Miracle-dz/UniFAR-FTUs huggingface dataset:
GEOGRAPHIC VARIATION IN THE TRADE-OFF BETWEEN NESTLING GROWTH RATE AND BODY CONDITION IN THE TREE SWALLOW

Abstract Nestlings can exhibit considerable variation in developmental patterns both within and among locations due to differences in environmental conditions and parental investment. I investigated trade-offs between nestling growth rate and residual body mass (body condition) at three locations across the range of the Tree Swallow (Tachycineta bicolor). Nestlings at the northern extreme of the range in Alaska had slower growth rates, lower body mass, and higher residual body mass than nestlings in New York and Tennessee. High insect availability was correlated with increased growth rates of nestlings in New York and Tennessee, but not in Alaska. Conversely, nestlings in Alaska showed increased residual body mass with high insect availability, but nestlings in New York and Tennessee did not. The trade-off between growth rate and residual body mass varied among sites, with fast-growing nestlings in Tennessee maintaining a higher residual body mass than those in Alaska. These results suggest that factors affecting offspring growth and condition vary among sites, leading to geographical differences in offspring development trajectories.
The Complete Mitochondrial Genome of Suidasia nesbitti and Phylogenetic Relationships of Astigmata

Astigmata Sarcoptiformes is an important suborder of mites due to their economic and public health impacts. Astigmata mites are commonly found in house dust, stored food products, or decaying organic matter. They negatively affect the quality of stored goods and can trigger an allergic response in humans. There are 13 species of Astigmata in GenBank with complete mt genomes. The positions of some mite genes relative to each other exhibit rearrangement, such as in Histiostomatidae mites (Lee and Wang, 2016; Xue et al., 2018). In addition, tRNAs loss has been observed in Trouessartia rubecula (Trouessartiidae) and two Tyrophagus mites (Acaridae; Que et al., 2014; Yang and Li, 2015; Esteban et al., 2018). The mite, Suidasia nesbitti, belongs to the Suidasiidae. However, the Suidasiidae mitochondrial genome has not been reported. The taxonomy of Suidasia remains unclear, and molecular data may be helpful for species classification and phylogenetic analyses (Ernieenor et al., 2018). The genus Suidasia was created in 1905 and placed in the family Rhizoglyphidae (Hora, 1948). Suidasia was later transfered to the Acaridae (Krantz, 1971). Suidasia mites possess a wrinkled cuticle and differ from other genera of Acaridae. Because of this, the genus Suidasia was proposed to be in a separate family (OConnor et al., 1982). Suidasia was placed in Suidasiidae of the Acaroidea by Krantz and Walter (2009). Classification studies solely based on morphological identification are often controversial. Mitochondrial genomes are useful for phylogenetic analyses and can improve the reliability of phylogenetic inference relative to short sequences (Boore, 1999). We obtained the complete sequence of the mitochondrial DNA (mtDNA) of S. nesbitti using next-generation sequencing approaches and de novo assembly. This represents the first complete mitochondrial genome sequenced from the genus Suidasia. A preliminary phylogenetic analysis was constructed based on the 13 PCGs data.
Resistive Approach for Extraction of Bias-Dependent Parasitic Resistance, Mobility and Virtual Gate Length in GaN HEMT

In this work, we introduce a resistive approach to extract various device performance parameters such as contact resistance, mobility and effective gate length. Without passivation of the un-gated region, HEMT device leads to forming of an extra gate length either side of gate called virtual gate length (δ<inf>LG</inf>). Carrier mobility (µ<inf>C</inf>) of 2DEG and δ<inf>LG</inf> also depends upon V<inf>GS</inf> (gate bias). The depleted channel also reduces the device current causing a significant increase in source/drain resistance (R<inf>S</inf>/R<inf>D</inf>).
LSTMSA: A Novel Approach for Stock Market Prediction Using LSTM and Sentiment Analysis

Stock market prediction is one of the most popular use cases for machine learning models. A general model that can predict the rise and fall of stocks is an arduous task as there maybe multifarious factors that can affect stock prices. This paper attempts to create a model by emulating the approach traders, investors and analysts take to evaluate stock investment strategy. A conjunction of both technical analyses using available numerical data about stocks and fundamental analysis using news headlines are attempted to understand and predict market behavior for the Google stock. For this purpose, sentiment analysis is used to understand news data regarding the stock along with existing time series data as input for an LSTM neural network. It is observed that such an approach yields a more intuitive and accurate yet generalized model that can be used for prediction of the stock market.
Weather effects on corn response to in-season nitrogen rates

Xie, M. , Tremblay, N. , Tremblay, G. , Bourgeois, G. , Bouroubi, M. Y. and Wei, Z. 2013. Weather effects on corn response to in-season nitrogen rates. Can. J. Plant Sci. 93: 407-417. The response of corn yield to in-season nitrogen rate (ISNR) fertilizer applications in a temperate humid climate is conditioned to a great extent by prevailing weather conditions, which affect nitrogen use efficiency and raise the level of uncertainty for making management decisions. A better understanding of the effects of temperature, expressed as accumulated corn heat units (CHU), and precipitation would help to ensure that a “closer-to-optimal” nitrogen rate is supplied at side-dressing. A meta-analysis was performed using a database of nitrogen response trials conducted from 1997 to 2008 in 60 locations in the corn grain production area of Québec, in conjunction with a weather database. Meta-analysis is a statistical procedure for combining results from a series of studies that is used in many fields of research. It is used to assess treatment effect (also called effect size) in a group of studies or experiments. Corn yield response to ISNR was negatively correlated with overall CHU accumulation, but positively correlated with CHU accumulation before side-dressing. Responses also showed a stronger relationship with cumulative precipitation (PPT) before side-dressing than after side-dressing. High and evenly distributed precipitation before side-dressing tended to increase responses to ISNR. It can be concluded that low CHU, low precipitation and low precipitation evenness before side-dressing reduce the impact of ISNR on corn yield.
Exercise Interventions in Polycystic Ovary Syndrome: A Systematic Review and Meta-Analysis

Background: Polycystic ovary syndrome (PCOS) is a common and complex endocrinopathy with reproductive and metabolic manifestations. Exercise training has consistently been found to result in improved clinical outcomes in women with PCOS, but shortfalls with exercise prescription are evident. The aim of this systematic review and meta-analysis was to identify exercise intervention characteristics that provide favourable outcomes in women with PCOS. Methods: A systematic review of published literature was conducted using EBSCOhost and Ovid Medline up to May 2019. The review adheres to the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) guidelines as per our PROSPERO protocol (CRD42018088367). Randomised controlled trials, non-randomised controlled trials, and uncontrolled trials that evaluated an exercise intervention of at least moderate intensity in women with PCOS were included. Meta-analyses were performed using general linear mixed modelling and Bayesian inferences about effect magnitudes. Results: Thirty-three articles were identified for systematic review of which 19 were meta-analysed. Intervention duration ranged from 6 to 26 weeks. A total number of 777 women were included in the meta-analysis. The meta-analysis found that improvements in health outcomes are more dependent on exercise intensity rather than dose. Fixed effects analysis reported a moderate increase in VO2peak (24.2%; 90% CL, 18.5–30.1), and small reductions in HOMA-IR (−36.2%; 90% CL, −55.3 to −9.0), and waist circumference (−4.2%; 90% CL −6.0 to −2.3) as a result of vigorous intensity exercise. These results are confirmed in the predicted analysis which reported the greatest improvements in VO2peak, BMI, and waist circumference after vigorous intensity exercise alone or when combined with diet, particularly for women with clinically adverse baseline values. Conclusions: Exercise training in the management of PCOS is becoming more common. Results from our analysis support the use of exercise and suggest that vigorous intensity exercise may have the greatest impact on cardiorespiratory fitness, body composition, and insulin resistance. Our results indicate that, a minimum of 120 min of vigorous intensity per week is needed to provide favourable health outcomes for women with PCOS with studies of longer duration required to evaluate outcomes with sustained exercise.
mTOR Inhibitors as Radiosensitizers in Neuroendocrine Neoplasms

Peptide receptor radioligand therapy (PRRT) has evolved as an important second-line treatment option in the management of inoperable and metastatic neuroendocrine neoplasms (NEN). Though high radiation doses can be delivered to the tumors, complete remission is still rare. Radiosensitization prior to PRRT is therefore considered to be a promising strategy to improve the treatment effect. In this study, effect and mechanism of mTOR inhibitors were investigated in a comprehensive panel of five NEN cell lines (BON, QGP-1, LCC-18, H727, UMC-11), employing assays for cellular proliferation, clonogenic survival, cell cycle modification and signaling. mTOR inhibition lead to growth arrest with a biphasic concentration-response pattern: a partial response at approximately 1 nM and full response at micromolar concentrations (8-48 μM). All cell lines demonstrated elevated p70S6K phosphorylation yet also increased phosphorylation of counterregulatory Akt. The pulmonary NEN cell line UMC-11 showed the lowest induction of phospho-Akt and strongest growth arrest by mTOR inhibitors. Radiation sensitivity of the cells (50% reduction versus control) was found to range between 4 and 8 Gy. Further, mTOR inhibition was employed together with irradiation to evaluate radiosensitizing effects of this combination treatment. mTOR inhibition was found to radiosensitize all five NEN cells in an additive manner with a moderate overall effect. The radiation-induced G2/M arrest was diminished under combination treatment, leading to an increased G1 arrest. Further investigation involving a suitable animal model as well as radioligand application such as 177Lu-DOTATATE or 177Lu-DOTATOC will have to demonstrate the full potential of this strategy for radiosensitization in NEN.
GREATER EMPATHIC ABILITIES AND THEIR CORELATION WITH RESTING STATE BRAIN CONNECTIVITY IN PSYCHOTHERAPISTS COMPARED TO NON-PSYCHOTHERAPISTS

Psychotherapists constantly regulate their own perspective and emotions to better understand the “other’s” state. We compared 52 psychotherapists with 92 non-psychotherapists to characterized psychometric constructs like, Fantasy (FS) and Perspective Taking (PT), and the emotion regulation strategy of Expressive Suppression (ES), which hampers the empathic response. Psychotherapists showed greater FS, PT and lower ES scores. In a subsample (36, 18 ea.), we did a functional connectivity (FC) study. Psychotherapists showed greater FC between the left anterior insula and the dorsomedial prefrontal cortex; and less connectivity between rostral anterior cingulate cortex and the orbito prefrontal cortex. Both associations correlated with the PT scores and suggest a cognitive regulatory effect related to the empathic response. Considering, that the psychometric differences between groups were in the cognitive domain and that the FC associations are related to cognitive processes, these results suggest that psychotherapists have a greater cognitive regulation over their empathic response.
Growth, yield and reproduction of dwarf tomato grown under simulated microgravity conditions

Abstract A closed hydroponic system combined with a horizontal uniaxial clinostat has been used to grow tomato plants (Solanum lycopersicum L.) under simulated microgravity conditions. The study was carried out to evaluate the quanti-qualitative traits (growth, yield and quality) of the dwarf tomato variety ‘Micro-Tom’ grown under simulated microgravity conditions and to determine if tomato plants would complete their life cycle (‘seed-to-seed’). Morphological and growth characteristics of ‘Micro-Tom’ were modified during clinorotation treatment. The ‘Micro-Tom’ plants grown under simulated microgravity exhibited a spreading growth and an increasing of the internode length. Total fruit yield, small fruit yield, leaf area, leaf dry weight, fruit dry weight, total dry weight and shoot – root ratio were lower in the clinorotated tomato plants than those grown in the control treatment. Foliar amount of carotenoids, and chlorophyll a and b were also substantially reduced under simulated microgravity conditions. Quality parameters (total soluble solids and fruit dry matter) of tomato plants were also negatively affected by clinorotation. The number of flowers per plant was increased by 32% in clinorotated plants versus controls. Fruit setting was reduced by 46% under clinorotation, while no significant difference was recorded for the pollen fertility and the seed number in small and large fruits. Clinorotation-exposed and control seeds were used in a germination trial in order to evaluate whether the seeds so formed were viable and if subsequent generations might be obtained in microgravity. Seeds formed under simulated microgravity proved to be biologically and functionally complete (germination = 78.6%) showing that ‘Micro-Tom’ plants could realize complete ontogenesis, from seed to seed in microgravity.
Population density and temperature influence the return on maternal investment in wild house mice

In mammals, reproduction is influenced by competitive stress, temperature and food availability and these factors might be crucial already during early life. Favourable early life environment and high maternal investment are expected to improve survival and reproduction. In mammals, maternal investment via lactation predicts offspring growth. As body mass is often associated with fitness consequences, females have the potential to influence offspring fitness through their level of investment, which might interact with effects of population density and temperature. Here, we investigate the relationship between pup body mass at day 13 (used as approximation for weaning mass) and individual reproductive parameters as well as longevity under natural variation in population density and temperatures. Further, we assess the extent to which mothers influence the body mass of their offspring until weaning. We analysed life data of 384 house mice (Mus musculus domesticus) from a free-living wild population that was not food limited. We found a complex effect of population density, temperature and maternal investment on life-history traits related to fitness: Shorter longevity with increasing pup body mass at day 13; delayed reproduction of heavier pups when raised at warmer temperatures; and increased lifetime reproductive success for heavier pups at high densities. House mice could use population density and temperature as cues for predicting future environmental conditions, allowing a mother to adjust her investment according to the environment in which offspring will breed in order to maximise fitness. This study highlights the importance of considering ecological conditions in combination with maternal effects.
VELCRO-IP RNA-seq explores ribosome expansion segment function in translation genome-wide

Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units scattered across multiple chromosomal loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. Emerging evidence suggests that expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may provide platforms for the binding of proteins and mRNAs. Here, we develop VELCRO-IP RNA-seq: a versatile methodology to generate species-adapted ESs and map specific mRNA regions across the transcriptome that preferentially associate with ESs. By applying VELCRO-IP RNA-seq to a mammalian ES, ES9S, we identified a large array of mRNAs that are selectively recruited to ribosomes via an ES. We further characterize a set of specific 5’ UTRs that facilitate cap-independent translation through ES9S-mediated ribosome recruitment. These data provide a novel technology for studying the enigmatic ESs of the ribosome in gene-specific translation.
Analysis of slaughter value and muscle fibre thickness of selected muscles in geese broilers as related to feeding applied during the rearing period

Used were 180 White Koluda® W31 geese divided into three groups, 60 birds each, reared as broilers in an intensive system up to the age of 10 weeks. Feeding, which included partial replacement of soybean post-extractive meal with rapeseed or sunflower post-extractive meals and yellow lupin meal, did not significantly differentiate final body weight and the weight of breast and leg muscles of birds. Moreover, it did not significantly affect the superficial breast muscle diameter of the geese, simultaneously changing, however, the diameter of their thigh biceps muscle.
Human bone mesoscale 3D structure revisited by plasma focused ion beam serial sectioning

Visualizing bone mineralization and collagen microfibril organization at intermediate scales between the nanometer and the 100s of microns range, the mesoscale, is still an important challenge. Similarly, visualizing cellular components which locally affect the tissue structure requires a precision of a few tens of nanometers at maximum while spanning several tens of micrometers. To address this issue, we employed a plasma focused ion beam (PFIB) equipped with a scanning electron microscope (SEM) to sequentially section nanometer-scale layers of demineralized and mineralized human femoral lamellar bone over volumes of approximately 46 × 40 × 9 μm3, and 29 × 26 × 9 μm3, respectively. This large scale view retained high enough resolution to visualize the collagen microfibrils while partly visualizing the lacuno-canalicular network (LCN) in three-dimensions (3D). We showed that serial sectioning can be performed on mineralized sections, and does not require demineralization. Moreover, this method revealed ellipsoidal mineral clusters, noted by others in high resolution studies, as a ubiquitous motif in lamellar bone over tens of microns, suggesting a heterogeneous and yet regular pattern of mineral deposition past the single collagen fibril level. These findings are strong evidence for the need to revisit bone mineralization over multi-length scales. Graphical Abstract
Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression

The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.
Map of SARS-CoV-2 spike epitopes not shielded by glycans

The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics in epitope mapping.
Retrieval of Surface Soil Moisture From Sentinel-1 Time Series for Reclamation of Wetland Sites

Soil moisture is a key factor in the reclamation of wetland habitats. Understanding the distribution and relative amount of water can be critical in reintroducing trees and grasses to disturbed soils. Soil moisture is also one of the main factors affecting microwave radar backscatter from the ground; while there are other factors determining backscatter levels (for instance, surface roughness, vegetation, and incident angle), relative variations in soil moisture can be estimated using space-based, high resolution, multitemporal synthetic aperture radar (SAR). In this work, relative soil moisture indicators are derived from a time series of Sentinel-1 SAR data over previously mined oil sands in Alberta, Canada. The algorithm provides a relative assessment of soil moisture and requires calibration over wet and dry periods. An evaluation of the soil moisture product is validated using in situ measurements at multiple sites with observations showing agreement from May to August. Comparisons with precipitation records show that SAR derived surface soil moisture is influenced by discreet precipitation events; that is, rainfall that is coincident with the satellite observation reduces the effectiveness of the measurement. The resulting algorithm controls for rain events by including local weather records to adjust estimates based on the known precipitation.
Predicting the Influence of MicroRNAs on Drug Therapeutic Effects by Random Walking

The emergence of drug resistance is one of the main reasons for the failure of disease treatment. More and more studies have shown that miRNAs are associated with the resistance or sensitivity of certain therapeutic drugs by regulating target genes. However, only a few associations have been reported between miRNAs and drug resistance or sensitivity. In this study, we first constructed a heterogeneous network by integrating the miRNA similarity network, drug similarity network and miRNA-drug effect associations network. Subsequently, we predicted the potential miRNA-drug effect associations by the Bi-Random walk (BiRW) algorithm. The cross-validation and De novo validation methods were applied to verify the prediction performance. Results show that the proposed method can effectively predict potential miRNA-drug effect associations. This study will enhance our understanding of the important roles of miRNAs in drug therapeutic effects and provide a valuable resource for designing effective therapeutic strategies.