护”和“植物医学”2个概念模糊不清、混为一谈.本文试图从植物保护学科及其专业招生与人才培养存在的问题着手,讨论植物医学与植物保护学科与专业的内涵与外延,深入分析植物保护与植物医学的不同特点及联系,意在强调在我国农林高校设置植物医学专业、建立植物医学学科、最终构建现代化植物医学教育体系的重要性和必要性.     

Effects of fragmentation on vascular plant diversity in a Mediterranean forest archipelago

Abstract

We analysed the effects of patch size and isolation on vascular plants in Quercus cerris forest surrounding Rome (Italy). We randomly sampled 96 plots within 18 forest patches with homogeneous environmental variables; the patches ranged from 1.4 ha to 424.5 ha and were divided into four size classes. We performed the analyses at the patch level using linear regression. At the size class level, the analysis of species richness response to fragmentation (area effect) was performed with ANOVA, while the effect on community composition was analysed by means of PERMANOVA. We also investigated which species could be used as indicator species for each size class. Lastly, to evaluate the advantages of conserving several small patches as opposed to few large ones, we used a cumulative area approach ranking forest fragments. The correlation between species richness and patch area was positive, with a significant difference between the “large” and “small” size classes, while analysis on community composition showed that “large” versus “medium” and “large” versus “small” were significantly different. Nemoral species were recognised as indicators in the “large” class, and shrub and edge species in the “small” class. Our results indicate that 10 ha may be a suitable forest size threshold for planning and conservation.     

Partial amino acid sequence of two forms of human post-gamma-globulin.

We have purified two different electrophoretic forms of Post-γ-globulin defined by electrophoresis as “native slow” form and “fast” form respectively. Amino acid sequences of the first fifty-two residues of the “native slow” form and twenty-nine of the “fast” form were determined. The sequence shows that the “fast” form lacks the first nine amino acids of the “native slow” form.This observation is consistent with the existence of a “native slow” form that is degraded into other more acidic forms of Post-γ-globulin by loss of basic amino acids.     

REPRODUCTIVE COMPATIBILITY AND RDNA SEQUENCE ANALYSES IN THE SELLAPHORA PUPULA SPECIES COMPLEX (BACILLARIOPHYTA)1

We tested whether internal transcribed spacer (ITS) rDNA sequence differences are correlated with sexual compatibility in the Sellaphora pupula complex, a model system for investigations of the species concept and speciation in diatoms. The phylogenetic relationships among the demes and the systematic position of the genus within the raphid diatoms were also investigated. The division of clones of S. pupula and S. laevissima into groups, based on sequence similarities and phylogenetic analyses, resembled groupings based on sexual compatibility: A high ITS sequence divergence, making full alignment difficult or impossible, was found among clones whose gametangia do not interact, whereas there was little sequence divergence among interfertile clones. This is clearly consistent with the idea that “Z clades” exhibit less intraclade than interclade variation in ITS and, as comparisons of secondary structure models for the RECT and PSEUDOCAP clones showed, that there is an equivalence of “CBC” and Z clades in the rectangular and pseudocapitate demes of S. pupula, as earlier hypothesized for chlorophytes. Intraclonal, presumably intraindividual, variation in ITS was found in S. pupula, though with a degree of variation less than that found within a single Z clade; it was too minor to affect the interclonal relationships in the ITS phylogeny. Sellaphora, which appears monophyletic in 18S phylogenies, with Pinnularia and “Navicula”pelliculosa as its closest allies, may also include some species currently classified in Eolimna. The S. pupula–S. laevissima group began to diversify in or before the Miocene.     

Constraints Shape Cell Function and Morphology by Canalizing the Developmental Path along the Waddington's Landscape

Studies performed in absence of gravitational constraint show that a living system is unable to choose between two different phenotypes, thus leading cells to segregate into different, alternative stable states. This finding demonstrates that the genotype does not determine by itself the phenotype but requires additional, physical constraints to finalize cell differentiation. Constraints belong to two classes: holonomic (independent of the system's dynamical states, as being established by the space-time geometry of the field) and non-holonomic (modified during those biological processes to which they contribute in shaping). This latter kind of “constraints”, in which dynamics works on the constraint to recreate them, have emerged as critical determinants of self-organizing systems, by manifesting a “closure of constraints.” Overall, the constraints act by harnessing the “randomness” represented by the simultaneous presence of equiprobable events restraining the system within one attractor. These results cast doubt on the mainstream scientific concept and call for a better understanding of causation in cell biology.     

The gamification of elementary school biology: a case study on increasing understanding of plants

ABSTRACT

This study presents a new technique, the “Which plant am I?” game, which helps to increase pupils’ plant knowledge, while motivate them to become familiar with more plants. On the other hand pupils’ plant knowledge was tested in Serbia.

The “Which Plant Am I?“ game was tested with two groups of pupils (in average 11 years old). Pupils in the experimental group took part in outdoor classes and played the ”Which plant am I?” game. Pupils of the control group observed plants only in the classroom. This technique can deliver significant improvement in pupils’ knowledge about plants and motivate them through an active and playful learning process. This technique can be one possible solution of plant blindness.     

Innervation of the human upper primary dentition: Implications for understanding tooth initiation and rethinking growth and eruption patterns

Recent comparisons of humans with apes and early fossil hominids have prompted renewed interest in the study of sequences of dental growth and development. Such comparisons, however, rely on certain assumptions about tooth development and dental homology and the biological reality of distinguishing “deciduous” from “permanent” teeth. In light of earlier suggestions by Schwartz that there might be a correlation between nerves and the stem progenitors of tooth classes, and thus between nerve branch number and number of tooth classes, we studied a large sample of ～ 3 month fetuses to elucidate the nature of nerve branching patterns and the development of the primary dentition (i.e., the “deciduous” incisors, canine, and molars, and the first “permanent” molar). Contrary to expectation, variation in nerve branch patterning was the rule. If nerve fibers do have a role in tooth development, it can only be at the time of initiation, with definitive innervation occurring late in tooth development. In taking into consideration the entire span of tooth development—from initiation to innervation to eruption—and the process by which successional teeth arise (each from the external dental epithelium of a predecessor tooth), we suggest that dividing tooth growth and eruption into patterns of the “deciduous” teeth vs. those of the “permanent” is artificial and that a more meaningful approach would be the study of the entire dentition.