Miracle-dz/UniFAR-FTUs huggingface dataset:
Sharing enemies: evidence of forest contribution to natural enemy communities in crops, at different spatial scales

The increase in cultivated lands has led to ecosystem and biodiversity loss. Arthropod natural enemies, involved in the ecosystem service of biological control, benefit from non‐crop habitat and may be affected by its proximity and amount in the landscape. We have evaluated natural enemy richness and composition in relation to forest cover in the landscape and distance from the forest, for a Chaco Serrano forest‐soybean crop system. Forest contribution to natural enemies on soybean was also investigated, by assessing similarities between forest and crop assemblages, and examining body size of shared enemies in relation to distance from the forest. In nine landscape circles, yellow pan traps were placed in forest and soybean crops (5, 25, 50 and 100 m from forest edge), which collected 8041 specimens representing 290 species. Species richness of natural enemies was positively related to forest cover and declined from the forest to the furthermost soybean locations, with both forest cover and its proximity affecting community composition. Also, similarity of forest and crop assemblages increased with forest cover and proximity. Finally, forest‐crop shared assemblages showed larger average body size at greater distances from the forest, indicating dispersal limitations on forest contribution to the crop. Our results suggest that forest species are important components of natural enemy communities on soybean, and that both the amount of natural habitat and its proximity may influence agroecosystems. We emphasise the importance of non‐crop habitat to help maintain natural enemy communities and ensure the ecosystem service of pest control.
LC-MS/MS Quantification of Zn-α2 Glycoprotein: A Potential Serum Biomarker for Prostate Cancer

Background: Zn-2 glycoprotein (ZAG) is a relatively abundant glycoprotein that has potential as a biomarker for prostate cancer. We present a high-flow liquid chromatography–tandem mass spectrometry (LC-MS/MS) method for measuring serum ZAG concentrations by proteolytic cleavage of the protein and quantification of a unique peptide. Methods: We selected the ZAG tryptic peptide 147 EIPAWVPEDPAAQITK 162 as the intact protein for quantification and used a stable isotope-labeled synthetic peptide with this sequence as an internal standard. Standards using recombinant ZAG in bovine serum albumin, 50 g/L, and a pilot series of patient sera were denatured, reduced, alkylated, and digested with trypsin. The concentration of ZAG was calculated from a dose–response curve of the ratio of the relative abundance of the ZAG tryptic peptide to internal standard. Results: The limit of detection for ZAG in serum was 0.08 mg/L, and the limit of quantification was 0.32 mg/L with a linear dynamic range of 0.32 to 10.2 mg/L. Replicate digests from pooled sera run during a period of 3 consecutive days showed intraassay imprecision (CV) of 5.0% to 6.3% and interassay imprecision of 4.4% to 5.9%. Mean (SD) ZAG was higher in 25 men with prostate cancer [7.59 (2.45) mg/L] than in 20 men with nonmalignant prostate disease [6.21 (1.65) mg/L, P 0.037] and 6 healthy men [3.65 (0.71) mg/L, P 0.0007]. Conclusions: This LC-MS/MS assay is reproducible and can be used to evaluate the clinical utility of ZAG as a cancer biomarker. © 2007 American Association for Clinical Chemistry
Comparing Life Histories Using Phylogenies

The comparative method as recently developed can be used to identify statistically independent instances of life-history evolution. When life-history traits show evidence for correlated evolutionary change with each other or with ecological differences, it is often possible to single out the trade-offs and selective forces responsible for the evolution of life-history diversity. Suites of life-history characters often evolve in concert, and recent optimality models incorporating few variables show promise for interpreting that evolution in terms of few selective forces. Because hosts provide well-defined environments for their parasites, when host-parasite phylogenies are congruent it is possible to test ideas about the evolution of particular life-history and size-related traits.
Development of Chrysanthemum Cuttings: The Influence of Age and Position of the Axillary Buds

Abstract In three experiments (twoin-vivo, onein-vitro), an attempt was made to separate the possible effects of age and position of axillary buds of chrysanthemum on bud outgrowth and the subsequent quality of cuttings. In thein-vivoexperiments, bud age and bud position were not significant factors in bud outgrowth and subsequent quality of cuttings. Nevertheless, most outgrowth parameters showed slightly higher values for the lower positioned buds and the time needed to produce a cutting tended to decrease with the age of the axillary bud. In thein-vitroexperiment, the relationship between age and the various parameters showed an optimum.
Overestimation of respiration rates in commercially available clamp-on leaf chambers. Complications with measurement of net photosynthesis

The possible interference when measuring gas exchange with respiratory CO2 produced under the gasket of commercially available clamp-on leaf chambers was investigated. Two of these chambers were compared with a leaf chamber that accommodated an entire leaf without clamping it under a gasket. An overestimation of dark respiration rate (RD) by 55% was found with Plantago major leaves, a species with homobaric leaves that have high resistance for lateral gaseous transport. The percentage was similar in the heterobaric Ficus benjamina, but was 32% in the highly porous homobaric Nicotiana tabacum. Net photosynthetic rate at low photon flux density was underestimated by 35% in the clamp-on chamber. However, the gasket effect was not detectable at light saturation because the error was small in comparison with the high photosynthetic rates. Estimation of respiration in the light (RL) in Nicotiana as derived from CO2 exchange at low CO2 concentrations was complicated by three factors. The inward diffusion of respiratory CO2 from under the gasket was added to a diffusion of CO2 from outside through the gasket material and through the leaf, which produced an even larger error in RL in comparison with RD at ambient CO2. These errors are significant for estimations of carbon gain at whole plant and canopy level and also at the leaf level when photosynthetic rates are low. Possible improvements in gasket design and corrections of CO2 exchange measurements for the gasket effect are discussed.
Bird diversity and land use on the slopes of Mt Kilimanjaro and the adjacent plains, Tanzania

ABSTRACT This study of bird distribution in the main land-use categories of the slopes of Mt Kilimanjaro, Tanzania, aims at understanding potential impacts of the land-use changes on birds. A land-use map of the study area was derived from a Landsat image, and land-use change information came from an earlier study by the author. Bird data were collected by observations along timed, standardized walks. Shannon (1948) indices of bird diversity for highlands, bushland and lowlands were 3.29, 2.99, and 2.62. The highland category was divided into two subcategories, homegarden and highland garden, as bird populations of the two were distinct. Highland garden had a higher diversity (3.15) than homegarden (3.07). The lower species diversity and number of individuals in homegardens was probably due to lower niche diversity and more human disturbance. Lowland fields had low diversity indices as they are dominated by large flocks of birds. The equitability indices for highlands, bushlands and lowlands were 0.82, 0.80 and 0.65, respectively. Each land-use type had many species that were not seen in the others. As bushland is disappearing, the species currently threatened are the 15 bushland species that are not found in other land-use types. Growing population pressure leading to deagrarianization of the homegarden area is likely to affect homegarden bird populations, though it is not clear whether the very high human population density will prevent it from supporting a highland garden type of a bird population.
Variation of Coagulase-Negative Staphylococci in the Skin Flora of Healthy Individuals during One Year

In order to investigate the variation and turnover time of coagulase-negative staphylococci (CNS) in the skin flora and whether CNS strains were transmitted over the body, we studied CNS in the skin flora of seven healthy persons during a period of one year. From 134 samples, collected approximately monthly, 547 CNS were isolated. All isolates were typed by PhP-CS, a biochemical fingerprinting method and, if further discrimination was required, also by pulsed-field gel electrophoresis of DNA. We found 109 different strains out of which 63% were transient, i.e. isolated only once, but the majority (77%) of isolated CNS belonged to resident strains, isolated at least twice. The CNS flora of the toes showed a high variation compared to the nares and axillas. Eighty percent of the resident strains colonized the skin for more than three months and two strains were isolated during the whole study period. Different strains were normally found on different persons, although several persons belonged to the same households. Transmission over the body of the same strain is very uncommon. It is concluded that although many different strains can be found on a body location, most of them are only found occasionally. However, certain strains may colonize the skin and become permanent members of the normal flora. Keywords: colonization, coagulase-negative staphylococci, skin flora.
Genetic structure of rheophytic and nonrheophytic populations of Farfugium japonicum on Yaeyama Islands, Japan

Farfugium japonicum (L.f.) Kitam. , a facultative rheophyte occupying both dryland and riparian habitats within the species range, exhibits various shapes of leaves ranging from stenophyllous to round. The present study assesses variability in leaf morphology (five leaf characters) and genetics (305 AFLP markers) for populations from dryland and riparian habitats on Yaeyama Islands, Japan. Results from the two datasets produced somewhat different patterns indicating that selection for habitat type is effective on leaf shape attributes, while lack of differentiation was observed for neutral markers caused by extensive gene flow. Leaf-shape attributes were clustered into three groups: shade (round), sun (round), and narrow (stenophyllous) leaves. Narrow leaves were only found in riparian populations, indicating that flood intensity acts as a selective agent for this attribute. Although high within-population variation was demonstrated by AMOVA, the populations were distinct enough to be classified in separat.
Does ecological filtering across a productivity gradient explain variation in species pool‐richness relationships?

Concerns about the impact of species diversity loss has heightened the importance of determining what limits local diversity and the relative roles of the available species pool and local interactions. Recent theory suggests that local diversity may exhibit linear or asymptotic responses to regional variation in species pools depending resource supply rates. We tested this idea by augmenting species pools in three sites along a natural productivity gradient (a surrogate for resource supply) in a mid-successional old-field. Augmentation of the species pool, enhanced local diversity more at medium than low productivity sites in this field and seed addition had no effect at high productivity, suggesting that diversity was saturated in high resource areas of this field. These results suggest that resource supply rates may mediate species pool-richness relationships. Species additions into cleared plots demonstrated that the observed differences in species recruitment along this gradient were largely driven by abiotic filtering at low and competitive filtering at high productivity. Furthermore, we observed that augmentation of the species pool shifted the productivity -diversity relationship
Gametophyte life-history dominance of Chondrus crispus (Gigartinaceae, Rhodophyta) along the Atlantic coast of Nova Scotia, Canada

adeceased December 2010 Similar to other species of Gigartinaceae Chondrus crispus has an alternation of perennial, isomorphic gametophytic and sporophytic generations. As these two generations co-exist independently within populations and obtain their resources in a similar manner, intraspecific competition is expected. In populations within the southern Gulf of St. Law rence, fronds of both generations of C. crispus occur in similar numbers. This equivalency can be related to substratum instability, where the population is dynamic with a high turn-over rate of genets. These observations support a stochastic hypothesis to account for distribution of gametophytes and sporophytes in this area. Along the Atlantic coast of Nova Scotia, where the substratum is stable, gametophytes are overwhelmingly predominant. Gametophytic predominance is greatest in the lower littoral zone where C. crispus is abundant and space is limited. Under the fucoid canopy where “free-space” exists, the gametophyte to sporophyte ratio is lower. Gametophytic and sporophytic fronds are distributed equally among different size-classes and size-distribution is not considered a competitive factor. Previous studies have shown that sporophytic fronds of C. crispus are more susceptible to infections by endophytic algae and other pathogens, and are more heavily grazed by herbivores than are gametophytic fronds. Thus, mechanistic factors are strongly implied in the selection of gametophytes in the Atlantic population.
Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure

Abstract We inferred phylogenetic relationships using Bayesian and maximum likelihood approaches for two genera of lichenized fungi, Hypogymnia and Cavernularia (Parmeliaceae). Based on the combined ITS and GPD1 dataset from 23 species (49 specimens) of Hypogymnia and two species (8 specimens) of Cavernularia, we conclude that Hypogymnia is paraphyletic, and that it should include Cavernularia to retain its monophyly. Hypogymnia hultenii ( = Cavernularia hultenii) and H. lophyrea ( = C. lophyrea) are accepted here. Five species of Hypogymnia represented by more than a single individual were found to be monophyletic and significantly supported. The phylogeny reflects a statistically significant biogeographic pattern where continental-scale endemic taxa tend to occur within the same phylogenetic group. Sorediate taxa, which have worldwide or broader geographical ranges than affiliated species lacking soredia, are spread across the phylogenetic tree. Hypogymnia contains three species pairs: H. krogiae and the sorediate counterpart H. incurvoides, H. minilobata and the sorediate H. mollis, and H. lophyrea and the sorediate H. hultenii. In the case of H. minilobata, both members of the pair are restricted to a small area in southern California. In the other two cases, the fertile counterpart occurs only in North America, while the sorediate species occurs in both North America and Fennoscandia. This suggests but not proves an origin of each species pair in North America, with migration of the sorediate member to Fennoscandia following the prevailing wind direction.
A systematic review uncovers a wide-gap between COVID-19 in humans and animal models

Background: Animal models of COVID-19 have been rapidly reported after the start of the pandemic. We aimed to assess whether the newly created models reproduce the full spectrum of humans COVID-19. Methods: We searched the Medline, as well as BioRxiv and MedRxiv preprint servers for original research published in English from January 1, to May 20, 2020. We used the search terms COVID-19 OR SARS-CoV-2 AND, animal models, hamsters, nonhuman primates, macaques, rodent, mice, rats, ferrets, rabbits, cats, and dogs. Inclusion criteria were the establishment of animal models of COVID-19 as an endpoint. Other inclusion criteria were assessment of prophylaxis, therapies, or vaccines, using animal models of COVID-19. Findings: 13 peer-reviewed studies and 14 preprints met inclusion criteria. The animals used were nonhuman primates (n=13), mice (n=7), ferrets (n =4), hamsters (n= 4), and cats (n =1). All animals supported high viral replication in the upper and lower respiratory tract associated with mild clinical manifestations, lung pathology and full recovery. Older animals displayed relatively more severe illness than the younger ones. No animal models developed hypoxemic respiratory failure, multiple organ dysfunction, culminating in death. All species elicited a specific IgG antibodies response to the spike proteins, which were protective against a second exposure. Transient systemic inflammation was observed occasionally in Rhesus macaques, hamsters, and mice. Notably, none of the animals unveiled cytokine storm or coagulopathy. Conclusions: Most of the animal models of COVID-19 recapitulated mild pattern of human COVID-19 with full recovery phenotype. No severe illness associated with mortality was observed, suggesting a wide gap between COVID-19 in humans and animal models.
Applying Multiple Level Cell to Non-volatile FPGAs

Static random access memory– (SRAM) based field programmable gate arrays (FPGAs) are currently facing challenges of limited capacity and high leakage power. To solve this problem, non-volatile memory (NVM) is proposed as the alternative to build non-volatile FPGAs (NVFPGAs). Even though the feasibility of NVFPGA has been confirmed, the utilization of multiple level cells (MLCs) has not been fully exploited yet. In this article, we study architecture of MLC-based NVFPGAs, and propose five cluster structures. To give detailed comparisons and extensive discussions, we conduct experiments for area, performance and leakage power evaluation. Based on explorations of the characteristics of MLC-based NVFPGAs, we further present MLC-aware timing-driven packing method to improve delay. In critical paths, our proposed method reduces the overhead of the additional delay in slow MLC cells. Experiments show that, compared to SRAM-based FPGAs, the proposed architecture with the proposed CAD flow can reduce the area, critical path delay and leakage power by 31%, 10%, and 95%, respectively.
Population Trends in Royal Catchfly (Silene regia) at Wilson's Creek National Battlefield, Missouri

Abstract. Royal catchfly (Silene regia, Caryophyllaceae) is a rare, tap-rooted, perennial forb known to occupy Midwestern prairies, glades, and savannas, which are increasingly fragmented. Though not federally listed, it is recognized as rare, threatened, or endangered in six states. We resurveyed 15 populations identified in 1980s–1990s monitoring at Wilson's Creek National Battlefield, Republic, MO. Abundance at each site was collected in 6 y (1988–1989, 1998–2000, 2019); measures of plant height and stems browsed were collected in 4 y (1998–2000, 2019). Fire history and precipitation were also explored. Mean royal catchfly abundance per population declined significantly over the study period, and only five of 15 populations supported extant populations in 2019. Year, site location, and the interaction between the two were highly significant factors in explaining variation of height measures and proportion of stems browsed. Plant height was significantly higher in 2019 than any other year, corresponding with overgrowth of competing vegetation and a wet spring. Prescribed fires became less frequent over the study period, and the mean fire return interval was higher than the historical regime of the region (9.7 y vs. 4–8 y). The decline of royal catchfly at Wilson's Creek National Battlefield and similar sites points to the need for fire management and restoration of prairie and savanna ecosystems for the persistence of this rare species.
Public's perceived importance of non-pharmacological interventions for COVID-19 control in Greece: preliminary evidence from a cross-sectional study

Background: In the early stages of coronavirus disease 2019 (COVID-19) pandemic, while effective pharmaceutical approaches are pending, COVID-19 management relies primarily on non-pharmaceutical interventions (NPIs), such as social distancing,which requirepublic's engagement and behavioral adjustment. This study aims to evaluate public's perceived importance of the NPIs imposed for COVID-19 control in personal and public health protection in Greece. Methods: This cross-sectional online study, enrolled 657 adult participants from the general Greek population in order to assess their beliefs and evaluate possible factors that influence their perceptions as regards NPI importance in personal and public health protection. Results: Overall, Greeks considered NPIs important for health protection. The participants who were less likely to consider NPIs important were men (OR versus females=1.64, 95% CI:1.15 to 2.36, p=0.007), people younger than 40 years old (OR between ages over 40 versus ages below 40=0.48, 95% CI:0.34 to 0.68, p<0.001), and people who did not chose the Hellenic National Public Health Organization (EODY) to get informed about COVID-19 (OR of EODY versus other sources of information = 0.65, 95% CI:0.46-0.92, p= 0.014). Conclusions: This study profiled Greek people who do and do not consider NPIs important, mainly as of their demographic features. Focused communicational strategies in certain population subgroups are recommended.
Comparative Effectiveness of Knowledge Graphs- and EHR Data-Based Medical Concept Embedding for Phenotyping

ABSTRACT Objective: Concept identification is a major bottleneck in phenotyping. Properly learned medical concept embeddings (MCEs) have semantic meaning of the medical concepts, thus useful for feature engineering in phenotyping tasks. The objective of this study is to compare the effectiveness of MCEs learned by using knowledge graphs and EHR data for facilitating high-throughput phenotyping. Materials and Methods: We investigated four MCEs learned from different data sources and methods. Knowledge-graphs were obtained from the Observational Medical Outcomes Partnership (OMOP) common data model. Medical concept co-occurrence statistics were obtained from Columbia University Irving Medical Center's (CUIMC) OMOP database. Two embedding methods, node2vec and GloVe, were used to learn embeddings for medical concepts. We used phenotypes with their corresponding concepts generated and validated by the Electronic Medical Records and Genomics (eMERGE) network to evaluate the performance of learned MCEs in identifying phenotype-relevant concepts. Results: Precision@k% and Recall@k% in identifying phenotype-relevant concepts based on a single concept and multiple seed concepts were used to evaluate MCEs. Recall@500% and Precision@500% based on a single seed concept of MCE learned using the enriched knowledge graph were 0.64 and 0.13, compared to Recall@500% and Precision@500% of MCE learned using the hierarchical knowledge graph (0.61 and 0.12), 5-year windowed EHR (0.51 and 0.10), and visit-windowed EHR (0.46 and 0.09). Conclusion: Medical concept embedding enables scalable identification of phenotype-relevant medical concepts, thereby facilitating high-throughput phenotyping. Knowledge graphs constructed by hierarchical relationships among medical concepts learn more effective MCEs, highlighting the need of more sophisticated use of big data to leverage MCEs for phenotyping.