Miracle-dz/UniFAR-FTUs huggingface dataset:
Intra and inter-annual climatic conditions have stronger effect than grazing intensity on root growth of permanent grasslands

Background and Aims Understanding how direct and indirect changes in climatic conditions, management, and species composition affect root production and root traits is of prime importance for grassland C sequestration service delivery. Methods We studied during two years the dynamics of root mass production with ingrowth-cores and annual above- and below-ground biomass (ANPP, BNPP) of upland fertile grasslands subjected for 10 years to a gradient of herbage utilization by grazing. Results We observed strong seasonal root production across treatments in both a wet and a dry year but response to grazing intensity was hardly observed within growing seasons. In abandonment, spring and autumn peaks of root growth were delayed by about one month compared to cattle treatments, possibly due to later canopy green-up and lower soil temperature. BNPP was slightly lower in abandonment compared to cattle treatments only during the dry year, whereas this effect on ANPP was observed the wet year. In response to drought, the root-to-shoot biomass ratio declined in the abandonment but not in the cattle treatment, underlining higher resistance to drought of grazed grassland communities. Conclusions Rotational grazing pressure and climatic conditions variability had very limited effects on root growth seasonality although drought had stronger effects on BNPP than on ANPP.
Focal electrical stimulation of human retinal ganglion cells for vision restoration

Objective. Vision restoration with retinal implants is limited by indiscriminate simultaneous activation of many cells and cell types, which is incompatible with reproducing the neural code of the retina. Recent work has shown that primate retinal ganglion cells (RGCs), which transmit visual information to the brain, can be directly electrically activated with single-cell, single-spike, cell-type precision – however, this possibility has never been tested in the human retina. In this study we aim to characterize, for the first time, direct in situ extracellular electrical stimulation of individual human RGCs. Approach. Extracellular electrical stimulation of individual human RGCs was conducted in three human retinas ex vivo using a custom large-scale, multi-electrode array capable of simultaneous recording and stimulation. Measured activation properties were compared directly to extensive results from macaque. Main results. Precise activation was in many cases possible without activating overlying axon bundles, at low stimulation current levels similar to those used in macaque. The major RGC types could be identified and targeted based on their distinctive electrical signatures. The measured electrical activation properties of RGCs, combined with a dynamic stimulation algorithm, was sufficient to produce an evoked visual signal that was nearly optimal given the constraints of the interface. Significance. These results suggest the possibility of high-fidelity vision restoration in humans using bi-directional epiretinal implants.
Dynamic expression of brain functional systems disclosed by fine-scale analysis of edge time series

Functional connectivity (FC) describes the statistical dependence between brain regions in resting-state fMRI studies and is usually estimated as the Pearson correlation of time courses. Clustering reveals densely coupled sets of regions constituting a set of resting-state networks or functional systems. These systems manifest most clearly when FC is sampled over longer epochs lasting many minutes but appear to fluctuate on shorter time scales. Here, we propose a new approach to track these temporal fluctuations. Un-wrapping FC signal correlations yields pairwise co-fluctuation time series, one for each node pair/edge, and reveals fine-scale dynamics across the network. Co-fluctuations partition the network, at each time step, into exactly two communities. Sampled over time, the overlay of these bipartitions, a binary decomposition of the original time series, very closely approximates functional connectivity. Bipartitions exhibit characteristic spatiotemporal patterns that are reproducible across participants and imaging sessions and disclose fine-scale profiles of the time-varying levels of expression of functional systems. Our findings document that functional systems appear transiently and intermittently, and that FC results from the overlay of many variable instances of system expression. Potential applications of this decomposition of functional connectivity into a set of binary patterns are discussed.
Meta-Transcriptomic Discovery of a Divergent Circovirus and a Chaphamaparvovirus in Captive Reptiles with Proliferative Respiratory Syndrome

Viral pathogens are being increasingly described in association with mass morbidity and mortality events in reptiles. However, our knowledge of reptile viruses and their role in population health remains limited. Herein, we describe a meta-transcriptomic investigation of a mass morbidity and mortality event in a colony of central bearded dragons (Pogona vitticeps) in 2014. Severe, extensive proliferation of the respiratory epithelium was consistently found in affected dragons. Similar proliferative lung lesions were identified in bearded dragons from the same colony in 2020 in association with increased intermittent mortality. Total RNA sequencing of bearded dragon tissue identified two divergent DNA viruses: a reptile-infecting circovirus, denoted bearded dragon circovirus (BDCV), and the first exogeneous reptilian chaphamaparvovirus - bearded dragon chaphamaparvovirus (BDchPV). Phylogenetic analysis revealed that BDCV was most closely related to bat-associated circoviruses, exhibiting 70% amino acid sequence identity. In contrast, the newly discovered BDchPV showed approximately 35-40% identity in the non-structural (NS) protein to parvoviruses obtained from tilapia fish and crocodiles in China. Subsequent specific PCR assays detected BDCV exclusively and comprehensively within animals with proliferative pulmonary lesions and respiratory disease. This study expands our understanding of viral diversity in the context of diseased reptiles in captivity.
Malaria mosquitoes acquire and allocate cattle urine to enhance life history traits

Background Nutrient acquisition and allocation integrate foraging and life-history traits in insects. To compensate for the lack of a particular nutrient at different life stages, insects may acquire these through supplementary feeding, for example, on vertebrate secretions, in a process known as puddling. The mosquito Anopheles arabiensis emerges undernourished, and as such, requires nutrients for both metabolism and reproduction. The purpose of this study was to assess whether An. arabiensis engage in puddling on cattle urine to obtain nutrients to improve life history traits. Methods To determine whether An. arabiensis are attracted to the odour of fresh, 24 h, 72 h and 168 h aged cattle urine, host-seeking and blood-fed (48 h post-blood meal) females were assayed in a Y-tube olfactometer, and gravid females assessed in an oviposition assay. Combined chemical and electrophysiological analyses were subsequently used to identify the bioactive compounds in all four age classes of cattle urine. Synthetic blends of bioactive compounds were evaluated in both Y-tube and field assays. To investigate the cattle urine, and its main nitrogenous compound, urea, as a potential supplementary diet for malaria vectors, feeding parameters and life history traits were measured. The proportion of female mosquitoes and the amount of cattle urine and urea imbibed, were assessed. Following feeding, females were evaluated for survival, tethered flight and reproduction. Results Host-seeking and blood-fed An. arabiensis were attracted to the natural and synthetic odour of fresh and aged cattle urine in both laboratory and field studies. Gravid females were indifferent in their response to cattle urine presence at oviposition sites. Host-seeking and blood-fed females actively imbibed cattle urine and urea, and allocated these resources according to life history trade-offs to flight, survival or reproduction, as a function of physiological state. Conclusions Anopheles arabiensis acquire and allocate cattle urine to improve life history traits. Supplementary feeding on cattle urine affects vectorial capacity directly by increasing daily survival and vector density, as well as indirectly by altering flight activity, and thus should be considered in future models.
Gene Families With Stochastic Exclusive Gene Choice Underlie Cell Adhesion in Mammalian Cells

Exclusive stochastic gene choice combines precision with diversity. This regulation enables most T-cells to express exactly one T-cell receptor isoform chosen from a large repertoire, and to react precisely against diverse antigens. Some cells express two receptor isoforms, revealing the stochastic nature of this process. A similar regulation of odorant receptors and protocadherins enable cells to recognize odors and confer individuality to cells in neuronal interaction networks, respectively. We explored whether genes in other families are expressed exclusively by analyzing single cell RNA-seq data with a simple metric. Chromosomal segments and families are more likely to express genes concurrently than exclusively, possibly due to the evolutionary and biophysical aspects of shared regulation. Nonetheless, gene families with exclusive gene choice were detected in multiple cell types, most of them are membrane proteins involved in ion transport and cell adhesion, suggesting the coordination of these two functions. Thus, stochastic exclusive expression extends beyond the prototypical families, permitting precision in gene choice to be combined with the diversity of intercellular interactions.
Alterations of the rewarding actions of amphetamine by prior nicotine and alcohol treatment: The role of age and dopamine

Rationale Nicotine and alcohol each can serve as the gateway to other drugs. Objective The current study was sought to determine if prior nicotine and alcohol exposure alters amphetamine reward and if age and dopaminergic neurotransmission are involved. Methods Male and female adolescent and adult C57BL/6J mice were tested for baseline place preference, received six conditioning with saline/nicotine (0.25 mg/kg) twice daily followed by six conditioning with saline/ethanol (2 g/kg) in a counterbalance manner. Control mice were conditioned with saline/saline throughout. Finally, mice were conditioned with amphetamine (3 mg/kg) once in the nicotine-alcohol-paired chamber and then tested for CPP 24 h later. The following day, mice were challenged with amphetamine (1 mg/kg) and tested for CPP under a drugged state. Mice were then immediately euthanized, brain removed and nucleus accumbens isolated and processed for the expression of dopamine receptors and transporter, and glutamate receptors. Results We observed a greater amphetamine-induced CPP in adolescent than adult mice but no change in state-dependent CPP between the two age groups. In contrast, amphetamine-induced CPP in mice with prior nicotine-alcohol exposure was greater in adult than adolescent mice under both drug-free and drugged states. The enhanced response in adult mice was associated with greater expression of dopamine-transporter, reduced D2 receptors, and increased D1 receptors with no changes in glutamate receptors. Conclusions These results suggest that prior nicotine and alcohol exposure differentially alters the rewarding action of amphetamine in adult and adolescent mice and alterations in dopaminergic neurotransmission may be involved in this phenotype.
Statistics and classification of spatial rotations and projection directions considering molecular symmetry in 3D electron cryo-microscopy

Electron cryo-microscopy (cryoEM) three-dimensional (3D) reconstruction is based on estimations of orientations of projection images or 3D volumes. It is common that the macromolecules studied by cryoEM have molecular symmetry. However, for neither spatial rotations nor projection directions, currently there is no statistics and classification method which takes molecular symmetry into consideration. This limits the applications of advanced statistical methods in cryoEM. In this research, based on the concept of non-unique-games (NUG), we propose statistics and classification methods of both spatial rotations and projection directions when molecular symmetry is considered. Such methods are realized in the open-source python package pySymStat.
Statistics for the Macintosh

The aim of this ection isto evaluate the character, content, cost, and hardware quirements of new software programs invarious fields of the biological sciences, and in appropriate related areas. All programs submitted to The Quarterly are given careful consideration, a dcompetent a d conscientious reviewers a e selected toassess the software for originality, efficacy, and suitability of various applications by our readers. The price of a software program reviewed was the publisher' suggested list price when the program was releasedfor review. Unless otherwise noted, documentation is included with each program. Authors and publishers ofbiological software who wish to have their biological software programs consideredfor review should submit complete programs and documentation o The Editor, Biological Software, The Quarterly Review of Biology, State University of New York, Stony Brook, NY 11794-5275 USA.
DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid

Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition. ABSTRACT Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering of primary material, laboratory methods, data analysis, and interpretation. The focus of this study is on gathering the primary material, in this case, DNA. We used bovine milk as a model to (i) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk, (ii) evaluate host DNA depletion methods for use with milk, and (iii) develop and evaluate a selective lysis-propidium monoazide (PMA)-based protocol for host DNA depletion in milk. Our results suggest that magnetically based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting the finding that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety, where the detection of Gram-negative pathogens and hygiene indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host. IMPORTANCE Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around 1,000 times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods for the ability to detect specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
Estimating encounter location distributions from animal tracking data

Ecologists have long been interested in linking individual behavior with higher-level processes. For motile species, this ‘upscaling’ is governed by how well any given movement strategy maximizes encounters with positive factors, and minimizes encounters with negative factors. Despite the importance of encounter events for a broad range of ecological processes, encounter theory has not kept pace with developments in animal tracking or movement modeling. Furthermore, existing work has focused primarily on the relationship between animal movement and encounter rates while no theoretical framework exists for directly relating individual movement with the spatial locations of encounter events in the environment. Here, we bridge this gap by introducing a new theoretical concept describing the long-term encounter location probabilities for movement within home ranges, termed the conditional distribution of encounters (CDE). We then derive this distribution, as well as confidence intervals, implement its statistical estimator into open source software, and demonstrate the broad ecological relevance of this novel concept. We first use simulated data to show how our estimator provides asymptotically consistent estimates. We then demonstrate the general utility of this method for three simulation-based scenarios that occur routinely in biological systems: i) a population of individuals with home ranges that overlap with neighbors; ii) a pair of individuals with a hard territorial border between their home ranges; and iii) a predator with a large home range that encompassed the home ranges of multiple prey individuals. Using GPS data from white-faced capuchins (Cebus capucinus) tracked on Barro Colorado Island, Panama, and sleepy lizards (Tiliqua rugosa) tracked in Bundey, South Australia, we then show how the CDE can be used to estimate the locations of territorial borders, identify key resources, quantify the location-specific potential for competition, and/or identify any changes in behaviour that directly result from location-specific encounter probability. This novel target distribution enables researchers to better understand the dynamics of populations of interacting individuals. Notably, the general estimation framework developed in this work builds straightforwardly off of home range estimation and requires no specialised data collection protocols. This method is now openly available via the ctmm R package.
A pilot study on the beneficial effects of additional selenium supplementation to methimazole for treating patients with Graves’ disease

Background/aim The aim of this study was to assess the effect of a combination use of methimazole (MMI) and selenium (Se) in the treatment of Graves’ disease (GD). Materials and methods A total of 103 newly diagnosed hyperthyroidism patients were randomized to MMI and MMI + Se combination groups. After treatment for 6 months, the levels of triiodothyronine (FT3), free thyroxine (FT4), thyrotropin receptor antibody (TRAb), thyroid peroxidase antibody (TPOAb), and thyroglobulin antibody (TGAb) were observed. An in vitro culture model of thyroid cells was established and the protein expression and mRNA levels of TRAb, TPOAb, and TGAb were determined by western blot and RT-PCR. Results A significant decrease in the levels of FT3, FT4, TRAb, TPOAb, and TGAb were observed in both groups along with a marked increase in TSH levels. Furthermore, the in vitro experiments showed that the protein expression and mRNA levels of TRAb, TPOAb, and TGAb decreased significantly. Also, compared to the MMI group, there was a greater improvement of these indices in the MMI + Se group. Conclusion We suggest that the combined use of MMI and Se could improve the thyroid activity in patients, which may provide an effective therapy for the treatment of GD in clinical settings.
Hallucination of moving objects revealed by a dynamic noise background

We show that on a dynamic noise background, the perceived disappearance location of a moving object is shifted in the direction of motion. This “twinkle goes” illusion has little dependence on the luminance- or chromaticity-based confusability of the object with the background, or on the amount of background motion energy in the same direction as the object motion. This suggests that the illusion is enabled by the dynamic noise masking the offset transients that otherwise accompany an object’s disappearance. While these results are consistent with an anticipatory process that pre-activates positions ahead of the object’s current position, additional findings suggest an alternative account: a continuation of attentional tracking after the object disappears. First, the shift was greatly reduced when attention was divided between two moving objects. Second, the illusion was associated with a prolonging of the perceived duration of the object, by an amount that matched the extent of extrapolation inferred from the effect of speed on the size of the illusion (~50 ms). While the anticipatory extrapolation theory does not predict this, the continuation of attentional tracking theory does. Specifically, we propose that in the absence of offset transients, attentional tracking keeps moving for several tens of milliseconds after the target disappearance, and this causes one to hallucinate a moving object at the position of attention.
Identifying Taxonomic Units in Metagenomic DNA Streams

With the emergence of portable DNA sequencers, such as Oxford Nanopore Technology MinION, metagenomic DNA sequencing can be performed in real-time and directly in the field. However, because metagenomic DNA analysis is computationally and memory intensive, and the current methods are designed for batch processing, the current metagenomic tools are not well suited for mobile devices. In this paper, we propose a new memory-efficient method to identify Operational Taxonomic Units (OTUs) in metagenomic DNA streams. Our method is based on finding connected components in overlap graphs constructed over a real-time stream of long DNA reads as produced by MinION platform. We propose an efficient algorithm to maintain connected components when an overlap graph is streamed, and show how redundant information can be removed from the stream by transitive closures. Through experiments on simulated and real-world metagenomic data, we demonstrate that the resulting solution is able to recover OTUs with high precision while remaining suitable for mobile computing devices.