Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution patterns and conservation status of Crocus species in Iran, one of the diversity centers of Crocus in the Middle East

Abstract Assessing distribution patterns of valuable taxa plays an important role in the biodiversity conservation of these taxa. The genus Crocus L. (Iridaceae) comprises about 100 species that are distributed mainly in the Mediterranean region and western Asia. The present study purposed to assess the distribution patterns of Iranian Crocus species (including C. sativus L. and 8 wild species) and their conservation status in Iran as one of diversity centers of Crocus in the Middle East. A set of geographic distribution data was compiled through field studies, and reviews of herbarium specimens, iNaturalist, and various Flora. Localities were marked on geo-referenced maps (1/106) of Iran using ArcView version 3.2 (Esri, 2000). The distribution patterns of the taxa were mapped per 0.25° × 0.25° universal transverse Mercator grid cells (25 km2 with the exception of boundary area). Based on the species distribution (SDI) (33%) and species specialization (SSI) (44%) indices, those Iranian Crocus species that are threatened are mainly distributed in Irano-Turanian region. The mountainous ecosystems of Almeh and Western Alborz are important distribution centers of these taxa. Iranian Crocus species with SSI < 0.5 (C. almehensis, C. gilanicus, C. michelsonii, and C. caspius) have the highest conservation value.
Correction factor between two calcitonin assays: DiaSorin LiaisonXL and Cobas E601

Abstract Introduction: Calcitonin measurement is important for the diagnosis and monitoring of medullary thyroid carcinoma. Unfortunately, in clinical practice, different detection systems assays are used in the follow-up of the patients, which can be misleading. Objective: To identify the correction factor for calcitonin measurement on two different immunoanalysers: DiaSorin-LiaisonXL (immunochemiluminescence) and CobasE601 (electro-immunochemiluminescence). Methods: We selected 89 registered CT samples (28-from men; 61-from women), that were analysed on CobasE601 with reported values between 0.5 pg/ml and 2812 pg/ml (128.5±513.98). These CT samples were selected randomly to cover as wide a range of values as possible, and represented either basal CT (n=38) or selected from CT stimulation tests (n=51). Samples were evaluated subsequently on DiaSorin-LiaisonXL. All patients gave their informed consent. Results: Between the two assays a segmented linear correlation was noted. We identified the following general linear regression equation: 1.108x+19.337 (p<0.05). The bias increased at high calcitonin values. Therefore, for a better accuracy we analysed the regression equation segmentally. A statistic difference (p<0.05) was noted for CT values ranged between 350-2600 pg/ml (n=31) on DiaSorin-LiaisonXL, for which the linear regression equation for CobasE601 becomes 1.009x+169.796. Conclusions: Calcitonin correction factors are highly important in the dynamic follow up of a patient suffering from medullary thyroid carcinoma when different detection systems assays are used to determine calcitonin. We identified the correction factors for calcitonin determination between two different frequently used chemiluminescence immunoanalysers: DiaSorin-LiaisonXL and CobasE601. However, it is strongly advisable to use the same analyser in order to establish biochemical evolution of calcitonin.
A comparative study between state‐of‐the‐art MRI deidentification and AnonyMI, a new method combining re‐identification risk reduction and geometrical preservation

Deidentifying MRIs constitutes an imperative challenge, as it aims at precluding the possibility of re-identification of a research subject or patient, but at the same time it should preserve as much geometrical information as possible, in order to maximize data reusability and to facilitate interoperability. Although several deidentification methods exist, no comprehensive and comparative evaluation of deidentification performance has been carried out across them. Moreover, the possible ways these methods can compromise subsequent analysis has not been exhaustively tested. To tackle these issues, we developed AnonyMI, a novel MRI deidentification method, implemented as a user-friendly 3D Slicer plugin-in, which aims at providing a balance between identity protection and geometrical preservation. To test these features, we performed two series of analyses on which we compared AnonyMI to other two state-of-the-art methods, to evaluate, at the same time, how efficient they are at deidentifying MRIs and how much they affect subsequent analyses, with particular emphasis on source localization procedures. Our results show that all three methods significantly reduce the re-identification risk but AnonyMI provides the best geometrical conservation. Notably, it also offers several technical advantages such as a user-friendly interface, multiple input-output capabilities, the possibility of being tailored to specific needs, batch processing and efficient visualization for quality assurance.
Evolutionary Dynamics of Asexual Hypermutators Adapting to a Novel Environment

How microbes adapt to a novel environment is a central question in evolutionary biology. While adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects the effects of genetic draft under strong linkage. Despite these linkage effects, the evolved populations exhibit parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results generally negate the presumed relationship between high mutation rates and high adaptive speed of evolution, providing insight into how clonal adaptation occurs in novel environments. Significance statement While mutations are critical source for the adaptation in a new environment, whether or not the elevated mutation rates can empirically lead to the elevated adaptation rates remains unclear, especially when the environment is more heterogenous. To answer this question, we evolved E. coli populations with different starting mutation rates in a complex medium for 900 days and then examined their fitness and genome profiles. In the populations that have a higher starting mutation rate, despite faster genome evolution, their fitness improvement is not significantly faster. Our results reveal that the effect of elevated mutation rates is only very limited, and the mutations accumulated in hypermutators are largely due to linkage effect.
The timescale and magnitude of 1/f aperiodic activity decrease with cortical depth in humans, macaques, and mice

Cortical dynamics obey a 1/f power law, exhibiting an exponential decay of spectral power with increasing frequency. The slope and offset of this 1/f decay reflect the timescale and magnitude of aperiodic neural activity, respectively. These properties are tightly linked to cellular and circuit mechanisms (e.g. excitation:inhibition balance and firing rates) as well as cognitive processes (e.g. perception, memory, and state). However, the physiology underlying the 1/f power law in cortical dynamics is not well understood. Here, we compared laminar recordings from human, macaque and mouse cortex to evaluate how 1/f aperiodic dynamics vary across cortical layers and species. We report that 1/f slope is steepest in superficial layers and flattest in deep layers in each species. Additionally, the magnitude of this 1/f decay is greatest in superficial cortex and decreases with depth. We could account for both of these findings with a simple model in which superficial cortical transmembrane currents had longer time constants and greater densities than those in deeper layers. Together, our results provide novel insight into the organization of cortical dynamics, suggesting that the amplitude and time constant of local currents control circuit processing as a function of laminar depth. This may represent a general mechanism to facilitate appropriate integration of fast sensory inputs (infragranular) with slow feedback-type inputs (supragranular) across cortical areas and species.
Muscarinic receptors mediate motivation via preparatory neural activity in humans

Motivation depends on dopamine, but might be modulated by acetylcholine which influences dopamine release in the striatum, and amplifies motivation in animal studies. A corresponding effect in humans would be important clinically, since anticholinergic drugs are frequently used in Parkinson’s disease, a condition that can also disrupt motivation. Reward and dopamine make us more ready to respond, as indexed by reaction times (RT), and move faster, sometimes termed vigour. These effects may be controlled by preparatory processes that can be tracked using EEG. We measured vigour in a placebo-controlled, double-blinded study of trihexyphenidyl (THP), a muscarinic antagonist, with an incentivised eye movement task and EEG. Participants responded faster and with greater vigour when incentives were high, but THP blunted these motivation effects, suggesting that muscarinic receptors facilitate invigoration by reward. Preparatory EEG build-up (contingent negative variation; CNV) was strengthened by high incentives and by muscarinic blockade. The amplitude of preparatory activity predicted both vigour and RT, although over distinct scalp regions. Frontal activity predicted vigour, whereas a larger, earlier, central component predicted RT. Indeed the incentivisation of RT was partly mediated by the CNV, though vigour was not. Moreover, the CNV mediated the drug’s effect on dampening incentives, suggesting that muscarinic receptors underlie the motivational influence on this preparatory activity. Taken together, these findings show that a muscarinic blocker used to treat Parkinson’s disease impairs motivated action in healthy people, and that medial frontal preparatory neural activity mediates this for RT.
WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat

Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Integrating results from this study and previous findings, we show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheats, so it might be particularly useful in durum wheat where H2 is rare. AUTHOR SUMMARY A region on wheat chromosome 7A has been previously shown to affect the number of spikelets and grains per spike as well as total grain yield in multiple breeding programs. In this study, we show that loss-of-function mutations in the WAPO1 gene located within this region reduce the number of spikelets per spike and that additional transgenic copies of this gene increase this number. These results demonstrate that WAPO1 is the gene responsible for the differences in grain number and yield associated with the 7A chromosome region. Among the three main variants identified for this gene, we demonstrate in field experiments that the H2 variant is associated with the largest increases in number of spikelets and grains per spike. The H2 WAPO1 variant is frequent in bread wheat breeding programs but is almost absent in modern pasta wheat varieties. Therefore, the introgression of the H2 represents a promising opportunity to improve grain yield in pasta wheat breeding programs.
The META tool optimizes metagenomic analyses across sequencing platforms and classifiers

A major challenge in the field of metagenomics is the selection of the correct combination of sequencing platform and downstream metagenomic analysis algorithm, or ‘classifier’. Here, we present the Metagenomic Evaluation Tool Analyzer (META), which produces simulated data and facilitates platform and algorithm selection for any given metagenomic use case. META-generated in silico read data are modular, scalable, and reflect user-defined community profiles, while the downstream analysis is done using a variety of metagenomic classifiers. Reported results include information on resource utilization, time-to-answer, and performance. Real-world data can also be analyzed using selected classifiers and results benchmarked against simulations. To test the utility of the META software, simulated data was compared to real-world viral and bacterial metagenomic samples run on four different sequencers and analyzed using 12 metagenomic classifiers. Lastly, we introduce ‘META Score’: a unified, quantitative value which rates an analytic classifier’s ability to both identify and count taxa in a representative sample.
Pharmacokinetics and biodistribution of extracellular vesicles administered intravenously and intranasally to Macaca nemestrina

Extracellular vesicles (EVs) have great potential as novel drug carriers for the treatment of various diseases. These lipid bilayer vesicles are naturally abundant in mammalian tissues and circulation, can be loaded with therapeutic small molecule drugs, (si)RNA, proteins and CRISPR/Cas9, and may be engineered for retention by specific tissues. However, many questions remain on the optimal dosing, administration route, and pharmacokinetics of EVs. Previous studies have addressed biodistribution and pharmacokinetics in rodents, but little evidence is available from larger animals. Here, we investigated the pharmacokinetics and biodistribution of Expi293F-derived EVs labelled with a highly sensitive nanoluciferase reporter (palmGRET) in a non-human primate model (Macaca nemestrina), comparing intravenous (IV) and intranasal (IN) administration over a 125-fold dose range. We report that EVs administered IV had markedly longer circulation times in plasma than previously reported in mice, and were detectable in cerebrospinal fluid (CSF) after 30-60 minutes. Already after one minute following IV administration, we observed EV uptake by PBMCs, most notably B-cells. EVs were detected in liver and spleen within one hour of IV administration. None of the IN doses resulted in readily detectable EV levels in plasma, CSF, or organs, suggesting that IN delivery of EVs in large animals including humans may require reconsideration or pretreatment approaches. Furthermore, EV circulation times strongly decreased after repeated IV administration, possibly due to immune responses and with clear implications for xenogeneic EV-based therapeutics. We hope that our findings from this baseline study in macaques will help to inform future research and therapeutic development of EVs.
Visual exposure enhances stimulus encoding and persistence in primary cortex

Significance Experience shapes sensory responses, already at the earliest stages of cortical processing. We provide evidence that, in the primary visual cortex of anesthetized cats, brief repetitive exposure to a set of simple, abstract stimuli expands the range and decreases the variability of neuronal responses that persist after stimulus offset. These refinements increase the stimulus-specific clustering of neuronal population responses and result in a more efficient encoding of both stimulus identity and stimulus structure, thus potentially benefiting simple readouts in higher cortical areas. Similar results can be achieved via local plasticity mechanisms in recurrent networks, through self-organized refinements of internal dynamics that do not require changes in firing amplitudes. The brain adapts to the sensory environment. For example, simple sensory exposure can modify the response properties of early sensory neurons. How these changes affect the overall encoding and maintenance of stimulus information across neuronal populations remains unclear. We perform parallel recordings in the primary visual cortex of anesthetized cats and find that brief, repetitive exposure to structured visual stimuli enhances stimulus encoding by decreasing the selectivity and increasing the range of the neuronal responses that persist after stimulus presentation. Low-dimensional projection methods and simple classifiers demonstrate that visual exposure increases the segregation of persistent neuronal population responses into stimulus-specific clusters. These observed refinements preserve the representational details required for stimulus reconstruction and are detectable in postexposure spontaneous activity. Assuming response facilitation and recurrent network interactions as the core mechanisms underlying stimulus persistence, we show that the exposure-driven segregation of stimulus responses can arise through strictly local plasticity mechanisms, also in the absence of firing rate changes. Our findings provide evidence for the existence of an automatic, unguided optimization process that enhances the encoding power of neuronal populations in early visual cortex, thus potentially benefiting simple readouts at higher stages of visual processing.
Ultrasonic Ring Array-Based Transient Triplet Differential Photoacoustic Imaging for Strong Background Removal

Photoacoustic imaging (PAI) is a fast evolving imaging technology enabling in vivo imaging with high specificity and spatial resolution. However, due to strong background signals from various intrinsic chromospheres such as melanin, photoacoustic imaging of targeting objects labeled by contrast agents remain a challenge. The transient triplet differential (TTD) method has shown a significant potential for background-free photoacoustic imaging. Here, we develop a photoacoustic system using an ultrasonic semicircular ring array for transient triplet differential imaging. Pt(II) Octaethylporphine (PtOEP) and black ink are used as the contrast agent and the phantom of melanoma, respectively. Using the TTD method, we could remove the strong background signal from black ink. The ratio between contrast agent signal and background signal is increased to about 10 times the previous one. Our finding demonstrates the potential of the TTD method on molecular imaging for strong background removal.
Peak Fat Oxidation Rate Is Closely Associated With Plasma Free Fatty Acid Concentrations in Women; Similar to Men

Introduction: In men, whole body peak fat oxidation (PFO) determined by a graded exercise test is closely tied to plasma free fatty acid (FFA) availability. Men and women exhibit divergent metabolic responses to fasting and exercise, and it remains unknown how the combined fasting and exercise affect substrate utilization in women. We aimed to investigate this, hypothesizing that increased plasma FFA concentrations in women caused by fasting and repeated exercise will increase PFO during exercise. Then, that PFO would be higher in women compared with men (data from a previous study). Methods: On two separate days, 11 young endurance-trained women were investigated, either after an overnight fast (Fast) or 3.5 h after a standardized meal (Fed). On each day, a validated graded exercise protocol (GXT), used to establish PFO by indirect calorimetry, was performed four times separated by 3.5 h of bed rest both in the fasted (Fast) or fed (Fed) state. Results: Peak fat oxidation increased in the fasted state from 11 ± 3 (after an overnight fast, Fast 1) to 16 ± 3 (mean ± SD) mg/min/kg lean body mass (LBM) (after ~22 h fast, Fast 4), and this was highly associated with plasma FFA concentrations, which increased from 404 ± 203 (Fast 1) to 865 ± 210 μmol/L (Fast 4). No increase in PFO was found during the fed condition with repeated exercise. Compared with trained men from a former identical study, we found no sex differences in relative PFO (mg/min/kg LBM) between men and women, in spite of significant differences in plasma FFA concentrations during exercise after fasting. Conclusion: Peak fat oxidation increased with fasting and repeated exercise in trained women, but the relative PFO was similar in young trained men and women, despite major differences in plasma lipid concentrations during graded exercise.
The Relationship Between “Protect People's Livelihood” and “Promote the Economy:” Provincial Evidence From China

This study focused on medical care in a single country (China) and in regions with different economic backgrounds and different economic development levels to determine the effect of healthcare expenditure on short- and long-term economic growth. The study supported some interesting conclusions: (1) For most areas of China, increasing healthcare expenditure has a negative impact on economic growth in the short term but promotes growth in the long run; (2) Under different levels of economic development within China, there is significant heterogeneity in the interaction between healthcare expenditure and economic growth; (3) The negative effects of healthcare expenditure on short-term economic growth are greater during periods of economic turbulence than during times of stability; and (4) Healthcare expenditure has a negative effect on underdeveloped areas through the accumulation of material capital, while in economically developed areas, this channel has the opposite effect. To improve the quality of medical and health protection and the quality of life and welfare, China needs to consider the development characteristics of different economic zones and establish a multilevel, systematic and diversified medical and health protection system.