Miracle-dz/UniFAR-FTUs huggingface dataset:
Forest fragmentation shapes the alpha–gamma relationship in plant diversity

Questions: Forest fragmentation affects biodiversity locally (alpha diversity) and beyond - at relatively larger scales (gamma diversity) - by increasing dispersal and recruitment limitations. Yet, does an increase in fragmentation affect the relationship between alpha and gamma diversity and what can we learn from it? Location: Northern France. Methods: We surveyed 116 forest patches across three fragmentation levels: none (continuous forest); intermediate (forest patches connected by hedgerows); and high (isolated forest patches). Plant species richness of both forest specialists and generalists was surveyed at five nested spatial resolutions across each forest patch: 1 m(2); 10 m(2); 100 m(2); 1,000 m(2); and total forest patch area. First, we ran log-ratio models to quantify the alpha-gamma relationship. We did that separately for all possible combinations of fragmentation level (none vs intermediate vs high) x spatial scale (e.g., alpha-1 m(2) vs gamma-10 m(2)) x species type (e.g., alpha-specialists vs gamma-specialists). We then used linear mixed-effects models to analyze the effect of fragmentation level, spatial scale, species type and all two-way interaction terms on the slope coefficient extracted from all log-ratio models. Results: We found an interaction effect between fragmentation level and species type, such that forest specialists shifted from a linear (i.e., proportional sampling) to a curvilinear plateau (i.e., community saturation) relationship at low and high fragmentation, respectively, while generalists shifted from a curvilinear to a linear pattern. Conclusions: The impact of forest fragmentation on the alpha-gamma relationship supports generalist species persistence over forest specialists, with contrasting mechanisms for these two guilds. As fragmentation increases, forest specialists shift from proportional sampling towards community saturation, thus reducing alpha diversity likely due to dispersal limitation. Contrariwise, generalists shift from community saturation towards proportional sampling, thus increasing alpha diversity likely due to an increase in the edge:core ratio. To ensure long-term conservation of forest specialists, one single large forest patch should be preferred over several small ones.
Evaluating Short-Term Impacts of Forest Management and Microsite Conditions on Understory Vegetation in Temperate Fir-Beech Forests: Floristic, Ecological, and Trait-Based Perspective

Forest understory vegetation is largely influenced by disturbances and given local abiotic conditions. Our research focuses on the early response of understory vegetation to various forest management intensities in Dinaric fir-beech forests in Slovenia: (i) control, (ii) 50% cut of stand growing stock, and (iii) 100% cut of stand growing stock. Apart from identifying overstory removal effects, we were interested in fine-scale variation of understory vegetation and environmental determinants of its species composition. Vegetation was sampled within 27 karst sinkholes, which represent a dominant landform in studied forests. Within each sinkhole, five sampling plots, varying in slope aspect (centre, north, east, south, west), were established (135 in total), where pre-treatment (in 2012) and post-treatment (in 2014) floristic surveys were conducted. The sampled understory species were characterized in terms of Ellenberg’s indicator values (EIVs) and plant functional traits (plant height, seed mass, specific leaf area, leaf dry matter content). Diversity metrics (species richness, total cover, Shannon index) increased in plots where the silvicultural measures were applied. Tree species richness also increased in 100% cutting. A redundancy analysis revealed that species composition was related to environmental variables, which are directly influenced by management interventions (overstory canopy cover, microclimate—maximum daily temperature, soil properties—thickness of organic soil layer) as well as by topographic factors (slope inclination and surface rockiness). EIVs for light were significantly affected by treatment intensity, whereas soil-related EIVs (moisture, reaction, nutrients) depended more on the within-sinkhole position. Canopy gaps, compared with uncut control plots, hosted a higher number of colonizing species with a higher plant height and smaller seeds, while leaf traits did not show a clear response. We found a negative correlation between pre-treatment species (functional) richness and post-treatment shifts in floristic (functional) composition. Plots with higher richness exhibited smaller changes compared with species-poor communities. Incorporating different perspectives, the results of this study offer valuable insights into patterns of understory vegetation response to forest management in fir-beech forests.
Top-down modulation of neural envelope tracking: the interplay with behavioral, self-report and neural measures of listening effort

When listening to natural speech, our neural activity tracks the speech envelope. Moreover, recent research has demonstrated that this neural envelope tracking can be affected by top-down processes. The present study was designed to examine if neural envelope tracking is modulated by the effort that a person expends during listening. Five measures were included to quantify listening effort: two behavioral measures based on a novel dual-task paradigm, a self-report effort measure and two neural measures related to neural phase synchronization and alpha power. Electroencephalography responses to sentences, presented at a wide range of subject-specific signal-to-noise ratios, were recorded in thirteen young, normal-hearing adults. A comparison of the five measures revealed different effects of listening effort as a function of speech understanding. Reaction times on the primary task and self-reported effort decreased with increasing speech understanding. In contrast, reaction times on the secondary task and alpha power showed a peak-shaped behavior with highest effort at intermediate speech understanding levels. We found a positive association between envelope tracking and speech understanding. While a significant effect of listening effort was found on theta-band envelope tracking, the effect size was negligible. Therefore, our results suggest that listening effort is not a confound when using envelope tracking to objectively measure speech understanding in young, normal-hearing adults.
Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Quality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato. Key Message A 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.
Penapisan Polimorfisme Nukleotida Tunggal Aterogenesis gen LDLR pada Macaca fascicularis dan Macaca nemestrina.

NENDEN SHANAZVIRA AZIZAH. Single Nucleotide Polymorphism Screening of LDLR Gene as Atherogenesis Markers on Macaca fascicularis and Macaca nemestrina. Supervised by RR DYAH PERWITASARI and UUS SAEPULOH. Long-tailed monkeys (Macaca fascicularis) has a variety of genetic backgrounds. M. fascicularis is the most commonly used primate species as a model in the study of atherosclerosis. In addition to M. fascicularis, M. nemestrina (beruk) also has the potential to be developed as an animal model of atherosclerosis. Genetic variation in the low density lipoprotein receptor gene (LDLR) has been associated with normal variations in plasma lipid profile and the risk of coronary heart disease (CAD) in humans. In this study screening was performed by analyzing haplotypes based on SNP regions of exon 6 LDLR genes and analyzing the kinship by constructing phylogenetic trees based on the sample groups according to their response to fat cholesterol diets (Hyper-responder, Hiporesponder, extreme). The LDLR gene of exon region 6 is amplified with a pair of forward and reverse primers. The nucleotide sequences of the amplicons is determined by the sequencing technique. Analysis of exon 6 region LDLR gene in M. fascicularis and M. nemestrina revealed no SNP in this exon. Based on the alignment results, the entire sample has a type of haplotype I. The type of haplotype owned by the six animals is related to the hyper-repons. The use of exon 6 as a genetic marker of M. fascicularis and M. nemestrina on a fat cholesterol diet makes the animal selection of hypofrom hyper-responder quicker and more efficient.
An insect invasion of Antarctica: the past, present and future distribution of Eretmoptera murphyi (Diptera, Chironomidae) on Signy Island

Rising human activity in Antarctica, combined with continued warming of the polar climate, means the risk of non‐native terrestrial species colonising and establishing in its biodiversity‐ and nutrient‐poor ecosystems is increasing. Of the five non‐native invertebrate species currently in terrestrial Antarctica, the flightless midge Eretmoptera murphyi (Schaeffer, The Museum of the Brooklyn Institute of Arts and Sciences 2:90–94, 1914) is perhaps the most persistent insect invader. Accidentally introduced to Signy Island (60°S) in the 1960s from sub‐Antarctic South Georgia (54°S), E. murphyi has steadily increased its distribution, however, its status has not been reassessed for a decade. Here, we update the distribution of E. murphyi on Signy, specifically assessing whether footpaths to regularly visited research sites represent dispersal corridors. Our findings show that both the abundance and range of E. murphyi have increased significantly since 2009, particularly along paths leading away from the original introduction site, and that the species is now on the cusp of moving into new valley systems. We identify a moderate association with soil/substrate and vegetation types and build Maximum Entropy (MaxEnt) models to predict areas of the island that may be at highest risk of future colonisation. As a detritivore with no competitors or predators, E. murphyi may have a major impact. For example, accelerating nutrient cycling which may have wider impacts on all levels of biodiversity. This study highlights the need for an assessment of current biosecurity protocols applied within the Antarctic Treaty system, as well as the need for systematic regular monitoring of introduced and invasive species in Antarctica.
Development of telomerase targeted gene therapy for treatment of cancer

Gene therapy is an area that is currently developing for treatment of various congenital and acquired diseases. The basic concept is that a transgene is expressed in a target cell resulting in alleviation of disease. In general there are certain obstacles limiting gene therapy regardless of the target disease. These include restriction of transgene expression to target cells, inadequate transgene expression and ineffective in vivo transgene delivery. Cancer is one of the leading diseases to cause death in the human and canine population. For this reason gene therapy has been studied as a potential novel treatment for cancer. Two step transcriptional amplification system is a system applied to gene therapy in order to improve efficacy. In this system a relatively weak tissue or disease specific promoter initiates the transcription of a transcriptional activator protein. This protein when expressed in target cells binds to binding sites upstream of a secondary promoter which then drives the transcription of the transgene of interest at a high level. By use of a two step amplification mechanism and a novel transcriptional activator fusion protein VP16E2, we increased transgene expression compared to the commonly used Gal4VP16 transcriptional activator fusion protein. By incorporating the human telomerase promoter hTERT as a primary promoter and the minimal 6xE23'BpTATA promoter as a secondary promoter, transgene expression is maintained in telomerase positive cells representing cancer cells, but is restricted in telomerase negative cell lines. By inserting the tumour necrosis factor apoptosis inducing ligand (TRAIL) gene as a transgene in this system we have shown that apoptosis is elicited in telomerase positive cells although not in telomerase negative cells. The similarities in incidence and nature of human and canine cancer forms and the need for a better translational model for human disease has put canines in focus for cancer studies and drug development. Conditionally replicative oncolytic viruses developed in humans are species specific and therefore can not be studied satisfactorily in rodent preclinical models. We have made a mutant adenovirus based on the canine adenovirus type 1. We have put the viral replication under control of our two step amplification mechanism making the viral replication dependent on telomerase activity of the infected cell. This virus is able to kill telomerase positive canine cells but not telomerase negative canine cells in vitro. This virus is a potential tool for studying a conditionally replicative oncolytic virus in vivo in naturally occurring canine cancer cases. This is a good translational model for human cancer treatment and thereby benefits both species.
Assessing the relative importance of temperature, discharge, and day length on the reproduction of an anadromous fish (
 Alosa alosa
 )

Climate change threatens anadromous fishes such as the allis shad (Alosa alosa) populations of which have declined since the 20th century in Europe. Sensitivity to climate change could be quantified by determining the fish’s spawning behaviour, defined as the timing of reproduction (i.e. spawning events) as a function of temporally variable environmental factors. The cues that fish use to time reproduction could determine their response to climate change. A machine learning technique (boosted regression tree) was calibrated using a 14‐year dataset composed of daily measures of environmental factors and fish occurrences during reproduction. The boosted regression tree provides complete insight into the complex relationship between the spawning probability, i.e. the probability for a fish to reproduce, and environmental factors that might evolve with climate change. The spawning probability was positively related to day length (44.6%) and water temperature (34.7%) and negatively related to river discharge (20.7%). Optimal reproductive conditions corresponded to a difference in day length between 0 and 0.04 hr, a water temperature between 15 and 26°C and a river discharge between 55 and 665 m³/s; these conditions are currently being utilised by allis shad populations in the Garonne and Dordogne rivers, France. This study highlights the relative influence of environmental factors on the observed spawning period as well as the evolution of habitat suitability during the 14‐year period. The novelty of this study stems from assessing population process data, i.e. the occurrence of fish reproduction, rather than mere occurrence data in an ecological niche model study. Climate change may lead to a shift in spawning phenology, as the water temperature and river discharge will also change. Therefore, conservation plans need to integrate these effects on spawning grounds.
Physiological Responses of Onion Varieties to varying Photoperiod and Temperature Regimes

We measured the gas exchange parameters of six onion varieties in two photoperiodic regimes. The photoperiods simulated early (long-day) and late (short-day) onion growing seasons of the high desert regions near Lancaster, California. We used six locally grown onion varieties: RedBull (RB), RedWing (RW), Hybrid Cometa (HC), Granero (YG), Hybrid Valero (HV) and Hybrid SR (HS). For both photoperiod regimes, daylength and temperature were changed weekly to represent the natural progression of field growing conditions. The results show that the onion plants grown under short-daylength (SD) and higher temperature regimes exhibited higher leaf photosynthetic rates and stomatal conductance than onion seedlings grown under the long-day (LD) regime. Onion plants also had different functional leaf traits depending on crop growth environment during the onset of bulbing. The higher photosynthetic rate of the short-day plants coincided with bulb initiation. Onion photosynthesis and stomatal conductance increased at bulb initiation, apparently to provide carbohydrates for growth and storage in the bulb.
A sparse observation model to quantify species interactions in time and space

Camera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time. Tomcat allows to learn about the environmental requirements and daily activity patterns of species while accounting for imperfect detection. It further implements a sparse model that deals well will a large number of potentially highly correlated environmental variables. By integrating both spatial and temporal information, we extend the notation of overlap coefficient between species to time and space to study niche partitioning. We illustrate the power of Tomcat through an application to camera trap data of eight sympatrically occurring duiker Cephalophinae species in the savanna - rainforest ecotone in the Central African Republic and show that most species pairs show little overlap. Exceptions are those for which one species is very rare, likely as a result of direct competition.
Integrating citizen science data with expert surveys increases accuracy and spatial extent of species distribution models

Information on species’ habitat associations and distributions, across a wide range of spatial and temporal scales, are a fundamental source of ecological knowledge. However, collecting biological information at relevant scales if often cost prohibitive, although it is essential for framing the broader context of more focused research and conservation efforts. Citizen-science data has been signaled as an increasingly important source of biological information needed to fill in data gaps needed to make more comprehensive and robust inferences on species distributions. However, there are perceived trade-offs of combining highly structured, scientific survey data with largely unstructured, citizen-science data. As a result, the focus of most methodological advances to combine these sources of information has been on treating these sources as independent. The degree to which each source of information is allowed to directly inform a common underlying process (e.g. species distribution) depends on the perceived quality of the data. In this paper, we explore these trade-offs by applying a simplified approach of filtering citizen-science data to resemble structured survey data, and analyze both sources of data under a common framework. To accomplish this, we explored ways of integrating high-resolution survey data on shorebirds in the northern Central Valley of California with observations in eBird for the entire region that were filtered to improve their quality. The integration of survey data with the filtered citizen-science data in eBird resulted in improved inference and predictive ability, and increased the extent and accuracy of inferences on shorebirds for the Central Valley. The structured surveys were found to improve the overall accuracy of ecological inference based only on citizen-science data, by increasing the representation of data collected from high quality habitats for shorebirds (e.g. rice fields). The practical approach we have shown for data integration can be also be used to improve the efficiency of designing biological surveys in the context of larger, citizen-science monitoring efforts, ultimately reducing the financial and time expenditures typically required of monitoring programs and focused research. The simple processing and filtering method we present can be used to integrate other types of data (e.g. camera traps) with more localized efforts (e.g. research projects), ultimately improving our ecological knowledge on the distribution and habitat associations of species of conservation concern worldwide.
Cisgenesis as a novel prospect for crop improvement. A review

Nowadays, the development of new biotechnological methods is necessary to satisfy requirements of market to produce enough good-quality food. Application of novel scientific approaches can be of great importance for improving the quality and quantity of plant crops. However, the most efficient strategies are based on genetic modification, which is still very controversial issue. GMO opponents do not accept the use of genetic engineering in crop improvement and production of new varieties suited for organic agriculture. Major discussion among various scientific and social issues concerns the possibility of existence of unintended effects of GMO both on human and world safety. Political, ethical, and social fears are related mostly to the best known transgenic approach, which is 'transgenesis'. Novel strategies and techniques are therefore required in the development of genetically engineered crops of the future. Nowadays, a new plant breeding technique, called 'cisgenesis' is intensively studied. In this paper, we review the most common strategies for crops improvement and describe cisgenesis as an alternative to transgenesis for safe and eco-friendly agriculture.