Miracle-dz/UniFAR-FTUs huggingface dataset:
The Influence of Fluctuating Resources on Life History: Patterns of Allocation and Plasticity in Female Guppies

We investigated how resources are allocated to reproduction and how vari- ations in resource availability influence reproductive allocation, offspring number, and offspring size in guppies (Poecilia reticulate). Our goal was to evaluate how plastic these variables are in response to environmental variation and to characterize the nature of this plasticity. Female guppies which had just given birth (litter 1) were assigned to either high or low levels of food availability until they gave birth to their next litter (litter 2, interval 1). They were then randomly reassigned to either high or low food with the constraint that there be equal numbers of individuals in each of four treatments: high-high, high-low, low-high, and low-low. They were maintained on this level of food availability until they produced their next litter (litter 3, interval 2). We analyzed variables that characterized the female after the birth of the third litter and the offspring in the third litter. These were two-way analyses, with intervals 1 and 2 as the main effects and high vs. low food as the levels of each effect. The qualities of the third litter were influenced by both interbrood intervals, indicating that the resources used for producing the litter were derived from both intervals. Specifically, higher food availability during either interval resulted in a significant increase in the number of offspring in litter 3, independent of the size of the mother. This result indicates that the number of offspring produced in a litter will be a function of both the immediate and the past environment. Lower food during either interval resulted in an increase in the number of days between the second and third litters, indicating that, if resource availability is low, the female may delay the initiation of the next litter, allowing her to acquire more resources. Resource availability during both intervals also influenced how resources were allocated to individual offspring. Females responded to low food during the first interbrood interval by producing heavier offspring in litter 3. This increase in mass was almost entirely at- tributable to an increase in fat reserves. Such a result could represent adaptive plasticity, if it can be demonstrated that maternal fitness increases through the production of heavier offspring in a low-food environment.
Morphology and cytology of aeciospores and aeciospore germ tubes of host-alternating and pine-to-pine races of Cronartium flaccidum in northern Europe

Host-alternating and pine-to-pine races of Cronartium flaccidum (Alb. & Schw.) Wint. (Peridermium pint Lev.) on Pinus sylvestris L. from northern Europe can be distinguished by differences in the morphology and cytology of aeciospores and aeciospore germ tubes. In the host alternating race, aeciospores were binucleate and, upon germination, two nuclei migrated into the germ tube. The nuclei remained undivided during migration. Septa were not observed and branching was dichotomous and irregular. Growth of germ tubes was indeterminate.In the pine-to-pine race, aeciospores were mostly binucleate but variable proportions (16% to 28%) were uninucleate. Upon germination nuclear division and septum formation occurred and the germ tubes were transformed into two, three, or four cells, each of which usually contained one nucleus. The germ tubes were straight and seldom exceeded 200 μ in length. One to three branches were observed. Despite the absence of basidiospores, the pine-to-pine race of C. flaccidum (= P. pi.
Review of Common Sequence Alignment Methods: Clues to Enhance Reliability

Today, in various aspects of molecular biology, sequence alignment has become an essential tool to study the structure-function relationships of proteins. With the impressive increase of the number of available sequences, alignments provide a substantial piece of information by way of various computational methods. These approaches have generally become a crucial tool to put forward working hypotheses for time-consuming bench work, as protein engineering and site directed mutagenesis. However alignment methods remain hugely perfectible. All methods are dramatically limited in the twilight zone, taking place around 25% of identity between pairs of sequences. More worrying is the very high rate of false positive results generated by most algorithms, depending of empirical parameters, and hard to validate by statistical criteria. After reviewing the main methods, this paper draws user's attention to the fact that algorithm performance evaluations are entirely limited to alignment power (sensibility) evaluation. In reference to a given truth defined from alignment of know structures, the power is defined as the proportion of truth restored in the solution. The power may be overestimated by a lack of independent sets of poorly related sequences and its value depends entirely on the criterion used to define the truth. On the other hand, confidence (selectivity) represents the proportion of the solution that is true. Depending on the method and the parameters used, confidence may be much lower than power, and is usually never evaluated. For non-trivial alignments, when the power is high, confidence is low, which means that correctly aligned positions are embedded in large regions unduly aligned. One possible solution to these problems is to use consensus of several multiple alignment methods, which will increase the confidence of the results. The addition of external information, such as the prediction of the secondary structure and/or the prediction of solvent accessibility is also an other way that should increase the performance of existing multiple alignment methods.
estim 1.0: a computer program to infer population parameters from one‐ and two‐locus gene identity probabilities

Estimating effective population size is an important issue in population and conservation genetics. Recently, we proposed a new method to infer effective size and migration rate from one- and two-locus identity probability measures. We now announce the release of a user-friendly Microsoft® Windows program that uses this method to provide joint estimates of local effective population size and immigration rate for each subpopulation in a population genetics data set.
Fine‐scale spatial structure in a grassland community: quantifying the plant’s‐eye view

1 The fine‐scale spatial patterns of Agrostis stolonifera, Holcus lanatus and Lolium perenne were recorded in an English lowland grassland as presence/absence maps from 400‐cell quadrats at two different scales (2 × 2 cm or 8 × 8 cm cells). 2 Local spatial structure in these patterns was quantified using spatial covariance functions. Distance‐ and direction‐dependent components were examined separately for both intra‐ and interspecific patterns. The significance of departures from randomness was determined using Monte Carlo techniques. 3 The smaller‐scale data showed that all three species were significantly aggregated, Agrostis to a greater distance (8 cm) than Holcus or Lolium(4 cm). The intensity of aggregation decreased in the order Lolium > Holcus > Agrostis. The larger‐scale data suggested that this aggregation extended to greater distances, and that it was most intense in Agrostis. 4 Despite the lack of visual directionality in the environment, Agrostis showed a directional pattern at both scales, with Lolium varying in the same direction at the larger scale. 5 Only Agrostis and Lolium showed a significant interspecific relationship (segregated to 2 cm at the small scale, but aggregated to 8 cm at the larger scale). There was no evidence of directionality in the interspecific components of pattern. 6 The nature of spatial structure appears to depend on the scale of observation, but the smaller‐scale data are more likely to provide a biologically interpretable measure of local spatial structure in this community.
Ontogenetic loss of phenotypic plasticity of age at metamorphosis in tadpoles

Amphibian larvae exhibit phenotypic plasticity in size at metamorphosis and duration of the larval period. I used Pseudacris crucifer tadpoles to test two models for predicting tadpole age and size at metamorphosis under changing environmental conditions. The Wilbur-Collins model states that metamorphosis is initiated as a function of a tadpole's size and relative growth rate, and predicts that changes in growth rate throughout the larval period affect age and size at metamorphosis. An alternative model, the fixed-rate model, states that age at metamorphosis is fixed early in larval life, and subsequent changes in growth rate will have no effect on the length of the larval period. My results confirm that food supplies affect both age and size at metamorphosis, but developmental rates became fixed at approximately Gosner (1960) stages 35-37. Neither model completely predicted these results. I suggest that the generally accepted Wilbur-Collins model is improved by incorporating a point of fixed developmental timing. Growth trajectories predicted from this modified model fit the results of this study better than trajectories based on either of the original models. The results of this study suggests a constraint that limits the simultaneous optimization of age and size at metamorphosis. 32 refs., 5 figs.,more » 1 tab. « less
The detection of Gram-negative bacterial mRNA from soil by RT-PCR

The method described extracts high quality RNA from a clay-rich soil for which other published extraction protocols have failed. Transcript encoding the enzyme β-glucuronidase could be reliably detected by reverse transcriptase polymerase chain reaction in soil seeded with a genetically modified Rhizobium leguminosarum containing the uidA gene.
Predicting Microbial Growth In Anaerobic Digester Using Gompertz And Logistic Models - IRE Journals

Models plays a vital role in understanding microbial growth in wastewater treatment and bioremediation processes, as is, in safe food production, microbe-mediated and mining among others. However, it is also gaining popularity in optimization designs. A study was undertaken to predict microbial growth in anaerobic digestor using Gompertz and logistic models. The objective was to determine the growth parameters and compare the performance of these primary models in anaerobic digestion (AD). Three isolates from brewery waste water closely related to Bacillus subtilis, Bacillus methylotrophicus and Lysinibacillus species were used as inoculum and their growth monitored based on optical density (OD) at the same conditions but different initial cell concentration. Microbial population growth data were fitted to the modified logistic function and Gompertz function using Marquardt algorithm and the comparison was based on both the Alkaike Information Criterion value (AIC), Residual Sum of Squares and R 2 values. All the models had a high goodness of fit (R 2 > 0.93) for all growth curves for three isolates, in all the cases. However, Gompertz model was accepted in 66.67% of the cases based on the AIC values and also supported by the R 2 > 0.95values and small RSS values. The models provided knowledge to define the growth of the methanogenic community in a bio-digester as a function of time, which could be used for maximum utilization of the exponential phase of the microbial growth for production of biogas. This indicates the practicality of applying Gompertz model to actual anaerobic digestion of brewery waste water. Growth parameters like the rate of increase in the number of cells per unit time and lag time were determined from the models. Indexed TermsAnaerobic digestion, Biogas, Gompertz, Logistic, Microbial growth Models.
TOWARDS MACHINE LEARNING APPROACHES TO IDENTIFY SHRIMP DISEASES BASED ON DESCRIPTION

: Shrimp farming is a key sector in economic development in Mekong Delta provinces. Unfortunately, there are many problems in shrimp farming, especially shrimp diseases which cause a considerable loss. Shrimp diseases are expressed through symptoms and manifestations of shrimp. Recognizing the importance of shrimp symptoms to help raise an early warning, in this research the authors apply several state-of-the-art text classification algorithms such as Logistic Regression, Random Forest, Naïve Bayes, Support Vector Machines, and Multilayer Perceptron on a collection of 1098 observations categorizing into 14 distinct classes. Several thorough evaluation scenarios have been conducted including a process tokenization and models’ comparison on the obtained data set with different ratios. The results show that Support Vector Machines achieves the highest classification accuracy (81.27%), followed by Multilayer Perceptron, Random Forest, Logistic Regression, and Naïve Bayes. Through the results of the study, it is feasible to apply machine learning algorithms to diagnose shrimp diseases entirely based on textual symptom descriptions.
Adrenal corticosteroids, their receptors and hypertension

Mineralocorticoids and glucocorticoids are primarily synthesized in the adrenal cortex, and play key roles in mediating physiological responses under stressful conditions, such as lack of water or nutrients. Both types of corticosteroid elevate blood pressure and elevated levels of these steroids are found in hypertensive patients. The major mineralocorticoid and glucocorticoid in humans are aldosterone and cortisol, respectively. Aldosterone activates the mineralocorticoid receptor (MR) and cortisol the glucocorticoid receptor (GR). In this overview, the clinical and genetic evidence that both MR and GR are involved in blood pressure regulation is reviewed as are the mechanisms by which MR and GR regulate blood pressure in response to agonists. MR antagonists have been used to treat hypertension. However, GR antagonists have not been fully explored in the clinic. Based on the prevalence of abnormal mineralocorticoid and glucocorticoid signaling in hypertension patients, it is proposed that antagonizing these adrenal corticosteroid receptors will provide benefit in treating hypertension. Drug Dev. Res. 67:871–883, 2006. © 2007 Wiley‐Liss, Inc.
GA Signaling: Genes and GTPases

The rich history of efforts to understand the biosynthesis and biological activity of gibberellins (GAs) began with Mendel (his stem length gene Le encodes a GA 3β-hydroxylase that activates GAs [[Lester et al., 1997][1]; [Martin et al., 1997][2]]). In the years since Mendel unknowingly got the
Environmental filtering of crustacean zooplankton communities in fishless boreal lakes: expectations and exceptions

To test the paradigm that large-bodied zooplankton species dominate in fishless lakes, we evaluated crustacean zooplankton composition of 53 fishless boreal lakes across a broad geographic scale (north-west Saskatchewan, Canada) in relation to contemporary environmental factors. Lake productivity, acid–base status and intensity of invertebrate predation were the three major environmental filters of crustacean zooplankton composition of the survey lakes, while lake morphometry and drainage basin characteristics likely had indirect effects by influencing the variations in above environmental factors. The traditionally expected dominance of large-bodied zooplankton species in fishless conditions only occurred in well-buffered shallow lakes with higher productivity and intense invertebrate predation. Daphnia pulex was dominant in more eutrophic lakes, while higher abundances of Holopedium gibberum were favored by relatively mesotrophic conditions. In exception to the traditional view, small-bodied species dominated in 57% of survey lakes as influenced by interactions of biotic and abiotic factors. Bosmina longirostris and cyclopoid copepods dominated less productive, deeper lakes with low invertebrate predation. Predominance of Leptodiaptomus minutus was supported under unfavorable environmental conditions for other species, i.e. poor buffering capacity and/or low calcium concentration. The present study demonstrates that exceptions to the generally expected species composition in fishless lakes can be caused by interactions among abiotic and biotic factors.
Systematics and Phylogeny of the Hatchet Head Plant Bug Genus Myrmecoroides Gross (Insecta: Heteroptera: Miridae: Orthotylinae)

Abstract Myrmecoroides Gross is revised and a new diagnosis is provided for the genus. The two previously recognized species, M. carinatus Gross and M. grossi Carvalho, are redescribed. Three new species are described: M. cassowary, M. monteithi, and M. rufescens. The male and female genitalia are documented and illustrated where specimens of each gender were available. Phylogenetic analysis of the species is given. The common name, Hatchet Head Plant Bug, is introduced for the genus, in recognition of the greatly bicompressed head.
Chlorophyll Measurements and Nitrogen Nutrition Index for the Evaluation of Corn Nitrogen Status

Plant-based diagnostic techniques are used to determine the level of crop N nutrition but there is limited comparative research on the different methods. Our objectives were to establish the relationship between chlorophyll meter (CM) readings and N nutrition index (NNI) during the corn (Zea mays L.) growing season, and to compare both methods as diagnostic tools for predicting grain yield response to N fertilization. The study was established at eight site-years using four to seven N fertilization rates. The CM readings from the youngest collared leaf were taken on five to eight sampling dates in 2004,2005, and 2006 along with NNI determinations. Generally, CM readings and NNI increased with increasing N rates. Chlorophyll meter readings and relative CM (RCM) readings were related to NNI, but the intercepts and/or slope of the response curves varied with site-year. Because they are site-specific, these relationships may not be reliable indicators of corn N status. The relationship between CM readings and relative grain yield (RY) at stage of development ≈V12 was also site-specific. Relative CM readings (RY = -0.64 + 1.65 RCM ifRCM ≤ 0,98 and RY = 0.97 if RCM > 0.98; R 2 = 0.60) and NNI (RY = -0.34 + 1.47 NNI ifNNI ≤ 0.88 and RY = 0.96 if NNI > 0.88; R 2 = 0.79) at stage of development ≈V12 were related to RY. These two relationships were stable across site-years and could be used to detect and quantify N deficiencies of corn.
The Classroom Management Approach in the Grammar Practice Class

The grammatical competence is a capacity that is considered necessary to organize words and sentences accurately. Since the teaching of grammar means training the students to improve their communicative competence as well, thus it requires a great deal of time. Although the adequate grammar learning classrooms have been managed, yet the additional grammar practice class is considered necessary to carry out. A number of studies related to traditional and modern grammar learning activities have been conducted. However, there are only a few interests on the classroom management approaches utilized in the grammar practice class. Hence, this study is conducted to analyze the systems, structures, and expectations of the grammar practice class conducted by the English Department at a university in Indonesia. The four primary approaches of classroom management are selected as the main framework in this study. The case study research is chosen to portray the structure of grammar practice class to reveal a particular classroom management approach employed in this program. The process of data analysis discloses that the grammar practice class utilizes the assertive discipline. As a result, the grammar instructor is likely to be classroom leader to create a systematic classroom management.
Cephennula gen. nov. (Coleoptera, Scydmaenidae), with Four New Species from Malaysia and Indonesia

A new genus belonging to the tribe Cephenniini, Cephennula Jal⁄oszyński, is described. The type species is Cephennula multicarinata Jal⁄oszyński, occurring in Indonesia (Borneo: Kalimantan); the genus includes also three other new species: C. minuta (E Malaysia, Borneo: Sarawak), C. secunda (W Malaysia: Selangor), and C. scaphisoma (W Malaysia: Pahang). Diagnostic characters of the new genus and all new species are illustrated and discussed on the background of morphology of all other genera of the tribe.
A targeted study on possible free ammonia inhibition of Nitrospira

Batch tests were carried out with Nitrospira in mixed and pure cultures using concentrations of free ammonia widely believed to be inhibitory to nitrite-oxidizing organisms. The mixed culture batch tests were conducted with mixed liquor from a bench scale completely stirred tank reactor (CSTR) treating a synthetic wastewater having a low C:N ratio. Nitrospira were confirmed as the dominant nitrite oxidizers via RNA slot blotting. Nitrospira moscoviensis were used for the pure culture trials. The results from this study suggest that free ammonia (NH3-N) concentrations of up to 10 mg/L were not inhibitory to Nitrospira either in situ or in pure culture. Key words: fatty acid methyl esters, free ammonia inhibition, molecular methods, nitrification, nitrite, Nitrobacter, Nitrospira, nitrous acid, nitrous oxide, RNA slot blotting, wastewater treatment.
Private Matching for Compute

We revisit the problem of two-party private set intersection for aggregate computation which we refer to as private matching for compute . In this problem, two parties want to perform various downstream computation on the intersection of their two datasets according to a previously agreed-upon identifier. We observe that prior solutions to this problem have important limitations. For example, any change or update to the records in either party’s dataset triggers a rerun of the private matching component; and it is not clear how to support a streaming arrival of one party’s set in small batches without revealing the match rate for each individual batch. We introduce two new formulations of the private matching for compute problem meeting these requirements, called private-ID and streaming private secret shared set intersection (PS 3 I), and design new DDH-based constructions for both. Our implementation shows that when taking advantage of the inherent parallelizability of these solutions, we can execute the matching for datasets of size upto 100 million records within an hour.
THE TREND AND DIRECTION OF MATHEMATICS EDUCATION RESEARCH IN KOREA

To explain the overall research trend in mathematics education in Korea over the last 20 years, this paper presents an analysis of 3044 peer-reviewed papers published in seven domestic professional mathematics education journals. The papers were analyzed in terms of publication year, topic, research method, and target research population. In addition, papers on research conducted in the international context were analyzed. The results of this analysis showed rapid quantitative growth since the late 2000s and a diversity of research topics including learners’ abilities or characteristics, instruction or teaching methods, and curricula or textbooks. The most popular research methods included pedagogical analyses, case studies, and surveys. In terms of the target research population, students were more popular subjects than curricular materials and teachers in both elementary and secondary schools. A majority of the papers on research conducted in the international context were comparative studies dealing with foreign curricula or textbooks. The paper concludes with several implications regarding issues that need to be further considered to promote mathematics education research.