Miracle-dz/UniFAR-FTUs huggingface dataset:
A degree-day model of Cirsium arvense shoot emergence from adventitious root buds in spring

Abstract If decision-aid software models of weed emergence and growth are ever to help producers better time weed management, these models must be able to predict perennial weed shoot emergence from vegetative propagules. In this research, Cirsium arvense shoot emergence from adventitious root buds in spring was modeled using degree-day heat sums. Fractional C. arvense shoot emergence was best modeled as a logistic dose–response function of degree-day heat sum as follows: Y = 1.108/(1+[X/488.344]−5.161) where Y = fractional C. arvense shoot emergence (0 to 1) and X = heat sum in degree-days above 0 C after day 91 of the year (April 1) with an upper limit of 800 degree (C) days (r2 = 0.83). This empirical model was validated by graphing observed vs. model-predicted C. arvense shoot emergence using two independently gathered data sets, one of C. arvense emergence in autumn chisel-plowed Triticum aestivum (r2 = 0.82) and the other in no-till fallow (r2 = 0.63). The model slightly overestimated emergence at low fractional emergence (< ∼7% at 0.1 fractional emergence) and underestimated emergence at high fractional emergence (10 to 20% at 0.8 to 1.0 fractional emergence). Below an emergence fraction of 0.8, the model adequately estimated observed emergence to within about 10% of the predicted regression line. Using the model, about 1% and 80% of C. arvense shoots should emerge from adventitious root buds after a heat sum accumulates of about 197 and 587 C d, respectively, starting from day 91 of the year. Consequently, farmers should begin monitoring C. arvense patches for emergence and height growth after about 197 C d accumulate and expect to control C. arvense before about 587 C d accumulate, which is when about 80% of shoots have emerged. Nomenclature: Cirsium arvense (L.) Scop. CIRAR, Canada thistle; Triticum aestivum L. , wheat.
Ruff , Philomachus pugnax (Aves, Charadriiformes), Migration in Western Ukraine

Abstract In the paper we discuss migration dynamics, biometry and stopover ecology of Ruff (Philomachus pugnax Linnaeus, 1758) in the Cholgini ornithological reserve. Also the observations, made in other regions of the western Ukraine, were used in the analysis. Th e base materials for this paper were collected during 1995-2012 by West-Ukrainian ornithological station, by conducting regular bird counts, ringing and taking measurements of migrating waders using standard methods. During Ruff spring migration two major waves of passage occured: the first one is from the end of March till early April and the second - from the end of April to the end of May. Th e average number of a flock was equal 12 individuals. In the autumn passage dynamics of two waves can also be seen. Th e fist wave is observed in July with the peak in the middle of month. Second wave occurs in August and in fist two decades of September, with maximum bird numbers in the end of August. Th e passage dynamic of Ruff in the Cholgini reserve is very similar to the dynamic in other continental staging sites. Significant difference was found in the wing length between the adult and juvenile Ruff s. Th e potential flight range of juvenile females was 3236 km, juvenile males - 2380 km, adult females - 2740 km. Pезюме Рассматриваются динамика миграции, биометрия и особенности пребывания на месте миграционной остановки турухтана (Philomachus pugnax Linnaeus, 1758) на примере орни- тологического заказника «Чолгинский». Также анализируются данные, полученные во время на- блюдений на других территориях запада Украины. Базовый материал, лежащий в основе работы, собран путём проведения регулярных учётов птиц, кольцевания и промеров биометрических пара- метров общепринятыми методами. Во время весенней миграции турухтана выявлено две основных волны пролёта: первая приходится на период от конца марта до начала апреля, вторая - на конец апреля - конец мая. Средняя численность скоплений турухтана в заказнике весной составляла 12 особей. В динамике осеннего пролёта можно также выделить две волны. Первая в июле, с пиком численности в средине месяца. Вторая волна в августе, а также в первых двух декадах сентября с максимальной численностью птиц в конце августа. Динамика миграции турухтана в заказнике «Чолгинский» в общем сходна с таковой в других пунктах остановки. Обнаружены достоверно меньшие длина крыла и масса молодых самок относительно взрослых. Потенциальная дальность полёта турухтанов для молодых птиц рассчитана как 3236 км, молодых самцов - 2380 км, взрослых самок - 2740 км.
Biochemistry & Pharmacology: Open Access Biological and Solid-State Nanopores for DNA Sequencing

History and current developments of nanopores for DNA sequencing are reviewed. Discussions are primarily carried out on the two major categories of the devices, biological and solid-state nanopores. Hybrid nanopores are also mentioned. Difficulties defying practical applications are demonstrated as well as some possible improvements. A brief prospect is given in addition.
Knowledge Transfer Dehazing Network for NonHomogeneous Dehazing

Single image dehazing is an ill-posed problem that has recently drawn important attention. It is a challenging image process task, especially in nonhomogeneous scene. However, the existing dehazing methods are commonly designed to handle homogeneous haze which is easily violated in practice, due to the unknown haze distribution of real world. In this paper, we propose a knowledge transfer method that utilizes abundant clear images to train a teacher network to provide strong and robust image prior. The derived architecture is referred to as the Knowledge Transform Dehaze Network (KTDN), which consists of the teacher network and the dehazing network with identical architecture. Through the supervision between intermediate features, the dehazing network is encouraged to imitate the teacher network. In addition, we use attention mechanism to combine channel attention with pixel attention to capture effective information, and employ an enhancing module to refine detail textures. Extensive experimental results on synthetic and real scene datasets demonstrates that the proposed method outperforms the state-of-the-arts in both quantitative and qualitative evaluations. The KTDN ranks 2nd in NTIRE-2020 NonHomogeneous Dehazing Challenge [4], [5].
Leftovers in seed dispersal: ecological implications of partial seed consumption for oak regeneration

1. Successful seed dispersal by animals is assumed to occur when undamaged seeds arrive at a favourable microsite. Most seed removal and dispersal studies consider only two possible seed fates, predation or escape intact. Whether partial consumption of seeds has ecological implications for natural regeneration is unclear. We studied partial consumption of seeds in a rodent‐dispersed oak species.
Diversity reduces invasibility in experimental plant communities the role of plant species

Several studies have presented experimental evidence that diversity reduces invasibility in grassland communities. The interpretation of these results has been disputed recently and it was proposed that sampling effects were responsible for the observed decrease of invasibility with diversity. The experiments performed to date were not designed to adequately separate sampling from diversity effects. Using the establishment of native plant species in experimental plant communities as a model of invasibility, we show that the number of invaders decreased with increasing diversity. When the presence of particular species is included, their effects are dominant. Centaurea jacea showed a strong effect at low diversity, whereas Leucanthemum vulgare showed a very strong negative impact at each diversity level. The negative effect of the latter might be related to root-feeding nematodes that showed far higher abundance in plots with Leucanthemum. However, diversity remained a significant factor in determining the number of invading species and the numbers of an abundant invader.
The role of the rhesus macaque (macaca mulatta) apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) in lentiviral replication and persistence

The simian-human immunodeficiency virus (SHIV)/macaque model for human immunodeficiency virus type 1 (HIV-1) has become a useful tool to assess the role of accessory genes like virion infectivity factor (Vif), in lentiviral pathogenesis. In this study, we introduced two amino acid changes in the highly conserved SLQYLA domain (to AAQYLA) of the SIV Vif protein. The resulting virus SHIVVifAAQYLA, was used to infect three macaques, which were followed for over six months. Plasma viral loads and circulating CD4 T cell levels were assessed during the course of infection. The three macaques inoculated with SHIVVifAAQYLA did not develop significant CD4 T cell loss over the course of their infection, had plasma viral loads that were over 100-fold lower than macaques inoculated with parental SHIVKU-1bMC33, and developed no histological lesions in lymphoid tissues. DNA and RT-PCR analysis revealed that only a select number of tissues were infected with this virus. Sequence analysis indicates that the site-directed changes were stable during the first three weeks after inoculation but thereafter the S147A amino acid substitution changed to a threonine in two of the three macaques. However, the L148A substitution remained stable in the vif amplified from the PBMC of all three macaques. Sequence analysis of vif, vpu, env, and nef genes revealed G-to-A substitutions in the genes amplified from macaques inoculated with SHIVVifAAQYLA, which were higher than in a macaque inoculated with parental SHIVKU-1bMC33. We found that the majority (>85%) of the G-to-A substitutions were in the context of 5’-TC (minus
Productivity overshadows temperature in determining soil and ecosystem respiration across European forests

This paper presents CO2 flux data from 18 forest ecosystems, studied in the European Union funded EUROFLUX project. Overall, mean annual gross primary productivity (GPP, the total amount of carbon (C) fixed during photosynthesis) of these forests was 1380 ± 330 gC m−2 y−1 (mean ±SD). On average, 80% of GPP was respired by autotrophs and heterotrophs and released back into the atmosphere (total ecosystem respiration, TER = 1100 ± 260 gC m−2 y−1). Mean annual soil respiration (SR) was 760 ± 340 gC m−2 y−1 (55% of GPP and 69% of TER).
Effects of surface topography and rain intensity on splash dispersal of Colletotrichum acutatum

Effects of ground cover, plant canopy density, and rain intensity on the splash dispersal of Colletotrichum acutatum were studied using a rain simulator. In one experiment, three ground covers (soil, straw, and plastic) and two rain intensities (15 and 30 mm/hr) were evaluated by collecting splash droplets with conidia in sheltered gravity samplers consisting of petri plates with a selective medium for C. acutatum. Ground covers were characterized by random roughness, the standard deviation of surface elevation. Infected fruits with sporulating lesions were clustered on the ground to serve as the inoculum source (.)
EVIDENCE ON THE PATHWAYS OF PHOSPHORUS TRANSFER BETWEEN VESICULAR - ARBUSCULAR MYCORRHIZAL PLANTS.

Mycorrhizal hyphae can link one root to another, and it is possible that phosphorus passes from plant to plant by these links. We present evidence on whether this 'direct transfer pathway' is the major route between mycorrhizal plants, or whether most phosphorus passes from the roots of one plant to the soil before being taken up by the other plant's roots or its associated mycorrhizal hyphae (the 'soil pool pathway'). The time-course of loss of 32 P from Lolium perenne L. roots to solution was measured after 32 P had been fed to leaves. Another experiment indicated that the amount of 32 P lost to soil was not influenced by mycorrhizal infection. 32 P was applied to soil in which Plantago lanceolata L. , mycorrhizal or non-mycorrhizal, was growing and the time-course of uptake determined. Using these results, two alternative models, the 'direct transfer model' and the 'soil pool model', were used to predict the time-course and amount of 32 P transfer from L. perenne to P. lanceolata. The predictions were then compared with measured transfers between these two species presented here and in a previous paper. The soil pool model's predictions of both amount and time-course of transfer gave the better fit to observation. The evidence thus suggests that direct hyphal links between roots are not important in phosphorus transfer between these plants.
Pseudo‐nitzschia multistriata (Bacillariophyceae) in New Zealand

Abstract Pseudo‐nitzschia multistriata (Takano) Takano has been observed in seawater samples from the North Island and from the northern waters of the South Island, New Zealand, with blooms of >1.0 × 106 cells litre‐1 being recorded in December 1997 (austral summer), and minor blooms occurring in both summer and winter 1998 and 1999. The species is notable for its sigmoid form, and for its cross‐reactivity with oligonucleotide probes targeted at P. australis Frenguelli ribosomal RNA. The species is non‐toxic, and for biotoxin monitoring purposes needs to be discriminated from the highly toxic P. australis. It falls in the “delicatissima” complex of Pseudo‐nitzschia H. Peragallo species, and electron microscopy shows a close resemblance to P. delicatissima (Cleve) Heidin, except for the lack of a central larger interspace.
Ribosomal frameshifting directed by a potyvirid sequence motif in diverse translation systems

The family, Potyviridae, contains a third of all known plant viruses within eight genera. The genome is translated as one large polyprotein from which ten mature proteins are proteolytically cleaved. Recently, discovery of a protein translated from an overlapping reading frame (pipo) proved essential in systemic plant infection. It is hypothesized to translate via a ribosomal frameshift, change in reading frame during the elongation phase of translation. The cryptic programmed ribosomal frameshift signal had been undetected until now because it lacks the canonical characteristics: slippery sequence, spacer sequence, and RNA secondary structure, in that order. Only one of the three components, the slippery sequence, is present as a conserved eight base G1-2A6-7 motif at the 5’ end of pipo. Using Turnip mosaic virus, sequence surrounding the conserved putative frameshift signal was tested for efficiency of shifting in a dual luciferase cassette where the expression of the downstream firefly luciferase requires a -1/+2 change in frame. The conserved G_GAA_AAA_A sequence is inherently slippery with similar efficiency as other stretches of a single base, i.e. AAA_AAA_A. An added benefit is present when G2A6 is surrounded by viral sequence. This suggests a positively acting cis element like R secondary structure, but deletion analysis could not detect any specific elements. Also, addition of RNA secondary structure did not increase frameshift efficiency; rather it had minimal impact on the relative rate to the levels of G2A6 by itself. Sequence analysis will assist in identifying the directionality of the frameshift. This is a new signal for programmed -1 ribosomal frameshifting, or it could be the first +2 frameshift signal to be reported
Potential and realities of enhancing rapeseed- and grain legume-based protein production in a northern climate

SUMMARY Crop-based protein self-sufficiency in Finland is low. Cereals dominate the field cropping systems in areas that are also favourable for legumes and rapeseed. The present paper estimated the realistic potential for expanding protein crop production taking account of climatic conditions and constraints, crop rotation requirements, field sizes, soil types and likelihood for compacted soils in different regions. The potential for current expansion was estimated by considering climate change scenarios for 2025 and 2055. By using actual regional mean yields for the 2000s, without expecting any yield increase during the expansion period (due to higher risks of pests and diseases), potential production volumes were estimated. Since rapeseed, unlike grain legumes, is a not a true minor crop, its expansion potential is currently limited. Thus, most potential is from the introduction of legumes into cropping systems. The current 100000 ha of protein crops could be doubled, and areas under cultivation could reach 350000 and 390000 ha as a result of climate warming by 2025 and 2055, respectively. Such increases result mainly from the longer growing seasons projected for the northern cropping regions of Finland. Self-sufficiency in rapeseed could soon increase from 0·25 to 0·32, and then to 0·50 and 0·60 by 2025 and 2055, respectively. If legume production expands according to its potential, it could replace 0·50–0·60 of currently imported soybean meal, and by 2025 it could replace it completely. Replacement of soybean meal is suitable for ruminants, but it presents some problems for pig production, and is particularly challenging for poultry.
Construction and Analysis of a Large Caribbean Food Web

We document the construction of a relatively large food web (44 species) from the island of St. Martin in the northern Lesser Antilles, and compare it with patterns observed in other, generally smaller food webs. In constructing this web, we integrate data from a variety of studies, many of which focussed on Anolis lizards and their vertebrate predators. In addition to determining the links between predators and prey, we estimate the frequencies of predation (the link strengths), and find an approximately bell—shaped distribution with a majority of links of intermediate frequencies. Some of the properties of this web contrast strongly with those of webs in the ECOWeB compilation. In particular, our analysis shows this web to possess an unusual richness of intermediate species (relative to top predators or basal species) and of links between those intermediate species. The number and lengths of chains are also unusually high, as is the degree of omnivory. Nor does this web match the predictions of the cascade model, which predicts even higher proportions of intermediate species and links between them, and even more numerous chains. It appears that these and other differences are not due simply to the large number of species involved here, but it is not yet clear whether they should be ascribed to the completeness with which some of the diets are known, to differences between the ways this and other webs were constructed, or to unique ecological conditions on the island of St. Martin.
Isolation and Characterization of Methanolobus bombayensis sp. nov., a Methylotrophic Methanogen That Requires High Concentrations of Divalent Cations

Methanolobus bombayensis B-1T (= OCM 438T) (T = type strain) was isolated from Arabian Sea sediments obtained near Bombay, India. This strain grew on methylamines, methanol, and dimethyl sulfide, but it did not catabolize H2-CO2, acetate, or formate. The cells were nonmotile, irregular coccoids (diameter, 1.0 to 1.5 μm) and occurred singly. Electron micrographs revealed that a cell membrane and a protein cell wall were present. The cells grew fastest at mesophilic temperatures, at a neutral pH, and at salinity levels near the salinity level of the ocean, and they required about 30 mM divalent cations (Mg2+ and Ca2+). The cells grew in mineral medium, but growth was greatly stimulated by yeast extract and peptones. The guanine-plus-cytosine content of the DNA was 39.2 ± 0.1 mol%. A comparison of 16S rRNA sequences showed that strain B-1T was phylogenetically related to Methanolobus vulcani, but the sequences of these organisms differed by 2%.
A new species of vent associated Munidopsis (Crustacea: Decapoda: Anomura: Galatheidae) from the Western Pacific, with notes on its genetic identification

Munidopsis myojinensis n. sp. , herein described and illustrated from Myojin Knoll and Northwest Eifuku Seamount in the Western Pacific, is the tenth species of Munidopsis known to be associated with active hydrothermal vents. It resembles M. starmer Baba & de Saint Laurent, 1992 in general ornamentation and spination of the body but differs in the erectness of the eyespine and form of the telson plates. Information on genetic identification using mitochondrial sequences (COI) is provided. Distributions of the vent associated Munidopsis in the Western Pacific and the habitat of the new species are briefly described.
Effect of short day photoperiod on DNA methylation and expression of a gene in rice KDML105

Methylation-sensitive amplified polymorphism (MSAP) technique was adapted to screen a photoperiodresponsive gene of rice KDML105. Six out of thirty-two primer combinations gave twelve EcoRI/HpaIIgenerated MSAP markers from the genomic DNA of KDML105 after exposure to short-day (SD) photoperiod. These MSAP fragments were cloned and used as probes to hybridize to MSAP fingerprints. Positive fragments generating the signals correlated to the MSAP fingerprints were sequenced and aligned to the database. Ten out of twelve MSAP markers showed 93-100% homology to database sequences and the best homology fragment (F1) was chosen for complete gene cloning, sequencing, and alignment. This candidate gene fragment showed 98% homology to the sequences of rice genomic DNA gi|23237916 and rice cDNA gi|32986083. It also has an open reading frame (ORF) of 402 bp and deduced a polypeptide of 134 amino acid residues, while those of gi|23237916 and gi|32986083 have a deduced polypeptide of 137 amino acid residues resulting in the overall homology of 97%. In addition, RT-PCR products and the Southern blot hybridization of the genomic DNA of KDML105 digested with HpaII or MspI indicated that the expression of this candidate gene depends on DNA demethylation, which is induced by 10 days of SD photoperiod. It is speculated that this gene might belong to another class of regulatory gene for the flowering time or heading-time loci in rice or it is a downstream product of flower initiation