Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and monitoring of cabbage aphids (Hemiptera: Aphididae) in dryland canola (Brassicaceae: Brassicales)

Information on how herbivorous arthropods choose host plants is likely to improve the way practitioners locate arthropod infestations and estimate their densities. Based on cabbage aphid choice studies with canola plants in varying growth stages, it was demonstrated that alate aphids colonised fewer canola seedlings than post-seedling growth stages, but there was no colonisation preference amongst post-seedling growth stages. No colonisation preference was evident between canola plants already infested with cabbage aphids compared with those not infested. Also, cabbage aphids colonised 100% of plants when released in single-plant cages with no preference amongst seedling, stem elongation and budding growth stages. The aphids, which were released above the plants, consistently colonised the abaxial sides of canola leaves within the lower portion of the canopy. This preference for the lower leaves could not be explained by leaf tissue analysis, done at stem extension growth stage. These results have implications for early detection of aphids in canola, particularly in advanced growth stages (flowering to early podding), as flowering spikes are often inspected for aphids, rather than the lower canopy leaves, where colonisation may have taken place. Improved knowledge about mechanisms driving host plant selection and aphid colonisation in canola is likely to improve aphid sampling in canola.
Reproductive Output and Clutch Phenology of Female Agassiz's Desert Tortoises (Gopherus agassizii) in the Sonoran Desert Region of Joshua Tree National Park

Abstract: Agassiz's desert tortoise (Gopherus agassizii) reaches the southern edge of its range in the Sonoran Desert of California. The reproductive ecology of this wideranging species is understudied here compared to populations in the adjacent Mojave Desert. Understanding potential geographic variation in reproductive ecology is important for effective management of conservation-reliant species like G. agassizii. We studied the fecundity and clutch phenology of female G. agassizii at two study sites in the Sonoran Desert region of Joshua Tree National Park over five years (1997–1999, 2015–2016) spanning two of the strongest El Niño events on record and an epic drought. Across all years, mean clutch size was 4.3±1.5 eggs, mean clutch frequency was 1.78 clutches/female/year, and mean X-ray egg width was 36.51±1.56 mm, all of which are comparable to other published studies both in the Sonoran and Mojave deserts of California. Our results generally support earlier published findings that G. agassizii utilize a bet-hedging strategy of consistently producing small clutches almost every year, even during times of low annual primary productivity. A regionally warmer climate in the Sonoran Desert of California appears to have an effect on the timing of egg production, as the earliest dates of egg visibility in our study (April 6) were approximately two weeks earlier than the earliest dates reported for G. agassizii in the Mojave Desert. Shelled eggs were no longer visible in tortoises after mid-June in all years but the El Niño year 1998, when eggs were visible until mid-July.
Prestimulus Activity in the Cingulo-Opercular Network Predicts Memory for Naturalistic Episodic Experience

Human memory is strongly influenced by brain states occurring before an event, yet we know little about the underlying mechanisms. We found that activity in the cingulo-opercular network (including bilateral anterior insula and anterior prefrontal cortex) seconds before an event begins can predict whether this event will subsequently be remembered. We then tested how activity in the cingulo-opercular network shapes memory performance. Our findings indicate that prestimulus cingulo-opercular activity affects memory performance by opposingly modulating subsequent activity in two sets of regions previously linked to encoding and retrieval of episodic information. Specifically, higher prestimulus cingulo-opercular activity was associated with a subsequent increase in activity in temporal regions previously linked to encoding and with a subsequent reduction in activity within a set of regions thought to play a role in retrieval and self-referential processing. Together, these findings suggest that prestimulus attentional states modulate memory for real-life events by enhancing encoding and by dampening interference from competing memory substrates.
trackdem: Automated particle tracking to obtain population counts and size distributions from videos in r

The possibilities for image analysis in scientific research are substantial: the costs of digital cameras and data storage are sharply decreasing, and automated image analyses greatly increase the scale, reproducibility and robustness of biological studies. However, automated image analysis in ecological and evolutionary studies is still in its infancy. There is a clear need for easy to use and accessible tools. Here, we provide a general purpose method to obtain estimates of population densities, individual body sizes and behavioural metrics from video material of moving organisms. The methods are supplied as a new r‐package trackdem, which provides a flexible, easy to install and use, generally applicable and accurate way to analyse ecological video data. The package can detect and track moving particles, count individuals and estimate individual sizes using background detection, particle identification and particle tracking algorithms. Machine learning is implemented to reduce the influence of noise in lower quality videos or to distinguish a single species in multi‐species systems. We show that trackdem provides accurate population counts and body size distributions. Using a series of simulations, we show that our estimates are robust against high levels of noise in videos. When applied to live populations of Daphnia magna, our methods obtained accurate and unbiased estimates of population counts, individual sizes and size distributions, as verified by manual counting and measuring. The package trackdem is also directly usable for movement analysis, for instance in behavioural ecology, as illustrated by the tracking of insects, fish, cars and humans. Within 24 hr, we obtained 192 accurate population counts and body sizes of 22,154 individuals. Such results underscore that automated analysis can improve robustness and reproducibility, and greatly increase the scope of studies in ecology and evolution.
Real‐time decoding of dopamine concentration changes in the caudate–putamen during tonic and phasic firing

The fundamental process that underlies volume transmission in the brain is the extracellular diffusion of neurotransmitters from release sites to distal target cells. Dopaminergic neurons display a range of activity states, from low‐frequency tonic firing to bursts of high‐frequency action potentials (phasic firing). However, it is not clear how this activity affects volume transmission on a subsecond time scale. To evaluate this, we developed a finite‐difference model that predicts the lifetime and diffusion of dopamine in brain tissue. We first used this model to decode in vivo amperometric measurements of electrically evoked dopamine, and obtained rate constants for release and uptake as well as the extent of diffusion. Accurate predictions were made under a variety of conditions including different regions, different stimulation parameters and with uptake inhibited. Second, we used the decoded rate constants to predict how heterogeneity of dopamine release and uptake sites would affect dopamine concentration fluctuations during different activity states in the absence of an electrode. These simulations show that synchronous phasic firing can produce spatially and temporally heterogeneous concentration profiles whereas asynchronous tonic firing elicits uniform, steady‐state dopamine concentrations.
Population genetics and systematics of a species-rich clade of Neotropical reef fishes, the tubeblenny genus Acanthemblemaria

v CHAPTER 1 GENERAL INTRODUCTION.1 2 NUCLEAR AND MITOCHONDRIAL SEQUENCE DATA REVEAL AND CONCEAL DIFFERENT DEMOGRAPHIC HISTORIES AND POPULATION GENETIC PROCESSES IN CARIBBEAN REEF FISHES.3 3 THE PERFORMANCE OF BAYESIAN PHYLOGENETIC INFERENCE UNDER EXTREME SUBSTITUTION RATE VARIATION: EFFECTS ON CONCATENATED AND SPECIES TREE ANALYSES.36 4 A THORNY SITUATION: ACCOUNTING FOR CONFLICT BETWEEN MOLECULES AND MORPHOLOGY IN THE NEOTROPICAL REEF FISH CLADE ACANTHEMBLEMARIA (CHAENOPSIDAE) . 80 5 CONCLUSIONS.108 REFERENCES.112 APPENDIX 1: SUPPLEMENTARY DATA.131 APPENDIX 2: PERMISSION FROM EVOLUTION.143 VITA.149
Performance of the UKPDS Risk Engine and the Framingham risk equations in estimating cardiovascular disease in the EPIC-Norfolk cohort

This is an uncopyedited electronic version of an article accepted for publication in Diabetes Care. The American Diabetes Association, publisher of Diabetes Care, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisherauthenticated version will be available in a future issue of Diabetes Care in print and online at http://care.diabetesjournals. org. Diabetes Care Publish Ahead of Print, published online December 29, 2008
Phytosociological characteristics of Quercus cerris L. forests in east Slavonia (Croatia)

The following paper reports on the results of phytosociological research on Slavonian Quercus cerris forests in the woodlands of Zokovica – Đakovo and Cerik – Vucevci near Đakovo. 20 releves were recorded in accordance with the Braun-Blanquet classical method. The releves were set against the already published releves of thermophilous forests of Carpino betuli-Quercetum roboris quercetosum cerris from the area of east Slavonia, and numerical analysis was performed. The studied Quercus cerris forests had developed through anthropogenic degradation of the association Carpino betuli-Quercetum roboris quercetosum cerris or Carpino betuli-Quercetum roboris typicum. Both of these stages of degradation have not been phytosociologically studied enough and have not received a defined syntaxonomic status. Conditions of the habitat have changed so much in a degraded ass. Carpino betuli-Quercetum roboris quercetosum cerris, that urgent efforts ought to be put into the attempt to reintroduce Quercus robur into the stands. These stands are described as an association of Aceri campestri-Quercetum cerris ass. nova. It would require far less work to reintroduce the Quercus robur into degraded forests of association Carpino betuli-Quercetum roboris typicum, where habitat conditions have not been changed to a greater extent.
Development and characterization of EST-SSR markers for Taxus mairei (Taxaceae) and their transferability across species

Abstract Taxus is an important genus which is well-known for Taxol. Its genetic analyses were lagged behind those of other conifers due to lack of suitable molecular markers. In this paper, we explored polymorphic loci for Taxus mairei and tested their transferability across species based on 150 EST-SSR loci already developed for Taxus cuspidata previously. The results showed that 103 loci were polymorphic, the number of alleles per locus ranged from 2 to 11 over 16 individuals. The observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0 to 1 and 0.0625 to 0.891, respectively. The PIC values ranged from 0.11 to 0.754 with an average of 0.453. The average cross-species transferability was 96.07% among 5 species. Most of these loci can be used as universal markers in Taxus genus. The PCA results showed these markers have strong power to identify different species. These markers will be useful for further studies on genetic analysis and conversation of Taxus mairei.
Statistical design and analysis for plant cover studies with multiple sources of observation errors

Effective wildlife habitat management and conservation requires understanding the factors influencing distribution and abundance of plant species. Field studies, however, have documented observation errors in visually estimated plant cover including measurements which differ from the true value (measurement error) and not observing a species that is present within a plot (detection error). Unlike the rapid expansion of occupancy and N‐mixture models for analysing wildlife surveys, development of statistical models accounting for observation error in plants has not progressed quickly. Our work informs development of a monitoring protocol for managed wetlands within the National Wildlife Refuge System. Zero‐augmented beta (ZAB) regression is the most suitable method for analysing areal plant cover recorded as a continuous proportion but assumes no observation errors. We present a model extension that explicitly includes the observation process thereby accounting for both measurement and detection errors. Using simulations, we compare our approach to a ZAB regression that ignores observation errors (naïve model) and an “ad hoc” approach using a composite of multiple observations per plot within the naïve model. We explore how sample size and within‐season revisit design affect the ability to detect a change in mean plant cover between 2 years using our model. Explicitly modelling the observation process within our framework produced unbiased estimates and nominal coverage of model parameters. The naïve and “ad hoc” approaches resulted in underestimation of occurrence and overestimation of mean cover. The degree of bias was primarily driven by imperfect detection and its relationship with cover within a plot. Conversely, measurement error had minimal impacts on inferences. We found >30 plots with at least three within‐season revisits achieved reasonable posterior probabilities for assessing change in mean plant cover. For rapid adoption and application, code for Bayesian estimation of our single‐species ZAB with errors model is included. Practitioners utilizing our R‐based simulation code can explore trade‐offs among different survey efforts and parameter values, as we did, but tuned to their own investigation. Less abundant plant species of high ecological interest may warrant the additional cost of gathering multiple independent observations in order to guard against erroneous conclusions.
Previous pregnancy loss and gestational cardiovascular health: A prospective cohort of nulliparous women

Objectives To estimate the association of previous pregnancy loss with subsequent cardiovascular health during gestation and to examine the role of high-sensitivity C reactive protein (hs-CRP) in the association. Methods A total of 2,778 nulliparous pregnant women were recruited between March 2015 and November 2020 in Hefei city, China. Their cardiovascular health (CVH) including prepregnancy body mass index (BMI), blood pressure, total cholesterol, fasting plasma glucose, and smoke status were recorded at 24–28 weeks’ gestation, as well as their reproductive history. Multivariate linear and logistic regression were performed to examine the association of pregnancy loss with cardiovascular health. And the role of hs-CRP between pregnancy loss and CVH was assessed by the mediation analysis. Results Compared with women who have no pregnancy loss, women with a history of spontaneous or induced abortions had higher BMI (β, 0.72, 95% CI, 0.50 to 0.94) and fasting plasma glucose (β, 0.04, 95% CI, 0.01 to 0.07), and had lower total CVH scores after adjusting for confounders (β, −0.09, 95% CI, −0.18 to −0.01). CVH scores were most significantly decreased among women with 3 or more induced abortions (β, −0.26, 95% CI, −0.49, −0.02). The contribution of pregnancy loss to poorer gestational CVH mediated by increased hs-CRP levels was 23.17%. Conclusion Previous pregnancy loss was associated with poorer cardiovascular health during gestation, which may be mediated by their gestational inflammatory status. Exposure to miscarriage alone was not a significant predictor of poorer CVH.
Development of Chutney Powder from Spider Conch, Lambis lambis (Linne, 1758)

The spider conch, Lambis lambis is one of the important fishery resources in the Vellapatti Village, Tuticorin, Southeast Coast of India. These conches land as by catches from crab nets (a modified bottom set gill net). The meat of gastropods is considered as a delicacy, rich in protein and the fat content is very low. Only a small section of the fisher folk consume its flesh, as it is less popular among the coastal fisher folk. For the utilization of this meat, chutney powder (a side dish for Idli or Dhosai in South India) was prepared from the meat. Biochemical, microbiological and sensory analyses were made to assess the shelf life for a period of four months. The meat had a protein content of 5.2%, 0.5% of carbohydrate and lipid content of 1%. The shelf life assessment of the chutney powder for a period of four months was carried out and it was found out that the product was good until the end of the assessment period. Even the TMA and TVB levels were found to be within the limits (10.8 mg per 100g and 18.36 mg per 100g, respectively). The present work reveals that the chutney powder is microbiologically and organoleptically good until the end of the storage period and safe for human consumption.
Modelling indices of abundance and size-based indicators of cod and flounder stocks in the Baltic Sea using newly standardized trawl survey data

Modelling indices of abundance and size-based indicators of cod and flounder stocks in the Baltic Sea using newly standardized trawl survey data Alessandro Orio*, Ann-Britt Florin, Ulf Bergström, Ivo Sics, Tatjana Baranova, and Michele Casini Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Turistgatan 5, Lysekil 45330, Sweden Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Skolgatan 6, € Oregrund 74242, Sweden Department of Fish Resources, Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes Street 3, Riga, LV 1076, Latvia *Corresponding author: tel: þ46 725437988; e-mail: alessandro.orio@slu.se
Stocking of Common Carp ( Cyprinus carpio ) into Some Newly-Estab Reservoirs of North-West Anatolia May Enhance the Spread of Non-Native Fish

Stocking of water bodies with non-native fish species for fisheries enhancement is a common practice worldwide. However, overall limited benefits in terms of revenues for local communities have so far been reported in some countries, whilst accidental introductions of several non-native fish species have occurred. To evaluate the benefits vs. costs associated with common carp Cyprinus carpio stocking practices, a three-year sampling study (2009–2011) was carried out across twelve adjacent artificial reservoirs of the Kocaeli Peninsula (north-west Anatolia, Turkey). Apart from common carp, 18 fish species in total were recorded, of which 12 native and six non-native, the latter comprising more than half of the total catch and dominated by gibel carp Carassius gibelio. Even though the abundance of common carp, natives and non-natives increased over the study period, common carp was always comparatively less abundant relative to most of the other species. Overall, the present findings indicate that stocking of common carp into the studied reservoirs has not fully met with the proposed objectives, likely a result of less-than-optimal age-0 fish release strategies and limited availability of spawning grounds. On the other hand, invasion especially by gibel carp is thought to be under way and this may ultimately impact on the abundance of the native fish fauna.
THE USE OF VIRAL VECTORS IN GENE TRANSFER THERAPY

Gene therapy is strategy based on using genes as pharmaceuticals. Gene therapy is a treatment that involves altering the genes inside body's cells to stop disease. Genes contain DNA- the code controlling body form and function. Genes that do not work properly can cause disease. Gene therapy replaces a faulty gene or adds a new gene in an attempt to cure disease or improve the ability of the body to fight disease. Gene therapy holds promise for treating a wide range of diseases, including cancer, cystic fibrosis, heart disease, diabetes, hemophilia and AIDS. Various types of genetic material are used in gene therapy; double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), plasmid DNA and antisense oligodeoxynucleotides (ASON). The success of gene therapy depends on assuring the entrance of the therapeutic gene to targeted cells without any form of biodegradation. Commonly used vectors in gene therapy are: adenoviruses (400 clinical studies; 23.8%), retroviruses (344 clinical studies; 20.5%), unenveloped/plasmid DNA (304 clinical studies, 17.7%), adeno-associated viruses (75 clinical studies; 4.5%) and others. In this paper, we have reviewed the major gene delivery vectors and recent improvements made in their design meant to overcome the issues that commonly arise with the use of gene therapy vectors.
Identification of quantitative trait loci underlying seed oil content of soybean including main, epistatic and QTL × environment effects in different regions of Northeast China

Abstract. Oil content is a primary trait in soybean and determines the quality of soy food, feed and oil product. Increasing oil content is a major objective of soybean breeding. The aims of the present study were to identify quantitative trait loci (QTLs) and epistatic QTLs associated with oil content in soybean seed by using 129 recombinant inbred lines derived from a cross between cultivar Dongnong 46 (oil content 22.53%) and the semi-wild line L-100 (oil content 17.33%). Phenotypic data were collected from 10 tested environments including Harbin in the years 2012–15, Hulan in 2013–15 and Acheng in 2013–15. A genetic linkage map including 213 simple sequence repeat markers in 18 chromosomes (or linkage groups) was constructed, covering ∼3623.39 cM. Seven QTLs, located on five chromosomes (or linkage groups), were identified to be associated with oil content, explaining 2.24–17.54% of the phenotypic variation in multi-environments. Among these identified QTLs, five (qOIL-2, qOIL-4, qOIL-5, qOIL-6 and qOIL-7) were detected in more than five environments. Seven QTLs had additive and/or additive × environment interaction effects. QTLs with higher additive effects were more stable in multi-environments than those with lower additive effects. Moreover, five epistatic, pairwise QTLs were identified in different environments. The findings with respect to genetic architecture for oil content could be valuable for marker-assisted selection in soybean breeding programs for high oil content.