Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementary Material For Optimization Methods for Interpretable Differentiable Decision Trees Applied to Reinforcement Learning

In this section, we provide a derivation of the optimal policy for the MDP in Fig. 1. For this derivation, we use the definition of the Q-function described in Eq. 2, where s′ is the state resulting from applying action a in state s. In keeping with the investigation in this paper, we assume deterministic transitions between states (i.e., p = 1 from Eq. 1). As such, we can ignore P (s′|s, a) and simply apply Eq. 3.
Screening of Ecotoxicant Responsive Genes and Expression Analysis of Benzo(a)pyrene-exposed Rockfish (Sebastes schlgeli)

Benzo[a]pyrene is a representative ecotoxicant in marine environment and a model compound of polycyclic aromatic hydrocarbons, which has an ability to bioaccumulate in aquatic organisms. This study aimed to identify molecular biomarkers suitable for assessing environmental pollution using a microarray technique. We examined the effects of benzo [a]pyrene on gene expressions in the rockfish, Sebastes schlegeli. We constructed the subtractive cDNA library with hepatic RNA from benzo[a]pyreneexposed and non-exposed control fish. From the library 10,000 candidate clones were selected randomly and cDNA microarray was constructed. We determined benzo[a]pyrene-responsive genes using a high-density microarray. Statistical analysis showed that approximately 400 genes are significantly induced or reduced by benzo[a]pyrene treatment (2 µM). Especially gene expression changes of 4 candidate clones among the up- or down-regulated genes were investigated in 6, 12 and 24 hr BaP-exposed fish groups. Many methods have been developed to monitor marine environmental status, which depend on quantifying the levels of the toxic components in polluted seawater or on ecological accessing, such as species diversity or richness. However, those methods could not provide information on physiological or genetic changes induced by such environmental stresses. Comparing with the conventional methods, these data will propose that benzo[a] pyrene-responsive genes can be useful for biological risk assessment of polycyclic aromatic hydrocarbons on marine organism at molecular level.
Are Pine Plantations “Inhospitable Seas” around Remnant Native Habitat within South-western Cape Forestry Areas?

SYNOPSIS Some areas of forestry estates, including unplantable ones, may be zoned and managed for nature conservation. This paper is an analysis of the results of studies of plants, birds and small mammals at Jonkershoek, Stellenbosch, to determine whether pine plantations are “inhospitable” to ecological and demographic processes required for the persistence of these biota in native habitat “islands” within forestry areas. The present study indicates that pine plantations are not unqualified “inhospitable seas”. However, the human-assisted dominance of the pines over the indigenous vegetation eliminates many species of the original habitat and reduces the numbers, or the frequency of occurrence, of the remaining species. There were significantly fewer vertebrate-pollinated, indigenous, plant species in the plantation sample than in the mountain fynbos one, and significantly more vertebrate-dispersed, native, plant species. Vertebrate pollinators were infrequently recorded in, or absent from, mature pine .
Morphological and Molecular Characterization of a New Nearctic Species of Calligrapha Chevrolat, 1836 (Coleoptera: Chrysomelidae, Chrysomelinae) from Central Mexico

Abstract. In this study we use a combination of morphological, molecular (mtDNA cytochrome c oxidase subunit 1 gene), geographic and ecological (field observations and cpDNA sequences from ingested plant tissue) data to describe and diagnose a new southern Nearctic leaf beetle species of Calligrapha Chevrolat, 1836 (Chrysomelidae: Chrysomelinae): Calligrapha thermalis Gómez-Zurita, sp. nov., associated to Perymenium mendezii De Candolle (Asteraceae). This new species, restricted to the Sierra Madre Occidental, is closely related to the Texan endemic Calligrapha wickhami Bowditch, 1911 associated to Viguiera stenoloba Blake (Asteraceae) in the northern foothills of the Sierra Madre Oriental ecoregion. The evolutionary scenarios explaining this recent taxonomic split, dated in the Pleistocene, are laid out and discussed.
Effects of Temperature and Leaf Position on Leaf Area Expansion of Kiwifruit (Actinidia deliciosa) Shoots: Development of a Modelling Framework

Abstract This paper describes mathematically the effects of temperature and position on the expansion of leaves along a kiwifruit (Actinidia deliciosa) shoot, taking into account shoot morphology. The leaves were grouped into three zones along the shoot: initial cluster leaves (first zone); the rest of the leaves that were preformed during the previous season (second zone); and leaves that were initiated during the current season (third zone). After opening of the initial cluster, the leaves appeared at constant rates for each of the two temperature treatments considered. The expansion of individual leaves was modelled by a growth function with the parameters: final area; duration of the growth window; centre of the growth window (timing of expansion); and lower asymptote. Within the first two zones, the pattern of leaf expansion was affected by nodal position, with basal leaves having higher initial rates of expansion than distal leaves. The timing of expansion was linear with respect to the nodal position within each of the zones, with the slope independent of temperature for the first zone. The slopes of the timing of expansion for the second and third zones depended on temperature and were correlated for each temperature treatment. Final leaf area was a function of leaf position in the first zone and a function of timing of leaf expansion for distal leaves starting from leaf 10. Temperature had no effect on final leaf area in the first zone. For the rest of the leaves, temperature affected final leaf area indirectly, through the timing of leaf expansion. The effect of temperature on the growth window of individual leaves within the first zone was less than that for the rest of the leaves. However, simulated values for the total leaf area of shoots using the average shoot growth window showed good agreement with experimental values.
Characterization of Poultry Production Systems in Vietnam

4 Abstract: Poultry raising in Vietnam is widespread and common to smallholder farmers that keep chickens and ducks as a source of cheap animal protein and to derive income from the sale of eggs, meat and live birds. Three systems of poultry production are described: 1) traditional, extensive backyard/household poultry production, 2) semi-intensive, small to medium scale, market-oriented, commercial poultry production and 3) intensive, large scale, industrial poultry production.
An efficient secretion of the protein fused to the AgfA signal sequence in Salmonella

Signal sequence (SS) of surface or secreting proteins plays an important function for protein secretion in bacterial system. The SS of various proteins may mediate different level of protein excretion yield of the proteins. In order to examine the effect of SS types in protein secretion, signal sequences of Bla (β‐ lactamase), AgfA (thin aggregative fimbriae A), StfA (Salmonella typhimurium fimbriae A) and OmpW (outer membrane protein W) were selected for the secretion of PspA protein which was used as a test protein. The PCR-amplified DNAs corresponding to each SS were cloned into the plasmid pYA3342. A primer used in PCR was designed to insert a His6-tag at the C-terminal of SS for the convenient detection of expressed SS. The 0.8 kb EcoRI-HindIII pspA gene was cloned into the recombinant plasmids, resulting pMMP66, pMMP67, pMMP68 and pMMP70. The S. typhimurium strains harboring the recombinant plasmids expressed the His6-tagged PspA, demonstrating in-frame fusion of PspA to each SS. Depending upon the type of SS, cell lysate as well as secreted PspA of each Salmonella samples was found different. Relatively, S. typhimurium containing pMMP67 (carrying AgfA SS) secreted the highest level of PspA than others, and suggested that the AgfA SS mediates efficient translocation of the PspA. Conclusively, the AgfA SS mediated secretion system in pMMP67 can be used in variety fields required for the high level of protein secretion, especially antigen delivery in recombinant attenuated Salmonella vaccines.
Copepod grazing and its potential impact on the phytoplankton development in the Barents Sea

Compiled data from published and unpublished sources on copepod grazing of the large-sized copepods in the Barents Sea give wide ranges in grazing rates. Approximate average values indicate daily rations of 7–18% for copepodite stages V and VI and considerably higher values for the earliest copepodite stages. It is demonstrated that individual variability in gut fullness of copepods from a given locality is typically very high and not closely related to variable food abundance or depth of occurrence. There is no diel feeding rhythm during the summer, and even when relating copepod grazing to a number of biotic and abiotic factors through stepwise linear regression analysis, much of the variability remains unexplained. It is suggested that feeding behaviour, food quality and feeding history of the copepods all play important roles as factors which regulate copepod grazing. Model simulations on the phytoplankton succession, using literature data on laboratory-determined growth characteristics for solitary cells and colonies of the prymnesiophyte Phaeocystis pouchetii and large diatoms, indicate that the extent of the mixed layer and selective grazing by zooplankton are important factors that may explain the occurrence of dense blooms of P. pouchetii colonies, frequently observed during the spring.
Genetic Similarities among Winter Wheat Cultivars Determined on the Basis of RFLPs, AFLPs, and SSRs and Their Use for Predicting Progeny Variance

The efficiency of breeding programs could be increased by predicting the prospects of crosses for line development before producing and testing lines derived from them. In this study, we (i) assessed the level of genetic diversity among German and Austrian winter wheat (Triticum aestivum L.) cultivars using 117 restriction fragment length polymorphism (RFLP) probes, 16 amplified fragment length polymorphism (AFLP) primer combinations, and 21 simple sequence repeat (SSR) primer pairs, (ii) investigated the correlation between coancestry (f) and genetic similarity (GS ) estimated from molecular markers, and (iii) evaluated the use off and GS for predicting the genetic variance (σ 2 g ) within sets of 22 F kn (n = 7 or 8) lines derived from 30 crosses between these winter wheat cultivars. The average polymorphic information content (PIC) for polymorphic bands was not significantly different between the three marker systems (0.30 ≤ PIC ≤ 0.33), whereas the marker index was low for RFLPs and SSRs but high for AFLPs. Estimates off between all 55 cultivar combinations ranged from 0.01 to 0.53. GS-values varied between 0.52 and 0.89 for RFLPs, between 0.40 and 0.83 for AFLPs, and between 0.16 and 0.91 for SSRs. The Mantel Z test statistic revealed no common pattern between the four dendrograms obtained by cluster analyses. Significant (P < 0.05) correlations among f, GS-RFLP, GS-AFLP, and GS-SSR were detected only for related parent combinations (f ≥ 0.10). For all seven traits analyzed, estimates of σ 2 g were not significantly associated with any measure of GS between parents. On the basis of these results, we recommend AFLPs for fingerprinting wheat cultivars. However, predicting the progeny variance σ 2 g remains an unsolved problem.
1‐methylcyclopropene extends Cymbidium orchid vaselife and prevents damaged pollinia from accelerating senescence

Abstract A single postharvest application of 1‐methylcyclopropene (MCP) was effective in prolonging vaselife of Cymbidium orchids by 6 or 7 days, to c. 19 days. It also prevented repeated applications of ethylene shortening the vaselife of Cymbidium orchids. The anti‐ethylene effect of one MCP treatment persisted throughout three successive challenges with ethylene at 5‐day intervals. A supra‐optimal concentration of MCP (500 ppb) showed no adverse effects. MCP was also effective in protecting Cymbidium orchids against accelerated senescence caused by damage to the pollinia. Individual flowers with damaged pollinia senesced even more rapidly than ethylene‐treated intact flowers. In the presence of MCP, flowers with damaged pollinia had a vaselife almost equal to that of undamaged flowers. This is a significant finding for the orchid export industry.
Cranial structure in the Devonian lungfish Soederberghia groenlandica and its implications for the interrelationships of ‘rhynchodipterids’

ABSTRACT New cranial material of the ‘rhynchodipterid’ lungfish Soederberghia groenlandica from Upper Devonian (Famennian) strata in East Greenland is described. Previously unknown structures identified here include components of the hyoid arch (ceratohyal, hypohyal) and the lower jaw (prearticular, dentary). Earlier interpretations of the cheek and mandible of Soederberghia are reconsidered in the light of new fossil specimens. Some of the difficulties in assessing the homologies between cheek bones in Soederberghia and those of other lungfishes stem from confusion over the arrangement in Rhynchodipterus, and a revised interpretation of this genus is proposed. The single infraorbital bar found in Soederberghia probably originates, in part, from an expanded bone 10 (quadratojugal) of the kind found in Griphognathus. Hypotheses that posit ‘rhynchodipterid’ polyphyly seem unlikely in light of a set of derived cranial characters that define a coherent radiation of long-snouted, denticle-bearing lungfishes known from the Late Devonian. The hypothesis presented here places ‘rhynchodipterids’ as a paraphyletic grade with respect to fleurantiids. Rhynchodipterus, Soederberghia, and fleurantiids form a clade to the exclusion of the species of Griphognathus. G. minutidens is the sister taxon to this apical group, while G. sculpta and G. whitei are more remote from it.
Absence of nuclear DNA synthesis in vesicular–arbuscular mycorrhizal fungi during in vitro development

SUMMARY A study of the in vitro viability of VA mycorrhizal propagules [Glomus caledonium (Nicol. & Gerd.), Gigaspora margarita (Becher & Hall)], indicated that none could be used for continuous in vitro cultivation. Large numbers of nuclei (at least 20000 for G. margarita) were found in the chlamydospores. Nuclear division could not be demonstrated in vitro, during or after spore germination using various cell cycle inhibitors, or by direct isotope labelling of nuclear DNA. Manipulation of secondary messengers (cAMP, calcium) and the microtubule or micro-filament system did not increase the in vitro growth of the tested VA mycorrhizal strains.
Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat

The objectives of this study were to validate the major quantitative trait locus (QTL) for scab resistance on the short arm of chromosome 3B in bread wheat and to isolate near-isogenic lines for this QTL using marker-assisted selection (MAS). Two resistant by susceptible populations, both using ‘Ning7840’ as the source of resistance, were developed to examine the effect of the 3BS QTL in different genetic backgrounds. Data for scab resistance and simple sequence repeat (SSR) markers linked to the resistance QTL were analyzed in the F2:3 lines of one population and in the F3:4 lines of the other. Markers linked to the major QTL on chromosome 3BS in the original mapping population (‘Ning7840’/‘Clark’) were closely associated with scab resistance in both validation populations. Marker-assisted selection for the QTL with the SSR markers combined with phenotypic selection was more effective than selection based solely on phenotypic evaluation in early generations. Marker-assisted selection of the major QTL during the seedling stage plus phenotypic selection after flowering effectively identified scab resistant lines in this experiment. Near-isogenic lines for this 3BS QTL were isolated from the F6 generation of the cross ‘Ning7840’/‘IL89-7978’ based on two flanking SSR markers, Xgwm389 and Xbarc147. Based on these results, MAS for the major scab resistance QTL can improve selection efficiency and may facilitate stacking of scab resistance genes from different sources.
New Host and Distribution Records of the Leech Placobdella sophieae Oceguera-Figueroa et al., 2010 (Hirudinida: Glossiphoniidae)

ABSTRACT: Placobdella sophieae Oceguera-Figueroa et al., 2010 (Hirudinida: Glossiphoniidae) is reported from Oregon, California, and British Columbia for the first time. New hosts reported for P. sophieae include Taricha granulosa (rough-skinned newt), Rana pretiosa (Oregon spotted frog), and Anaxyrus boreas (western toad). Placobdella sophieae exhibits relatively low host specificity and all amphibians occurring in the Pacific Northwest are potential hosts.
Effects of Environmental Forcing on Age-Structured Populations: Northern California Dungeness Crab (Cancer magister) as an Example

Evaluation of potential environmental effects on recruitment requires knowing how environmental forcing can affect recruitment and subsequent catch, and how these effects depend on life history. General relationships between a time series of an environmental forcing variable, the resulting time series of recruitment, and the subsequent time series of catch or abundance are described here for a fishery in which environmental forcing affects density-dependent recruitment and the population is fished at a constant rate. For a stable population with overcompensatory, density-dependent recruitment, the recruitment time series will resemble the environmental time series except that frequencies near 1/(2 × mean age in the population) will be emphasized. The amount of selective emphasis will depend on the degree of overcompensation, harvest rate, and width of the cohort size distribution (in a size-selective fishery). For a population harvested at constant rate, the catch time series will resemble the recruitment.
Balanço de nitrogênio em cordeiros alimentados com rações contendo diferentes teores de concentrado

Evaluated the nitrogen intake, fecal and urinary nitrogen production and nitrogen balance (NB) in lambs fed levels increasing of concentrate (20.0%, 40.0%, 60.0% and 80.0 %) in the southwestern region of Mato Grosso. Were used four lambs mongrel (SRD), intact, with body weight (BW) averaged 19.3 ± 2.1 kg allocated to metabolism cages, fed twice daily, the concentrate was composed of ground corn and soybean and roughage utilized was corn silage. Were used a design in latin square 4X4, the leavings, faeces and urine were collected daily for six days, in each collection period. Each experimental period lasted 20 days. Intake data of nitrogen (N), fecal N, urinary N, absorbed N and NB expressed in g day-1;% of nitrogen intake (NI) and grams per kilogram of metabolic weight (g kg0,75 –1) were undergo analysis of variance (ANOVA) and tested using regression equation at 5% probability. It was observed that the inclusion of different levels of concentrate supplied the lambs, on the intake N, N absorbed and urinary in g day-1, g kg0.75 –1 and % NI presented a quadratic effect (P<0.05) with the maximum point obtained for the inclusion of 40.0% concentrate on experimental diets. For fecal nitrogen in g day –1, g kg0.75 –1 and % NI and nitrogen balance (NB), the inclusion of concentrate in the diet changed (P<0.05) linearly decreasing with better results for inclusion levels of 20.0% to 40.0% concentrate diet. Thus, it is concluded that the level of 40.0% concentrate in the diet of lambs provides the best values of nitrogen intake, urinary nitrogen and nitrogen absorbed in g day-1, g kg0.75 –1 and in % of nitrogen intake, and provide satisfactory results for the values of fecal nitrogen and nitrogen balance expressed in g day 1, g kg0.75-1 and in % of nitrogen consumed.
Root exudate is allelopathic in invaded community but not in native community: field evidence for the novel weapons hypothesis

1 Exotic invasive plants can have strong effects on native communities. Centaurea maculosa, a forb that is native to Eurasia, has created near‐monocultures in many parts of its invaded range in western North America and produces the root exudate (±)‐catechin. Controlled laboratory experiments suggest that the phytotoxic effects of (±)‐catechin may be stronger on some North American species than on some European species. 2 We conducted experiments in the field in two different years in the native (Romania) and invaded (MT, USA) ranges of C. maculosa, testing the effects of (±)‐catechin on species that co‐occur with C. maculosa in both ranges. 3 (±)‐Catechin reduced the growth of native plant species in Montana in both years, although there was some variability between species in the effect of (±)‐catechin on leaf growth in 2005. There was no effect of (±)‐catechin on plants in Romania. 4 This first in situ test of the novel weapons hypothesis supports the notion that novel biochemical constituents of some invasive species may contribute to their success. 5 Synthesis. In addition to providing information useful for understanding invasions, our results indicate that some species in the native range of C. maculosa may be adapted to its particular biochemical traits, raising the possibility that interactions among plant species may be affected by a common evolutionary history.
Pelacakan Kerusakan Akrosom Spermatozoa Domba Selama Proses Pembekuan dengan Teknik Histokimia Lektin (DETECTION OF ACROSOMAL DAMAGE OF RAM SPERMATOZOA DURING FREEZING PROCESS USING LECTIN HISTHOCHEMICAL TECHNIQUE)

Freezing process in ram spermatozoa caused damage of the plasma membrane and acrosome thatlead to the decrease of spermatozoa fertility. Research was conducted to evaluate acrosomal damageduring freezing process using lectin histochemical technique. Semen was collected twice a week usingartificial vagina from 1-2 years old Garut ram. Immediately after collection, characteristic of semenquality was evaluated then diluted with Niwa and Sasaki Freezing (NSF) medium. Semen was loadedinto 0.25 mL mini straws and equilibrated at 4oC for two hours. Straws were then frozen and stored inliquid nitrogen. Evaluation of sperm characteristic (motility, viability and plasma membrane integrity)and acrosomal integrity were done during the freezing process. Detection of acrosomal integrity was observedusing Fluorescens isothiocyanate (FITC) and Avidin-Biotin-Complex (ABC) staining methods. Data ofcharacteristic spermatozoa and acrosomal integrity were analyzed using ANOVA. Result of the experimentsshowed that the percentage of motility, viability and plasma membrane integrity of spermatozoa before freezing (83 ± 2.7%; 88.8 ± 2.6%; 88.2 ± 3.7%) were significantly decreased (P<0.05) after equilibration (71± 4.2%; 84.2 ± 5.0%; 76.2 ± 1.3%) and after thawing (40 ± 3.5%; 61.08 ± 3.3%; 51.2 ± 10.4%). The percentageof intact acrosomal spermatozoa using FITC and ABC methods during freezing process were 93.63 ±2.73%; 88.04 ± 3.2% and 81.73 ± 4.77% VS 94.54 ± 0.26%; 88.17 ± 0.38% and 79.38 ± 2.06%, respectively.In conclusion, the characteristic of spermatozoa were significantly decrease (P<0.05) during freezing process.Furthermore, the integrity of acrosome spermatozoa can be well analyzed during freezing process by usinglectin histochemical staining methods.