Miracle-dz/UniFAR-FTUs huggingface dataset:
Overcompensation and adaptive plasticity of apical dominance in Erysimum strictum (Brassicaceae) in response to simulated browsing and resource availability

In the cases where overcompensation has been observed in monocarpic herbs, overcompensation is associated with an apically dominant shoot architecture of intact plants, increased lateral branching following herbivory, and increased reproductive success as a consequence of damage. The compensatory continuum hypothesis expects overcompensation to be more prevalent in resource rich environments compared to poor environments. This is paradoxical since in resource rich conditions the intact plants should branch most vigorously and hence any further increase in branch number should lead to lower seed yield. An explanation could be that apical dominance is rather insensitive to changes in resource availability, and that overcompensation is possible in conditions where plants experience meristem limitation (due to apical dominance) in relation to available resources. We explored the branching patterns and fitness responses of tall wormseed mustard (Erysimum strictum ) to simulated browsing, soil nutrients, and competition in common garden. Competition increased apical dominance and reduced plant fitness whereas fertilization had the reverse effects. Simulated browsing increased lateral branching and had little impact on plant fitness. Fitness overcompensation was observed only among plants grown in competition and in the absence of fertilization � / the most resource poor treatment combination in the experiment. The results contradict both with the compensation continuum and the assumption that apical dominance shows no or very little plasticity in relation to growing conditions. Because directional selection gradients on branch number were invariantly positive irrespective of growing conditions, we propose that, in spite of phenotypic plasticity of apical dominance, the plants appear to be meristem rather than resource limited, and that meristem limitation is strongest in conditions where intact plants produce fewest lateral branches. Our results deviate from the compensation continuum because resource availability affected compensation ability more strongly through phenotypic plasticity of shoot architecture rather than via changes in resource availability per se.
Book Review

A thorough understanding of correlational techniques is essential for scholars in the organizational and psychological sciences. A cursory review of journals such as Organizational Research Methods, Academy of Management Journal, and Journal of Applied Psychology illustrates the heavy reliance on such methods. Published in 1983, the previous edition of the Cohen, Cohen, West, and Aiken book has served as an important stimulus for the increased use of correlational methods and as an outstanding reference and course textbook. Indeed, my copy of the previous edition of this text sits alternately on my shelf and desk with scraps of paper marking numerous passages that I have frequently consulted. To be fair, I opened the third edition of the Cohen et al. book with feelings of both optimism and skepticism. The positive expectations were largely due to the inclusion of new material (e.g., material related to the use of logistic regression procedures and updated chapters on causal modeling), the significant period of time since the last edition (1983), and the potential contributions of Stephen G. West and Leona S. Aiken. The negative expectations I had were related to concerns about the nature of the changes and to what extent the previous edition could be improved upon. From all-tofrequent revisions of computer operating systems and software to the latest “new and improved” household products, we have become a society accustomed to product upgrades. In many cases, such upgrades provide little, if any, real improvement over the previous version of the product. Thus, the question I found myself coming back to was, “Have the changes made to the text warrant a new edition? ” The stated audiences for the Cohen et al. book are students in classroom settings and researchers seeking to understand and use various correlational methods. This is an ambitious and difficult task because students (often seeing this material for the first time) need a more basic treatment of topics, whereas researchers are often seeking guidance with respect to a particular aspect of an analytic technique. The ability to balance these potentially competing goals was a chief strength of the previous edition. As was the case with the previous edition of this book, the first three chapters offer an explanation of the general model that underlies regression analyses (chapter 1), a review of the basic statistical terms and concepts related to the simple regression case involving one predictor and one criterion (chapter 2), and a discussion of how the simple regression case may be extended to include multiple predictors (chapter 3). Readers already familiar with previous editions will find these treatments to be largely unchanged. Chapter 4, new to this edition, addresses how to diagnose and remedy situations in which the researcher finds that one or more of the basic assumptions of regression have been violated. The authors start with the excellent recommendation that researchers first take a visual look at their data (e.g., scatterplots). Although this recommendation
Antimicrobial assessment of crude extracts of Fenugreek against Endodontic pathogens

Bacteria are the powerful causative agents in human dental problems. The performance of a standard irrigation agent depends on the ability in killing all bacteria and fungi present in the prepared root canal. The aim of this study was to evaluate the antibacterial activity of aqueous and organic solvent-extracts of stems, leaves, seeds and roots of Fenugreek on some selected human clinical isolates of
Big, Bad, and Beautiful: Phylogenetic Relationships of the Horned Frogs (Anura: Ceratophryidae)

Abstract. The horned frog family, Ceratophryidae, currently comprises three genera and 12 extant species, distributed from the Caribbean lowlands to the Pampean grasslands. Horned frogs are fossorial species that are remarkable in terms of their adult and larval morphology, karyotype, behavior, and other aspects of their biology. In this paper we present a molecular phylogenetic analysis with the goals of: (1) exploring the relationships among the species of Ceratophryidae; (2) studying the evolution of polyploidy; (3) studying the evolution of cocoon formation and larval development duration associated with surviving in semiarid environments; and (4) reviewing the ceratophryid fossil record that could be relevant as calibration points in molecular divergence estimations. The analysis included 11 of the 12 extant species and, when possible, multiple exemplars per species, as well as multiple outgroups. Sequence data were obtained on seven mitochondrial and six nuclear genes for up to 8200 bp per specimen. Our results indicate that the individual monophyly of Ceratophrys and Lepidobatrachus is well corroborated. The monotypic Chacophrys is recovered as the sister taxon of Lepidobatrachus, but with Jackknife frequency < 50%. Lepidobatrachus asper is the sister taxon of L. laevis + L. llanensis. Relationships within Ceratophrys are congruent with an earlier proposal, with a clade composed of the species possessing a dorsal bony shield (Ce. aurita, Ce. cranwelli, Ce. joazeirensis, and Ce. ornata), and another clade composed of Ce. stolzmanni, Ce. calcarata, and Ce. cornuta. Unlike earlier proposals, the octoploid species (Ce. aurita, Ce. joazeirensis, and Ce. ornata) are not monophyletic, as the diploid Ce. cranwelli, and Ce. ornata are sister taxa. This result implies an ambiguous optimization of ploidy levels, with either a single origin of octoploidy with a subsequent reversal to diploidy, or two independent origins of octoploidy being equally parsimonious; both alternatives are quite unusual from the perspective of chromosome evolution. Our results suggest that ceratophryids diversified in semiarid environments and three independent events resulted in three species subsequently occupying temperate or tropical humid areas. This early diversification in semiarid areas explains the retention of characteristics associated with these environments (like the production of a cocoon of dead skin during estivation, and possibly an accelerated larval period and development) in species present in humid areas. A revision of the fossil record of this family of frogs indicates that there are only two fossil remains that could serve as calibration points for molecular clock estimation, but a number of issues associated with them preclude their use.
Water quality status and phytoplankton composition in Soetendalvlei, Voëlvlei and Waskraalsvlei, three shallow wetlands on the Agulhas Plain, South Africa

Three wetlands on the Agulhas Plain, for which no limnological information was available, were investigated in order to provide baseline data on their present water quality and phytoplankton community structure. Physicochemical variables were assessed and phytoplankton biomass and community analyses were conducted seasonally in 2007. The water in all wetlands was well mixed with no thermal stratification at the time of sampling. Soluble reactive phosphorus levels corresponded to the eutrophic to hypertrophic category. Only Voëlvlei showed very high microalgal chlorophyll a levels (>400 μg l–1) due to the dominance of cyanobacteria. In the other wetlands, flagellates, chlorophytes and diatoms were the main microalgal groups. A high rainfall event in July–August 2007 considerably altered the phytoplankton community structure in Voëlvlei when cyanobacteria were completely replaced by chlorophytes. During August and November 2007 phytoplankton biomass was low in all the wetlands, and eutrophication signs were observed only in Voëlvlei. However, dense stands of both submerged and emergent macrophytes were present in two of the wetlands, the decomposition of which could lead to water quality changes. Voëlvlei had only large stands of emergent macrophytes (Phragmites and Schoenoplectus).
Cloning and characterization of ATP synthase CF1 α gene from sweet potato

ATP synthase CF1 α subunit protein is a key enzyme for energy metabolism in plant kingdom, and plays an important role in multiple cell processes. In this study, the complete atpA gene (accession no. JN247444) was cloned from sweet potato ( Ipomoea batatas L. Lam) by reverse transcriptasepolymerase chain reaction (RT-PCR). This atpA gene contains an open reading frame (ORF) of 1524 bp coding for a peptide of 507 amino acids with a molecular mass of 55.36 kD. Sequence analysis showed that atpA gene from sweet potato has high homology with the other plant chloroplast atpA. The transcript levels of the atpA gene in young leaves, mature leaves, stems and tuberous roots were examined by the digital gene expression profiling (DGE), and then confirmed by semi-quantitative RTPCR. The results demonstrate that the highest transcription of atpA gene was found in young leaves, but it was relatively lower in other three tissues. In addition, the atpA gene was successfully expressed in Escherichia coli. Key words: Sweet potato, atpA gene, gene expression, digital gene expression profiling, quantitative analysis
Planting Date and In-ground Time Affect Cut Flowers of Liatris, Polianthes, and Iris

Bulbous roots of Kansas gayfeather or liatris (Liatris spicata Wind.), tube- rose (Polianthes tuberosa L.), and Dutch iris (Iris × hollandica) were planted between Nov. 1986 and Mar. 1987. Late planting extended harvest times and resulted in highest yields and longest stem lengths for Liatris spicata and Polianthes tuberosa, but. results were cultivar-dependent with Iris × hollandica hybrids. Yield was highest for all cul- tivars of Dutch iris except 'White Bell' when bulbs were planted in December. Late planting extended harvest time but reduced yield for all cultivars except 'White Wedg- wood'. No differences due to planting time occurred after the first season for liatris and tuberose, but both species had higher yields the years after initial planting and may be left undisturbed for at least 3 years. Iris flowers were destroyed by late frosts in two successive years and longevity could not be determined. The yield and stem length were optimum for Liatris 10 to 15 days from beginning of harvest, 4 to 5 weeks for single-flowered tuberose, and 5 to 6 weeks from start of harvest for double tuberose. Stem length of tuberose increased over the seasons, regardless of cultivar. Dutch iris, Kansas gayfeather (syn. L. callilepis), and tuberose are well-established cut-flower crops- in many countries. These crops are forced under greenhouse condi- tions to meet peak consumer demands and also grown in the field under minimal pro- tection. One of the limitations to field pro- duction is the lack of control of flowering time. Many field-grown species flower only for 1 to 3 weeks, resulting in oversupply while in flower and an undersupply after flowering has terminated. Studies with Dutch iris have demonstrated the necessity of rel- atively high temperatures after lifting fol- lowed by relatively low temperatures for successful flower forcing (Rees, 1985). Ethephon has been used to reduce the per- centage of nonflowering bulbs (Durieux and Kamerbeek, 1973) and some growers use smoke from burning damp straw (Stuart et al., 1966). Tuberose production was studied by Brundell and Steenstra (1985) and re- viewed by Wilkins (1985). Tuberose is widely
Alternative Splicingof an Arabidopsis Gene, At2g24600, Encoding Ankyrin-Repeat Protein

In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrin repeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number of transmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other. Keywords—Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.
Habitat Patch Size Affects Demographics of the Florida Scrub Lizard (Sceloporus woodi)

Abstract Habitat destruction and fragmentation are often cited as primary causes for declines in reptile and amphibian populations. Smaller habitat patches constrain population size resulting in increased extinction risk caused by stochastic processes. However, patch size also may affect populations in a deterministic manner. We used mark and recapture techniques to examine effects of patch size on demographics of the Florida Scrub Lizard (Sceloporus woodi). We examined populations in eight scrub habitat patches that differed in size but were similar with respect to other habitat characteristics. Abundance, survivorship, and recruitment were positively associated with patch size for both sexes. Individual growth rate increased with patch size for males but was negatively associated with patch size for females. Although our data indicate that patch size strongly affects demographics of scrub lizards, mechanisms responsible for these patterns are unknown. We discuss conservation implications of area-sensitive demography for local and regional populations. In particular, we suggest caution when constructing metapopulation models that assume homogenous survival and fecundity rates for all patches regardless of patch size.
Foundations of systems biology

Systems biology is a new field in biology that aims at system-level understanding ​ ofbiological systems. While molecular biology has led to remarkable ​ progress in our understanding ofbiological systems, the current ​ focus is mainly on identification of genes and functions of their products ​ which are components ofthe system. The next major challenge is to ​ understand at the system level biological systems that are composed of ​ components revealed by molecular biology. This is not the first attempt at ​ system-level understanding, since it is a recurrent theme in the scientific ​ community. Description: TOC,ILL,290P URI: http://hdl.handle. net/123456789/1685 Date: 2001-01-01
A cytological study of pretreatments used to improve isolated microspore cultures of wheat (Triticum aestivum L.) cv. Chris

Isolated microspores of wheat can be induced in vitro to switch their development from the gametophytic pollen pathway to a sporophytic pathway, resulting in embryoid or callus formation. The influence of cold or mannitol pretreatment on karyokinesis and cytokinesis in isolated microspore culture responses were investigated. Anthers were pretreated in mannitol for 7 d at 28°C; spikes at 4°C for 28 d. Microspores often completed the 1st mitotic nuclear division during pretreatment while cytokinesis was delayed. During mannitol pretreatments, the 1st mitotic nuclear division was mostly symmetrical while only asymmetric 1st nuclear divisions were seen during or after cold pretreatment. Following the symmetrical division, the two similar nuclei often appeared to fuse to form a diploid nucleus. Subsequently, these nuclei underwent rapid nuclear divisions to form multinucleate, and later, multicellular structures in induction medium. Cold pretreatments also induced muticellular structures but frequencies were l.
Shape from local and global analysis of texture

We demonstrate methods for estimating shape from texture $\dagger $ , for textures which are neither isotropic nor homogeneous. Whereas earlier work assumed either isotropy or homogeneity, we make a more general assumption: the local tangent distribution of the surface texture is invariant with respect to position. We then present a taxonomy of texture types, and a set of methods that can be used to recover surface orientation for each texture type. We define two classes of methods for estimating shape from texture: invariance-seeking methods, and value-seeking methods. These definitions are used to account for the performance of new methods on different classes of texture. The approach outlined in this paper provides a general strategy for generating methods for obtaining shape from texture for known classes of texture.
The Effect of pH on the Antioxidative Activity of Melanoidins Formed from Glucose and Fructose with L and D-Asparagine in the Maillard Reaction

In this study, the effect of pH on the antioxidative activities of melanoidins formed as a result of the reaction between sugars, glucose (Glc) or fructose (Fru), and amino acids, L-asparagine (L-Asn) and D-asparagine (D-Asn) are examined. For this purpose, antioxidative activities were evaluated on the basis of reducing power, including ferric reducing/antioxidant power (FRAP) and free radical scavenging activity includes 1,1-diphenyl-2-picryl- hydrazil (DPPH) and 2,2'-azinobis(3-ethylbenothiazoline-6-sulfonic acid) diammonium salt (ABTS) and ferrous ion chelating activity. Ethylene diamine tetraacetate (EDTA) and trolox, a water-soluble analog of tocopherol, were used as reference antioxidant compounds. The antioxidative activities of the melanoidins at a pH of 7.0 were greater than those with a pHs of 4.0 and pH 10.0. Especially, it was found that the melanoidins formed from D-isomers are more effective antioxidants in different in vitro assays. The reducing power and chelating activity of the melanoidins formed from the Fru systems were higher than those of the melanoidins formed from the Glc systems. However, the ABTS radical scavenging activity of the melanoidins formed from the Glc systems were higher than those of the melanoidins formed from the Fru systems. In particular, the DPPH radical scavenging activity and the FRAP of the melanoidins showed different antioxidative activities according to pH level.
Potential for Monitoring Eastern Small-footed Bats on Talus Slopes

Abstract Typical efforts to monitor bat populations in North America rely on winter hibernacula counts, but this method may be ill-suited for Myotis leibii (Eastern Small-footed Bat). Timing of reproduction, migration, and hibernation in this species also are poorly understood. We piloted novel techniques to monitor Small-footed Bats during the nonhibernation period, including catching bats in mist-nets placed directly on talus slopes, visually searching for roosting bats, surveying randomly distributed quadrats to estimate population size, and using skin temperature to study thermoregulation and seasonal activity. We efficiently documented bats with mist-nets and visual searches; the animals used crevices near the surface of talus slopes from early March until the end of October. Estimates from quadrats suggested one 3-ha talus slope had a maximum population of 196–343 bats. Use of torpor varied seasonally, but was similar between sexes. In mid-March, bats exhibited a hibernation-like pattern of torpor, hinting at the possibility that they may also overwinter on talus slopes. Monitoring of Small-footed Bats on rock outcrops during summer could resolve uncertainty about population trends. Thus, techniques described herein should be tested at suitable habitats in other parts of the range of Small-footed Bats.
Protocols for Evaluating Antioxidant Defence and Oxidative Stress Parameters in Rat Testis

This article describes the comprehensive methods and steps evaluating different antioxidant defence parameters and oxidative stress parameters of rat testis. Different antioxidant defence parameters include antioxidant enzymes like superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, glutathione S-transferase along with small antioxidant molecules like ascorbic acids and glutathione contents. Various oxidative stress parameters include hydrogen peroxide, protein carbonyl and lipid peroxide contents. Besides, methods for isolation of different testicular subcellular fractions, germ cell isolation and testis histological preparation were also described.
Aspects of the Life History of the Pacific Electric Ray, Torpedo californica (Ayres)

Abstract Pacific electric rays (n = 198) were collected from central and southern California from July 1994 through January 1996 for studies on their age and growth, reproduction, and demography. Whole vertebral centra with graphite microtopography band enhancement were used for ageing. Average percent error and percent error were 6.5% and 4.9% among readings. Maximum age was an estimated 16 yr. The von Bertalanffy growth model provided the best fit and predicted an asymptotic total length of 1372 mm for females and 921 mm for males, and K was estimated to be 0.073 for females and 0.137 for males. Female and male reproductive status was determined using two and three criteria, respectively. Median total length-at-maturity, determined using a logistic response function, was 645 mm (age estimate, 6 yr) for males and 731 mm TL (age estimate, 9 yr) for females. Fecundity of one female was estimated at approximately 17 young per litter. Time of parturition could not to be determined. Instantaneous mortality estimates ranged from 0.096–0.277, depending on longevity estimates. Best age-based demographic analyses indicate that the Pacific electric ray population has a net reproductive rate per generation of 2.6–8.9, a generation time of 11.2–13.0 yr, instantaneous rates of change of 0.09–0.18, and finite rates of change of 1.09–1.20.