Miracle-dz/UniFAR-FTUs huggingface dataset:
An Evaluation of Physically Based and Empirically Determined Evapotranspiration Models for Nursery Plants

A lysimeter study was conducted to determine the evapotranspiration (ET) rates of Red Sunset red maple (Acer Rubrum 'Red Sunset') nursery trees under outdoor conditions in August and September 1997. The average ET rate was 0.084 mm day-1. This measured ET rate was compared with calculated ET rates based on four physical ET (i.e., Penman, Penman-Monteith, Stanghellini and Fynn) and two empirically determined ET models (vapor pressure deficit (VPD) and solar radiation based empirical ET models). The Penman-Monteith and Penman models overestimated the measured ET rate by 15% and 31%, respectively while the Stanghellini and Fynn models underestimated the measured ET rates by 19.7% and 16.3% with R2 values of 0.70, 0.582, 0.645 and 0.644, respectively. The linear regression analyses showed that the single variables solar radiation and vapor pressure deficit each correlated with ET and R2 values of 0.750 and 0.650 respectively. This study showed that VPD or solar radiation based empirical ET models could be used to predict ET rates of nursery plants if there is difficulty in running the physically based ET model due to a lack of input parameters.
Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?

The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from December 24, 2019, to May 13, 2020, according to the GISAID database. Our analysis revealed the presence of 3,206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (> 10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein and one in each of three proteins: spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the RBD of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with mutational frequency dissimilarity and intra-genomic divergence of SARS-CoV-2 could indicate that the SARS-CoV-2 is not yet adapted to its host. Unlike the influenza virus or HIV viruses, the low mutation rate of SARS-CoV-2 makes the development of an effective global vaccine very likely.
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

Cell differentiation and function are regulated across multiple layers of gene regulation, including the modulation of gene expression by changes in chromatin accessibility. However, differentiation is an asynchronous process precluding a temporal understanding of the regulatory events leading to cell fate commitment. Here, we developed SHARE-seq, a highly scalable approach for measurement of chromatin accessibility and gene expression within the same single cell. Using 34,774 joint profiles from mouse skin, we develop a computational strategy to identify cis-regulatory interactions and define Domains of Regulatory Chromatin (DORCs), which significantly overlap with super-enhancers. We show that during lineage commitment, chromatin accessibility at DORCs precedes gene expression, suggesting changes in chromatin accessibility may prime cells for lineage commitment. We therefore develop a computational strategy (chromatin potential) to quantify chromatin lineage-priming and predict cell fate outcomes. Together, SHARE-seq provides an extensible platform to study regulatory circuitry across diverse cells within tissues.
Disrupted basal ganglia output during movement preparation in hemi-parkinsonian mice accounts for behavioral deficits

Parkinsonian motor deficits are associated with elevated inhibitory output from the basal ganglia (BG). However, several features of Parkinson’s disease (PD) have not been accounted for by this supra-inhibition framework, including the potentially therapeutically-relevant observation that movements guided by external stimuli are less impaired than otherwise-identical movements generated based on internal goals. Is this difference due to divergent processing within the BG itself, or to the recruitment of extra-BG pathways by sensory processing? In addition, surprisingly little is known about precisely when, in the sequence from selecting to executing movements, BG output is altered by PD. Here, we address these questions by recording activity in the SNr, a key BG output nucleus, in hemiparkinsonian (hemi-PD) mice performing a well-controlled behavioral task requiring stimulus-guided and internally-specified directional movements. We found that hemi-PD mice (n = 5, male) exhibited a bias ipsilateral to the side of dopaminergic cell loss, consistent with supra-inhibition of contralateral movements by BG output, and that this bias was stronger when movements were internally specified rather than stimulus guided, consistent with clinical observations in parkinsonian patients. We further found that changes in SNr activity during movement preparation could account for the ipsilateral behavioral bias, as well as its greater magnitude for internally-specified movements. These results suggest that parkinsonian changes in BG output underlying movement preparation contribute to the greater deficit in internally-specified in comparison to stimulus-guided movements. Significance Statement Parkinsonian patients exhibit the intriguing phenomenon that movements guided by external stimuli are often less impaired than otherwise-identical movements generated based on internal goals. For example, patients can exhibit a more normal gait when their steps are guided by patterned floor tiling than when traversing a featureless floor. Whether this difference in movement execution is due to distinct processing intrinsic to the basal ganglia (BG) or to compensation from other motor pathways is an open question with therapeutic implications. We addressed this question by recording BG output during behavior in a parkinsonian mouse model. We found that mice exhibited greater impairment in internally-specified than stimulus-guided movements, and that differences in BG output during movement preparation could account for this effect.
Single cell RNA sequence analysis of human bone marrow samples reveals new targets for isolation of skeletal stem cells using DNA-coated gold nanoparticles

There is a wealth of data indicating human bone marrow derived stromal cells (HBMSCs) contain the skeletal stem cell (SSC) with the potential to differentiate along the stromal osteogenic, adipogenic and chondrogenic lineages. However, despite these advances, current methods to isolate skeletal stem cells (SSCs) from human tissues have proved challenging as no single specific marker has been identified limiting understanding of SSC fate, immunophenotype and the widespread clinical application of these cells. While a number of cell surface markers can enrich for SSCs, none of the proposed markers, alone, provide a platform to isolate single cells with the ability to form bone, cartilage, and adipose tissue in humans. The current study details the application of oligonucleotide-coated nanoparticles, spherical nucleic acids (SNAs), to rapidly isolate human cells using mRNAs signatures detected in SSCs in real time, to identify stem and progenitor skeletal populations using single cell RNA sequencing. Based on scRNA-seq of samples from 11 patients, this method was able to identify novel targets for SSC enrichment, which were assessed in a total of 80 patients. This methodology was able to isolate potential SSCs found at a frequency of <1 in 1,000,000 in human bone marrow, with a capacity for tri-lineage differentiation in vitro. The current approach provides new targets and a platform to advance SSC isolation, enrichment with significant therapeutic impact therein.
Temporal dynamics of the neural mechanisms for encoding hue and luminance contrast uncovered by magnetoencephalography

Hue and luminance contrast are the most basic visual computations, and are reflected in the earliest layers of convolutional neural networks, yet the extent to which they are extracted by the same or separate circuits in the brain, and the timing of these neural computations, is unknown. Here we answer these questions using multivariate analyses of human brain responses measured with magnetoencephalography. We report three discoveries. First, hue and luminance contrast could be decoded independently, indicating these computations are somewhat separable. Hue was computed about 15-24ms after luminance contrast. Second, representations of hue showed relatively greater generalization across time and were more sustained, providing the first neural correlate of the perceptual preeminence of hue over luminance contrast in grouping objects. Finally, luminance contrast could be decoded less well for hues associated with daylight (orange and blue), suggesting that color-constancy mechanisms are adapted to natural lighting.
QTL mapping for aggressiveness variation in F. graminearum revealed one causal mutation in FgVe1 velvet protein

Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight in the world, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population, for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.
Erector spinae plane block and transversus abdominis plane block for postoperative analgesia in cesarean section: A prospective randomized comparative study

Background and Aims: Erector spinae plane (ESP) block is an interfascial plane block given at the paraspinal region and provides effective visceral and somatic analgesia. Transversus abdominis plane (TAP) block is also an interfascial block that provides adequate somatic pain control. We conducted this study to compare the analgesic efficacy of ESP and TAP blocks with ropivacaine for 48 h after the cesarean section. Material and Methods: Sixty patients scheduled for elective cesarean section under spinal anesthesia, randomly divided into ESP block (n = 30) or TAP block (n = 30) groups. After completion of surgery, ultrasound-guided ESP or TAP block was given using 0.2% ropivacaine (0.2 ml/kg on either side). Postoperatively visual analogue scale (VAS) score and analgesic requirement of each patient was assessed at regular interval for 48 h by a blinded investigator. Statistical analysis was done using SPSS version 21. Student's t-test and Chi-square test were used for demographic and other data. Results: ESP block provided prolonged analgesia compared to the TAP block, andthe mean time to first rescue analgesia was 43.53 h and 12.07 h, respectively (P < 0.001). The requirement for total analgesic was also significantly less in the ESP group compared to the TAP group (P < 0.001). Conclusion: ESP block provided prolonged analgesia with a significant decrease in analgesic requirement compared to TAP block and can be used as a standard technique for post-cesarean analgesia.
Predicting walking response to ankle exoskeletons using data-driven models

Despite recent innovations in exoskeleton design and control, predicting subject-specific impacts of exoskeletons on gait remains challenging. We evaluated the ability of three classes of subject-specific phase-varying models to predict kinematic and myoelectric responses to ankle exoskeletons during walking, without requiring prior knowledge of specific user characteristics. Each model – phase-varying (PV), linear phase-varying (LPV), and nonlinear phase-varying (NPV) – leveraged Floquet Theory to predict deviations from a nominal gait cycle due to exoskeleton torque, though the models differed in complexity and expected prediction accuracy. For twelve unimpaired adults walking with bilateral passive ankle exoskeletons, we predicted kinematics and muscle activity in response to three exoskeleton torque conditions. The LPV model’s predictions were more accurate than the PV model when predicting less than 12.5% of a stride in the future and explained 49–70% of the variance in hip, knee, and ankle kinematic responses to torque. The LPV model also predicted kinematic responses with similar accuracy to the more-complex NPV model. Myoelectric responses were challenging to predict with all models, explaining at most 10% of the variance in responses. This work highlights the potential of data-driven phase-varying models to predict complex subject-specific responses to ankle exoskeletons and inform device design and control.
A study of the influence of different rootstocks on the vegetative growth of almond cultivars

This study investigated different seed rootstocks (bitter almond, peach seedling and sweet almond seedling), the reactions of these rootstocks with three different almond cultivars (Shahrood cultivars of 15, 12 and 18) and their effect on vegetative growth as well as the effect of the rootstocks on nutrient absorption. The used research design was a split plot in the form of complete randomized block design in three replicates in which the original factor of scion cultivar and sub factor of rootstock type was applied. Features measured during the design included: plant height, trunk diameter, extension width and effect of rootstock on the absorption of nitrogen, phosphorus and potassium. The obtained results indicate that vegetative growth with rootstock of bitter almond, which is mostly used, was less than the other tested rootstocks in the early years and peach rootstock had more vegetative growth. Also, rootstock had a meaningful impact on nutrient absorption so that the greatest amount of nitrogen absorption was obtained by the peach rootstock and the highest amount of potassium absorption was achieved by sweet almond rootstock.
RUNX1 marks a luminal castration-resistant lineage established at the onset of prostate development

The characterization of prostate epithelial hierarchy and lineage heterogeneity is critical to understand its regenerative properties and malignancies. Here, we report that the transcription factor RUNX1 marks a specific subpopulation of proximal luminal cells (PLCs), enriched in the periurethral region of the developing and adult mouse prostate, and distinct from the previously identified NKX3.1+ luminal castration resistant cells. Using scRNA-seq profiling and genetic lineage tracing, we show that RUNX1+ PLCs are unaffected by androgen deprivation, and do not contribute to the regeneration of the distal luminal compartments. Furthermore, we demonstrate that a transcriptionally similar RUNX1+ population emerges at the onset of embryonic prostate specification to populate the proximal region of the ducts. Collectively, our results reveal that RUNX1+ PLCs is an intrinsic castration-resistant and self-sustained lineage that emerges early during prostate development and provide new insights into the lineage relationships of the prostate epithelium.
The Clear‐water Paradox of Aquatic Ecosystem Restoration

Anders is a ﬁ sheries scientist and an associate consultant with Cramer Fish Sciences and serves as afﬁ liate faculty in the University of Idaho’s Department of Fish and Wildlife Resources in Moscow, Idaho. He can be reached at anders@ﬁ shsciences.net. Ashley is a limnologist and environmental engineer with the Greater Vancouver Regional District and an adjunct professor in the Civil Engineering Department at the University of British Columbia, Vancouver.
Environmental conditions define the energetics of bacterial dormancy and its antibiotic susceptibility

Bacterial cells that stop growing but maintain viability and the capacity to regrow are termed dormant and have been shown to transiently tolerate high concentrations of antimicrobials. The proposed mechanism behind the enhanced survival capabilities of these cells is the reduced energy supply. However, not all reported results are in agreement, and the exact role of energetics remains unsolved. Because dormancy merely indicates growth arrest, which can be induced by various stimuli, we hypothesise that dormant cells may exist in a range of energetic states that depend on the environment. We first establish conditions that are capable of inducing dormancy, and subsequently measure the energy profiles they elicit in single dormant cells. Our simultaneous measurements of proton motive force (PMF), cytoplasmic pH and ATP concentrations confirm that dormant cells exhibit characteristic energetic profiles that can vary in level and dynamics, depending on the stimulus leading to growth arrest. We test whether the energetic makeup is associated with survival to antibiotics of different classes and find that, while growth arrest remains the dominant mechanism enabling survival, some correlations with cellular energetics exist. Our results pave the way to a classification of dormant states based on energy profiles, support a novel relationship between environment and drug susceptibility of dormant cells and suggest that knowledge of the conditions present at the infection site is necessary to design appropriate treatments.
Wildlife in dry lake and associated habitats in western New South Wales.

Intermittently and occasionally flooded lakes are common in arid and semi-arid Australia. The wetldry nature of these lakes means that they provide habitat for terrestrial fauna when dry and aquatic fauna when flooded. The fauna of dry lakes in western New South Wales is largely unknown. This study reports on species of small mammals and reptiles trapped in a dry lake in south-western New South Wales, and contrasts them with species trapped in surrounding woodland and shrubland habitats. Information on bird species in these habitats was also drawn on. Small mammals, reptiles and birds showed considerable partitioning between the habitats in the study area. The dry lake provided the main habitat for the two small mammals Smznthopsis crassicaudata and Planlgale gdesi. Reptiles were most speciose and most abundant in the blue bush (Maireana spp.) shrubland, but some reptile species were mainly or entirely confined to the dry lake habitats, or to black box (Eucalyptus largzjlorens) woodland. Birds in the study region were most abundant and most speciose in the black box woodland, with some species confined to blue bush shrubland. The study showed that conservation of all the habitats investigated is necessary to retain the suite of vertebrate species that occupy these landscapes. Key words: small mammals, reptiles, birds, arid zone, dry lake, shrubland, woodland, biodiversity: Australia
Soroprevalência de Borrelia burgdorferi latu sensu associada à presença de carrapatos em cães de áreas rurais do Estado do Rio de Janeiro, Brasil

The prevalence of antibodies against Borrelia burgdorferi latu sensu was investigated in dogs from rural areas of seven towns of the Rio de Janeiro State, Brazil, using an indirect enzyme-linked immunosorbent assay. All dogs were also examined for the presence of ticks. From the 199 dogs, 15.58% were seropositive, with titers that ranged from 400 (13.57%) to 1600 (0.5%). The positive cases were equally distributed among the seven studied towns. No differences (P > 0.05) were found among the age groups of over six months old. Ticks were found and collected from 71 (35.68%) dogs. From this total, 24.12% were infested with Amblyomma cajennense, 13.6% with Rhipicephalus sanguineus, 2.5% with Amblyomma aureolatum and 1.5% with Amblyomma ovale. Amblyomma cajennense was found in 38.7% and R. sanguineus in 22.6% of the dogs with B. burgdorferi antibodies, although no positive correlation between the ticks parasitism and positive serology was found.
The Influence of Axial Length Upon the Retinal Ganglion Cell Layer of the Human Eye

Purpose We examined the relationship between axial length and the thickness and volume of the ganglion cell layer (GCL) of the retina, and related these measures to the size of the optic chiasm. Methods We used optical coherence tomography to measure the thickness of the GCL over a 50° extent of the horizontal meridian in 50 normally-sighted participants with a wide range of axial lengths. Using a model eye informed by individual biometry, we converted GCL thickness to tissue volume per square degree. The volume of the optic chiasm was measured for 40 participants using magnetic resonance imaging. Results While GCL thickness decreases with increasing axial length, there is a positive relationship between GCL tissue volume and axial length, leading us to conclude that increasing axial length is associated with decreased retinal ganglion cell packing, increased cell size, or both. We characterize how retinal ganglion cell tissue varies systematically in volume and spatial distribution as a function of axial length. This model allows us to remove the effect of axial length from individual difference measures of GCL volume. We find that variation in GCL volume correlates well with the size of the optic chiasm as measured using magnetic resonance imaging. Conclusions Our results provide the volume of ganglion cell tissue in the retina, adjusted for the effects of axial length upon ganglion cell size and/or packing. The resulting volume measure accounts for individual differences in the size of the optic chiasm, supporting its use to characterize the post-retinal visual pathway.
Nutritional status and fecundity are synchronised by muscular exopheresis

Organismal functionality and reproduction depend on metabolic rewiring and balanced energy resources. However, the crosstalk between organismal homeostasis and fecundity, and the associated paracrine signaling mechanisms are still poorly understood. Using the Caenorhabditis elegans we discovered that large extracellular vesicles termed exophers, attributed in neurons and cardiomyocytes to the removal of damaged subcellular components, are released by body wall muscles to support embryonic growth. We found that exopher formation (exopheresis) is a non-cell autonomous process regulated by egg formation in the uterus. Our data suggest that exophers serve as transporters for muscle-generated yolk proteins used for nourishing and improving the growth rate of the next generation. We propose that the primary role of muscular exopheresis is to stimulate the reproductive capacity, thereby influencing the adaptation of worm populations to the current environmental conditions.