Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of Number of Amino Acid Substitutions when Back Mutations Can Occur

to estimate the mean number of amino acid substitutions per site, Di, occurring in the evolutionary pathway connecting a pair of species which are observed to differ in d amino acid sites for a protein of which T' sites are evolutionarily variable. A drawback of this approach is that, as pointed out by Zuckerkandl and Pauling (1965), it assumes that a site that has once been modified cannot revert to its original condition. The purpose of this note is to construct an estimator similar to expression (1) that avoids this difficulty. For a pair of modern species, E, and F, for which d is observed, inferring the corresponding am amounts to judging the most likely number of substitution events per site in the evolutionary path connecting E and F. I shall treat such a path formally as originating at E, proceeding through some number of substitutions, and terminating at F. The benefit of this convention is that it obviates any need to specify the condition of the common ancestor, G, of E and F. Note, however, that the "original" condition of a site under this terminology refers to the condition of E, not that of G. We first construct the probability that a specified site of F differs from the corresponding site of E given that x substitutions occur at that site in the path traced from E to F. Denote as bh, the amino acid present at the selected site after x substitutions have occurred in the path starting at E, so that bo is equal to the amino acid at the corresponding site of E. Write px for the probability that bh = bo. Let r denote the probability that bh -_ bo,
ESTIMATING SIZE AND ASSESSING TRENDS IN A COASTAL BOTTLENOSE DOLPHIN POPULATION

We used a case study of a coastal bottlenose dolphin population to present a framework for determining the number of individuals present and assessing the likely time scale over which trends in abundance may be determined. Such a framework is appropriate for animal species that possess natural markings sufficient for individual recognition, and may be valuable in the development and implementation of management and monitoring programs for vulnerable populations. Population abundance was estimated using mark–recapture methods applied to photoidentification data. This experiment was designed to minimize violation of method assumptions so as to allow use of the most parsimonious model for analysis. The data were examined critically to investigate mark–recapture assumptions, while analytical methods and data were selected to minimize and, where necessary, account for violations. The estimated number of animals with long-lasting marks from left and right side estimates were 73 ± 12 and 80 ± 11 individuals, res.
A comparative study of different temperature accumulation methods for predicting the start of the Quercus pollen season in Cordoba (South West Spain)

The aim of the present paper is to study the influence of air temperature on the start of Quercus pollination in Córdoba (Andalusia, Spain). Sixteen years of pollen counts were used. The start date of the pollen season in this period varied between 26th February and 7th April. Chilling requirements and heat accumulation were taken into account although no significant correlation between chilling hours and the start date was observed. Five different predictive methods based on heat accumulation were compared in this paper: 1) Number of days over a threshold; 2) Heat Units (accumulated daily mean temperature after deducting a base temperature); 3) Growing Degrees Days (Snyder 1988), as a measure of physiological growing time; 4) Accumulated maximum temperatures; and 5) Mean maximum temperature. Results indicated that the optimum base temperature for heat accumulation was 11 Co. This threshold was used in the first three methods mentioned above. Good statistical results were obtained with the five methods, yielding high levels of explanation (p∼99%). Nevertheless, the most accurate method appeared to be the Growing Degree Days (GDDo) method, which indicated that a mean of 127.3 GDDo must be accumulated from the end of the chilling period up to the beginning of the Quercus pollen season in Córdoba (South West Spain). Results were tested for predicting start dates in 1999 and 2000. The predicted dates were only one day after the actual dates.
Millieriinae, a new subfamily of Choreutidae, with new taxa from Chile and the United States (Lepidoptera, Sesioidea)

Heppner, John B. Millieriinae, A New Subfamily of Choreutidae, with New Taxa from Chile and the United States (Lepidoptera: Sesioidea). Smithsonian Contributions to Zoology, number 370, 27 pages, 63 figures, 1 table, 1982. —The new subfamily, Millieriinae, is described in Choreutidae and includes one European genus, Millieria Ragonot, with its single species Millieria dolosana (Herrich-Schaffer), as well as two new genera and species: Phormoestes, new genus, including Phormoestes palmettovora, new species, from Florida; and Nyx, new genus, including Nyx puyaphaga, new species, from central Chile. All taxa are described, illustrated, and discussed regarding their relationships. Host plants include Aristolochia clematitis Linnaeus and Aristolochia pistolochia Linnaeus (Aristolochiaceae) for Millieria, Sabal palmetto (Walter) Loddiges (Palmae) for Phormoestes, and Puya alpestris (Poeppig) Gay (Bromeliaceae) for Nyx. OFFICIAL PUBLICATION DATE is handstamped in a limited number of initial copies and is recorded in the Institution's annual report, Smithsonian Year. SERIES COVER DESIGN: The coral Montastrea cavernosa (Linnaeus). Library of Congress Cataloging in Publication Data Heppner, John B. Millieriinae: a new subfamily of Choreutidae, with new taxa from Chile and the United States (Lepidoptera: Sesioidea) (Smithsonian contributions to zoology ; no. 370) Bibliography: p. Supt. of Docs, no.: SI 1.27:370 1. Choreutidae—Classification. 2. Insects—Classification. 3. Insects—United States—Classification. 4. Insects—Chile—Classification. I. Title II Series QLI.S54 no. 370 [QL561.C47]. 591s [595.78'1] 82-600162 AACR2
Induced systemic resistance to blue mold: early induction and accumulation of β-1,3-glucanases, chitinases, and other pathogenesis-related proteins (b-proteins) in immunized tobacco

Increases in b-proteins were detected in controls only 6 days after challenge. A basal level of chitinases was always detected, but increases in chitinases above this level in immunized plants followed a profile similar to that of the β-1,3-glucanases and other b-proteins. It is likely that β-1,3-glucanases, chitinases, and other b-proteins are coordinately regulated in tobacco. The increases in these proteins coincided with the onset of immunization in plants injected with P. tabacina, and the levels were maintained during the period after challenge, when the development of P. tabacina was restricted
New combinations in Lactifluus, 3 : L. subgenera Lactifluus and Piperati

In this last of a series of three papers, new combinations in the genus Lactifluus are proposed. This paper treats Lactifluus subg. Lactifluus (an autonymous subgenus) and Lactifluus subg. Piperati (proposed as a new subgenus). In Lactifluus subg. Lactifluus, six sections are recognized (five of them as new combinations) and 46 new combinations are proposed at species level. In Lactifluus subg. Piperati, two sections are recognized (as new combinations) and nine new species combinations are proposed. In addition, new combinations are proposed for an unassigned section and its single species as well as for three unassigned species.
Quantifying physiological influences on otolith microchemistry

Trace element concentrations in fish earstones (‘otoliths’) are widely used to discriminate spatially discrete populations or individuals of marine fish, based on a commonly held assumption that physiological influences on otolith composition are minor, and thus variations in otolith elemental chemistry primarily reflect changes in ambient water chemistry. We carried out a long‐term (1‐year) experiment, serially sampling seawater, blood plasma and otoliths of mature and immature European plaice (Pleuronectes platessa L.) to test relationships between otolith chemistry and environmental and physiological variables. Seasonal variations in otolith elemental composition did not track seawater concentrations, but instead reflected physiological controls on metal transport and biokinetics, which are likely moderated by ambient temperature. The influence of physiological factors on otolith composition was particularly evident in Sr/Ca ratios, the most widely used elemental marker in applied otolith microchemistry studies. Reproduction also triggered specific variations in otolith and blood plasma metal chemistry, especially Zn/Ca ratios in female fish, which could potentially serve as retrospective spawning indicators. The influence of physiology on the trace metal composition of otoliths may explain the success of microchemical stock discrimination in relatively homogenous marine environments, but could complicate alternative uses for trace element compositions in biominerals of higher organisms.
Bacteria associated with early life stages of halibut, Hippoglossus hippoglossus L., inhibit growth of a pathogenic Vibrio sp.

Bacteria capable of inhibiting growth of a pathogenic Vibrio sp. were isolated from the gastrointestinal tract of cultured halibut larvae during the first feeding and weaning stages. No such bacteria were found among isolates from the surface of eggs or the gastrointestinal tract of yolk sac larvae. The fraction of pathogen-inhibitors among the total number of isolates ranged between 0–100% (first feeding) and 0–66% (weaning). All pathogen-inhibitors were Gram-negative rods, and 95% were oxidase and catalase positive fermentative isolates, capable of producing acid aerobically from a varying range of carbohydrates. These isolates possessed the characteristics of the Vibrio/Aeromonas-group, but only 19% were sensitive to the vibriostatic agent 0/129. Isolates from eggs and yolk sac larvae were dominated by bacteria belonging to the Cytophaga/Flexibacter/Flavobacterium- group. The high fraction of isolates with the ability to inhibit growth of the pathogenic Vibrio sp. among the total number of isolates indicates that pathogen inhibition may be an important mutualistic role of the intestinal flora of early life stages of halibut.
Taxonomy and molecular phylogeny of the Asian Paraleucophenga Hendel (Diptera, Drosophilidae)

This paper reports on nine Asian species of the genus Paraleucophenga, of which four are new to science: Paraleucophenga brevipenis sp. nov., Paraleucophenga hirtipenis sp. nov., Paraleucophenga longiseta sp. nov., and Paraleucophenga tanydactylia sp. nov. We also report on a new synonym, Paraleucophenga shanyinensis Chen & Toda, 1994 syn. nov. A key to all of the species examined, based on morphological data, is provided, together with a ‘molecular’ key to seven Paraleudophenga species based on DNA sequence data of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. The phylogenetic relationships among seven Paraleucophenga species are reconstructed based on DNA sequences of the mitochondrial ND2 gene, using two Leucophenga species as outgroups. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155, 615–629.
Variation in the Essential Oil Composition and Antimicrobial Activity of Baccharis spartioides (H. et A.) J. Rimy from Three Regions of Argentina.

Abstract Hydrodistilled oils of Baccharis spartioides from three populations of Argentina (Northwest, Central and Patagonia areas) were analyzed by using GC and GC/MS. Thirty-nine compounds were identified in the oils and a relatively high variation in their contents and in their antimicrobial activity was found. The main constituents of the oils were camphor (26.5–50%), limonene (4.3–35.8%), citronellal (12%), carvone (10%) and spathulenol (2.1–11.8%). The oil was tested against ten Gram-positive and Gram-negative bacteria and against the yeast Candida albicans. The best antimicrobial activity of the oils of B. spartioides was against S. aureus and B. cereus while P. aeruginosa was the most resistant bacteria to all the oils.
Note on the external features and sexual behavior of a wild hybrid Baikal Teal×Northern Pintail male found at Hyo-ko Waterfowl Park, Niigata, Japan

choice of potential mates is limited. This is particularly common among ducks. Among the dabbling ducks (Anas spp.), hybridization in the wild is also common; e.g., hybrids of Northern Pintail Anas acuta with Mallard A. platyrhynchos, Common Teal A. crecca, Baikal Teal A. formosa, Gadwall A. strepera, Eurasian Wigeon A. penelope, Northern Shoveler A. clypeata, and even Common Pochard Aythya ferina have previously been documented from Japan (Kuroda 1939; Tokikuni 1989; Shimizu 1993). In addition, hybrids of Baikal Teal with Common Teal, Northern Pintail, Cinnamon Teal A. cyanoptera and Eurasian Wigeon have also been reported (Johnsgard 1960, 1965, McCarthy 2006). It is generally known that hybridization causes sterility and reduces the survival of the hybrid and its offspring. Nevertheless, the dabbling ducks show remarkable interspecific hybrid fertility (Johnsgard 1960; McCarthy 2006). In this context, knowledge on morphology, degree of sterility/fertility, and sexual behavior of hybrid ducks (Johnsgard 1960, 1965; McCarthy 2006), together with genetic (Numachi et al. 1983) and cytogenetic data (Yamashina 1949) has contributed to our understanding of the systematics and evolutionary biology of the waterfowl. In the course of our field study (bird banding) at Hyo-ko Waterfowl Park, a local preserve in Niigata Prefecture, Japan, we came across males of a presumed hybrid between Baikal Teal and Northern Pintail and had, for the first time, an opportunity to observe sexual behavior of these hybrids in the wild. As a contribution to further knowledge of avian reproductive biology, this paper briefly describes the external features and sexual behavior of these hybrids and their transient mating (pair bond) with female Northern Pintail.
The evolution of the giant deer, Megaloceros giganteus (Blumenbach)

Abstract The giant deer, Megaloceros giganteus , is best known from its fossil occurrences in Ireland around 11 000 years ago, but has a history across Europe and Western Asia spanning 300 000-400 000 years. This paper reports a biometric study of variation and evolution in the giant deer through its history. Most early populations were as large in body size as the Irish sample, but some were distinctly smaller and others had markedly shorter limbs. Thickened skull and mandibular bones, especially marked in males, are constant throughout the species' history. Some earlier populations had antlers which were relatively smaller, more upright and differing in other details from the celebrated Irish specimens. Observed variation in body and antler form is discussed in terms of changing palaeoenvironments. Interpretation of the fighting or display roles of M. giganteus antlers needs to take account of their differing forms through time.
Comment on ‘Identification of trend and probability distribution for time series of annual peak flow in Tapi Basin, India’ by Timbadiya et al., Vol. 19, No. 1, p. 11-20

Şen’s ITAM. They have found increasing trend on all the gauging stations except Sarangkheda. However, in Figure 1(b)–(d), there is not equal data quantity in each period. For example, in Figure 1(b), first half of the series has 19 data values, whereas in the second half only 17 annual peak flows data exist. Similar cases can be seen in Figure 1(c) and (d), give rise to increasing on probability of occurrence of maximum or minimum flows for a period of larger data. In Figure 1(b), probability of maximum and minimum flow occurrences equal to 1/19 = 0.052 (5.2%) and 1/17 = 0.058 (5.8%) for first and second halves, respectively. This false approximation damages actual trend structure and gives rise to a false calculation on trend expectations. In this comment article such false applications are The paper being commented is Timbadiya et al. (2013). Şen (2012a) proposed an innovative trend analysis methodology (ITAM) to detect trend in any hydro-meteorological time series. The method is used for rainfall, temperature, streamflow, discharge, water quality, etc. data-sets by different researchers (Dabanli et al. 2016, Deng et al. 2017; Elouissi et al. 2016; Haktanir and Citakoglu 2014; Öztopal and Şen 2016; Saifullah et al. 2016; Şen 2012a,b, 2014, 2015, 2016, 2017; Timbadiya et al. 2013). The method is based on the comparison of the first and the second half pieces of a time series for trend identification. Timbadiya et al. (2013) investigated trend on observed annual peak flows at four stream gauging stations (Gopalkheda, Burhanpur, Sarangkheda, Ukai Reservoir) in Tapi Basin using
A computational approach to analyze the missense mutations in human angiogenin variants leading to amyotrophic lateral sclerosis

The most detrimental missense mutations of angiogenin causing Amyotrophic lateral sclerosis were identified computationally and the substrate binding efficiencies of these mutations were also analyzed. Out of 12 variants, I-Mutant 2.0, SIFT and PolyPhen programs identified 3 variants that were less stable, deleterious and damaging respectively. Modeling of these 3 variants was performed to understand the change in their conformations with respect to the native angiogenin by computing their RMSD and Total energy. The native and the 3 mutants were docked with ribonuclease inhibitor to explain the binding efficiencies of those detrimental missense mutations. The loss of binding affinity with their interacting protein namely ribonuclease inhibitor was investigated by computing the ﬂexibility of binding amino acids of angiogenin and computing the binding free energy (ΔG) between native and mutant complexes. DOI: http://dx.doi. org/10.3329/bjp.v8i4. 15259 Bangladesh Journal of Pharmacology Vol.8(4) 2013 382-389
Formation of ε-Formyllysine on Silver-stained Proteins

Considerable effort is focused presently on the detection and comprehensive assignment of post-translational modifications of proteins. Obviously attention must be paid to the possibility of chemical modifications that may occur to protein samples during sample handling and manipulation prior to analysis by tandem mass spectrometry. This is of particular concern when a modification is isobaric with the mass differential in common with a known post-translational analog. Here we provide evidence that silver staining protocols that use formaldehyde can result in ε-formylation of lysine residues. This modification is in fact isobaric with the important product of methyltransferases, ε,ε-dimethyllysine. Without exercising proper caution the analysis of silver-stained protein samples by mass spectrometry looking for dimethylation of lysine will yield a significant number of misassigned sites of modification. High accuracy measurements of the mass of the precursor ions and their fragments are required to eliminate this uncertainty. The occurrence of dimethylation of the ε-amino function of lysine residues has been reported often in histones. For histone samples excised from silver-stained gels, we found that most sites initially assigned to be dimethylated by automatic search engines under standard search parameters (100 ppm error tolerance) are actually in fact formylated. Caution must be exercised when data obtained from instruments unable to perform high accuracy mass measurements (better than 5 ppm) are to be interpreted.
First zoea of Pagurus japonicus (Crustacea: Decapoda: Anomura: Paguridae) reared in the laboratory

The first zoeal stage of Pagurus japonicus is described and illustrated. Its morphological characteristics are compared with those of other known species of the genus Pagurus. The first zoea of P. japonicus was very similar to that of P. similis. The zoeas of the two species could be distinguished from other pagurid zoeas by morphological characteristics of the carapace without posterolateral spine, two setae on the endopod of the antenna, and 3+3 setae on the endopod of the maxilla. They show affinities more to the species of the family Diogenidae than to the species of the genus Pagurus in respect of zoeal morphology.
Selenium: Biochemical Role as a Component of Glutathione Peroxidase

When hemolyzates from erythrocytes of selenium-deficient rats were incubated in vitro in the presence of ascorbate or H2O2, added glutathione failed to protect the hemoglobin from oxidative damage. This occurred because the erythrocytes were practically devoid of glutathione-peroxidase activity. Extensively purified preparations of glutathione peroxidase contained a large part of the 75Se of erythrocytes labeled in vivo. Many of the nutritional effects of selenium can be explained by its role in glutathione peroxidase.
Interannual variation in birth mass and postnatal growth rate of Juan Fernández fur seals

The objectives of this study were to establish body mass at birth, postnatal growth rate, and the factors that influence these parameters for the Juan Fernandez fur seal, Arctocephalus philippii. Females of this species have an unusual attendance pattern in which foraging trips and shore visits last, on average, 12.3 and 5.3 days, respectively. Pup mass was obtained from cohorts born during the reproductive seasons in 1988 through 1992. Birth masses of male and female pups were significantly different, averaging 6.1 and 5.5 kg, respectively (F = 13.2, P < 0.0003, n = 238). Birth masses also differed among cohorts, being lowest in 1992 and highest in 1990. During the first 2 months of life, male and female pups grew at the same rate (79 ± 61.5 g · day-1 (mean ± SD); F[1] = 0.03, P = 0.8562). Interannual differences in growth rate during the first month were significant (F[4] = 8.14, P < 0.0001), as was the interaction between month and year effects (F[2] = 6.81, P = 0.0012). Growth rates for the 1990 cohor.
Analysis of the Determinants of Consumption in Nigeria: An Autoregressive Distributed Lag Approach

The need for economic theory to address the problem of unsustainable consumption patterns in a developing economy, Nigeria cannot be overemphasized. The literature suggests that present consumption patterns which use up economic resources beyond the capacity of the environment to replenish may make development unsustainable. This study analyzed consumption behavior vis-à-vis the factors that weakly or strongly influence consumption decisions. This key objective of this study is to establish the determinants of consumption among individual households in Agyaragu community of Nasarawa and by inference Nigeria. The study also investigated the extent to which consumption behavior of individuals supported the predictions of conventional models of consumption. A sample of 500 households was drawn from the community population of 22,750, with a response rate of 97%. The model employed alongside others is the Autoregressive Distributed Lagged (ADL) model. The results and findings revealed that individuals do not behave according to the baseline models of consumption. Consumption patterns favored non-durable consumption and necessities. The study recommended the model used in this study as a model of consumption that should incorporate the additional factors revealed by this study. The study, therefore, called for an economic policy and programme that will switch consumption away from non-durables to durables. This recommendation would enhance wealth creation, savings, investment and economic growth and development.