Miracle-dz/UniFAR-FTUs huggingface dataset:
Ataxin 2-binding protein 1 is a context-specific positive regulator of Notch signaling during neurogenesis in Drosophila melanogaster

The role of the Notch pathway during the lateral inhibition that underlies binary cell fate choice is extensively studied, but the context specificity that generates diverse outcomes is less well understood. In the peripheral nervous system of Drosophila melanogaster, differential Notch signaling between cells of the proneural cluster orchestrates sensory organ specification. Here we report functional analysis of Drosophila Ataxin 2-binding protein 1 (A2BP1) during this process. Its human ortholog is linked to type 2 spinocerebellar ataxia and other complex neuronal disorders. Downregulation of Drosophila A2BP1 in the proneural cluster increases adult sensory bristle number, whereas its overexpression results in loss of bristles. We show that A2BP1 regulates sensory organ specification by potentiating Notch signaling. Supporting its direct involvement, biochemical analysis shows that A2BP1 is part of the Suppressor of Hairless [Su(H)] complex in the presence and absence of Notch. However, in the absence of Notch signaling, the A2BP1 interacting fraction of Su(H) does not associate with the repressor proteins Groucho and CtBP. We propose a model explaining the requirement of A2BP1 as a positive regulator of context-specific Notch activity. Summary: Drosophila A2BP1 regulates sensory organ specification by potentiating Notch signaling, forming part of the Suppressor of Hairless complex and acting in a context-dependent manner.
Exploiting Scene Context for Image Captioning

This paper presents a framework for image captioning by exploiting the scene context. To date, most of the captioning models have been relying on the combination of Convolutional Neural Networks (CNN) and the Long-Short Term Memory (LSTM) model, trained in an end-to-end fashion. Recently, there has been extensive research towards improving the language model and the CNN architecture, utilizing attention mechanisms, and improving the learning techniques in such systems. A less studied area is the contribution of the scene context in the captioning. In this work, we study the role of the scene context, consisting of the scene type and objects. To this end, we augment the CNN features with scene context features, including scene detectors, objects and their localization, and their combinations. We use the scene context features as an initialization feature at the zeroth time step in a LSTM model with deep residual connections. In subsequent time steps, the model, however, uses the original CNN features. The proposed language model, contrary to more conventional ones, thus has access to visual features through the whole process of sentence generation. We demonstrate that the scene context features affect the language formation and improve the captioning results in the proposed framework. We also report results from the Microsoft COCO benchmark, where our model achieves the state-of-the-art performance on the test set.
Methods to Improve Establishment and Growth of Bottomland Hardwood Artificial Regeneration

With ongoing attempts to reforest both cut-over and abandoned agricultural land in the lower Mississippi alluvial plain, it has become evident that there exists a need for an efficient regeneration system that makes biological and economic sense. Also, there is a need to address how to minimize oomoetitkm from invading weeds, to deter predation by small mammals, and to achieve adequate tree establishment. This study was designed as a randomized complete block experiment with treatments arranged as factors (3 species X 2 levels of protection X 4 weed control treatments) wlth three replications. to assess efficacy of seedling protection and weed control to improve seedling growth and survival. The study was conducted on a cleared area in the Delta Experimental Forest, Stoneville, MS. Three tree species, Nuttall oak (Quemus &&//ii Palmer), green ash (Fmxhus pennsylvanica Marsh.). and persimmon (Diospyros Virginia L) were planted as 1-O bareroot seedlings in March 1997. Each treatment plot had 25 seedlings, spaced at 0.75 meters X 0.75 meters. Shelter protection was installed on half of the seedlings. Shelters were 1 meter tall, 15 centimeter diameter plastic tree shelters. Each shelter treatment (with or without shelter) received one of four weed control treatments: mechanical mowing (gas-powered weed ctilter), fabric mat (woven, black polypropylene material), chemical herbicide (Oust, suffometurcin-rnethyl at 210 grams per hectare), or undisturbed (control). Response of shelters and weed control treatments on seedling survival, height and diameter were followed for one growing season. Seedlings in shelters had greater survival (98 percent) than seedlings without shelters (93 percent). For all three species, height growth was significantly greater for sheltered seedlings (43 centimeters) compared to unsheltered seedlings (15 centimeters). For the unsheltered seedlings, fabric mat weed control increased survival relative to chemical weed control. All seedlings had significantly greater height and dieter growth under the fabric mat weed control compared to growth under’the other treatments except for unsheltered oak seedlings.
Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Atmospheric nitrogen (N) deposition has enhanced soil carbon (C) stocks in temperate forests. Most research has posited that these soil C gains are driven primarily by shifts in fungal community composition with elevated N leading to declines in lignin degrading Basidiomycetes. Recent research, however, suggests that plants and soil microbes are dynamically intertwined, whereby plants send C subsidies to rhizosphere microbes to enhance enzyme production and the mobilization of N. Thus, under elevated N, trees may reduce belowground C allocation leading to cascading impacts on the ability of microbes to degrade soil organic matter through a shift in microbial species and/or a change in plant–microbe interactions. The objective of this study was to determine the extent to which couplings among plant, fungal, and bacterial responses to N fertilization alter the activity of enzymes that are the primary agents of soil decomposition. We measured fungal and bacterial community composition, root–microbial interactions, and extracellular enzyme activity in the rhizosphere, bulk, and organic horizon of soils sampled from a long‐term (>25 years), whole‐watershed, N fertilization experiment at the Fernow Experimental Forest in West Virginia, USA. We observed significant declines in plant C investment to fine root biomass (24.7%), root morphology, and arbuscular mycorrhizal (AM) colonization (55.9%). Moreover, we found that declines in extracellular enzyme activity were significantly correlated with a shift in bacterial community composition, but not fungal community composition. This bacterial community shift was also correlated with reduced AM fungal colonization indicating that declines in plant investment belowground drive the response of bacterial community structure and function to N fertilization. Collectively, we find that enzyme activity responses to N fertilization are not solely driven by fungi, but instead reflect a whole ecosystem response, whereby declines in the strength of belowground C investment to gain N cascade through the soil environment.
Laboratory evaluations of feed-grade and agricultural-grade phosphates.

Nine samples of pure, feed-grade (FP) and agricultural-grade (AP) phosphates were evaluated at seven laboratories (six in Brazil and one in the U.S.) for physical and chemical characteristics. Phosphates were one "standard" pure dicalcium phosphate; four FP, two dicalcium phosphates (FP-1 and FP-2) made in Brazil, one di-monocalcium phosphate (FP-3), and one defluorinated phosphate (FP-4) made in the U.S.; and four AP made in Brazil [single superphosphate (AP-1), triple superphosphate (AP-2) and monoammonium (AP-3), and thermomagnesium (AP-4) phosphates]. Average analytical values for FP and AP, respectively, were 3.3 and 6.3% moisture, 1.0 and 2.5% insoluble residue, 16.2 and 28.4% loss on ignition, 6.8 and 4.7 (pH), 1,028 and 1,023 g/L apparent density, 9.6 and 55.0% P solubility in water, 83.6 and 88.4% P solubility in 2% citric acid, and 85.2 and 97.0% P solubility in neutral ammonium citrate. Based on particle size, six products were classified as "fine," and three were classified as "irregular. " Atomic absorption and plasma spectrometry determinations were performed for 31 essential and potentially harmful or radioactive minerals. The Na level was high in FP-4 (6.03%). Mineral concentrations were safe for all FP as compared with NRC standards. Levels in AP were toxic, exceeding the tolerance limits for F, Fe, Mg, and Ba, and were particularly high as compared with FP for S, Ti, and radioactive Th. The AP-1 was high in F, Ba, S, and Th; AP-2 and AP-3 were high in F and S; and AP-4 was high in F, Ba, Fe, Mg, Ti, and Th. X-ray diffraction assays detected impurities for all commercial samples and identified as major components CaHPO4*2H2O (standard phosphate), CaCO3 and CaHPO4 (FP-1, FP-2, and FP-3), Ca(H2PO4)2*H2O (FP-3), Na2Ca3Al2(PO4)2(SiO4)2 and Ca3(PO4)2 (FP-4), CaSO4*nH2O and (NH4)Fe3P6O20*(PO4)2 (AP-1), Ca(H2PO4)2*H2O and KFe3P6O20*10H2O (AP-2), (NH4)H2PO4 and CaSO4*nH2O (AP-3), and no definite molecular structure for AP-4, an amorphous product. The biological consequences of feeding animals a mineral source with no definite molecular structure, an amorphous product, is not known. A biological evaluation of all phosphates included in this article is being published as a separate report (Fernandes et al., 1999).
Mucosal‐associated invariant T cells in autoimmune and immune‐mediated diseases

Autoimmune and inflammatory diseases have complex etiologies not fully understood. Both innate and adaptive immune cells are involved in the pathogenesis of these diseases. Mucosal‐associated invariant T (MAIT) cells express an invariant TCRα chain (Vα7.2‐Jα33 in humans and Vα19‐Jα33 in mice) and recognize the conserved MHC‐I‐related molecule MR1 presenting bacterial metabolites derived from the synthesis of vitamin B. MAIT cells harbor tissue homing properties and produce inflammatory cytokines, suggesting that MAIT cells may play a key role in autoimmune and inflammatory diseases. In this review, we described the current knowledge on MAIT cells in these pathologies, based on patients analyses as well as mouse models. While most of the studies support a deleterious role of MAIT cells in tissue inflammation and destruction, a few reports suggest a protective role of MAIT cells. MAIT cells could represent a new biomarker of disease progression, and a better knowledge of their function might open new avenues for therapeutic strategies based on their manipulation.
Predicting mechanical properties of hot-rolling steel by using RBF network method based on complex network theory

Recently, producing high-precision and high-quality steel products becomes the major aim of the large-scale iron and steel enterprises. Because of the internal multiplex components of products and complex changes in the production process, it is too difficult to achieve precise control in hot rolling production process. In this paper, radial basis function neural network is used to complete performance prediction. It has the advantage of fast training and high accuracy, and overcomes shortcomings of BP neural network used previously, such as local minimum. When determining the center of radial basis function we make use of complex network visualization which can clearly figure out the relationship between input vectors and receive the center and width according to the relationship of the nodes. Experiments show that the method that is combining community discovery algorithm and RBF enjoy high stability, small training time which means to be suitable to analysis large-scale data. More importantly, it can reach high accuracy.
Object Detection on Dynamic Occupancy Grid Maps Using Deep Learning and Automatic Label Generation

We tackle the problem of object detection and pose estimation in a shared space downtown environment. For perception multiple laser scanners with $360^{o}$ coverage were fused in a dynamic occupancy grid map (DOGMa). A single-stage deep convolutional neural network is trained to provide object hypotheses comprising of shape, position, orientation and an existence score from a single input DOGMa. Furthermore, an algorithm for offline object extraction was developed to automatically label several hours of training data. The algorithm is based on a two-pass trajectory extraction, forward and backward in time. Typical for engineered algorithms, the automatic label generation suffers from misdetections, which makes hard negative mining impractical. Therefore, we propose a loss function counteracting the high imbalance between mostly static background and extremely rare dynamic grid cells. Experiments indicate, that the trained network has good generalization capabilities since it detects objects occasionally lost by the label algorithm. Evaluation reaches an average precision (AP) of 75.9%.
Operative Management of Distal Tibial Extra-articular Fractures - Intramedullary Nail Versus Minimally Invasive Percutaneous Plate Osteosynthesis.

BACKGROUND The ideal treatment of distal tibial extra articular fractures remains controversial. Minimally invasive percutaneous plate osteosynthesis and intramedullary nailing are the two most commonly used methods. We did a prospective randomized controlled study to assess the functional outcome of distal tibial extra articular tibial fractures by comparing these treatment methods. MATERIALS AND METHODS Sixty patients with distal tibial extra articular fractures were randomly assigned to an IMN (intramedullary nailing) group and a MIPPO (minimally invasive percutaneous plate osteosynthesis) group. All patients were followed up for a period of one year. At final follow-up, clinical and radiological outcome was assessed by foot function index. Malunion, infection, implant removal, time to union and secondary interventions were compared between the two groups. The comparison of continuous variables was performed by using the Student t-test or Mann-Whitney U test in accordance with normality testing. A value of p less than 0.05 was considered statistically significant. RESULTS All patients were followed up for a period of one year. Time to callus formation was equal in both groups. There was no non-union in our series. Malunion was more common in the nailing group. The foot function index was similar in both groups. CONCLUSION MIPPO and intramedullary nailing are effective treatment options in the management of distal tibial extra particular fractures, with comparable functional outcomes.
Seismic Response of Adjacent Steel Structures Connected by Passive Device

In this study, the seismic response of adjacent steel structures linked to one another at different floor levels by passive devices is evaluated. Two types of connectors are considered: linear viscous dampers and linear springs. Various combinations of type and location of the connectors are analyzed for wide ranges of their characteristics. Influence of the structural properties (ratio of number of stories and ratio of fundamental periods) and the properties of the excitation (frequency) on the story response are also investigated. The results show that reduction of the story drift and the floor acceleration is not possible if the structures are connected to one another solely by the springs. However, it is feasible if the structures are linked to one another by either: (a) viscous dampers or (b) combinations of viscous dampers and springs. Herein, response reductions corresponding to case (b) are generally smaller than those corresponding to case (a). Also, the coupling control approach is more effective in controlling the response than the uncoupled approach.
Addressing small sample size bias in multiple‐biomarker trials: Inclusion of biomarker‐negative patients and Firth correction

In recent years, numerous approaches for biomarker‐based clinical trials have been developed. One of these developments are multiple‐biomarker trials, which aim to investigate multiple biomarkers simultaneously in independent subtrials. For low‐prevalence biomarkers, small sample sizes within the subtrials have to be expected, as well as many biomarker‐negative patients at the screening stage. The small sample sizes may make it unfeasible to analyze the subtrials individually. This imposes the need to develop new approaches for the analysis of such trials. With an expected large group of biomarker‐negative patients, it seems reasonable to explore options to benefit from including them in such trials. We consider advantages and disadvantages of the inclusion of biomarker‐negative patients in a multiple‐biomarker trial with a survival endpoint. We discuss design options that include biomarker‐negative patients in the study and address the issue of small sample size bias in such trials. We carry out a simulation study for a design where biomarker‐negative patients are kept in the study and are treated with standard of care. We compare three different analysis approaches based on the Cox model to examine if the inclusion of biomarker‐negative patients can provide a benefit with respect to bias and variance of the treatment effect estimates. We apply the Firth correction to reduce the small sample size bias. The results of the simulation study suggest that for small sample situations, the Firth correction should be applied to adjust for the small sample size bias. Additional to the Firth penalty, the inclusion of biomarker‐negative patients in the analysis can lead to further but small improvements in bias and standard deviation of the estimates.
Semen production, sperm quality, and their heritabilities as influenced by selection for fertility of frozen-thawed semen in the chicken.

Ejaculate volume, sperm concentration, and sperm number per ejaculate were measured six times from 8 to 15 months of age, and testes and body weight at 15 months of age, on Generation 9 males of a line of broiler breeders selected for fertility of frozen-thawed semen and those of a randombred control line. Sperm quality (percent normal, percent abnormal, and percent dead sperm) was determined on Generation 10 males at 11 months of age. Selection decreased (P less than .01) ejaculate volume and sperm number per ejaculate. The control line had 4.9% more abnormal (P less than .05) sperm than the selected line. The differences between the lines for sperm concentration, testes and body weights, and percent dead sperm were not significant (P greater than .05). The correlation coefficients of fertility of frozen-thawed semen with percent abnormal and percent dead sperm were negative but were positive with percent normal sperm. The heritability and repeatability estimates of ejaculate volume, sperm concentration, and sperm number per ejaculate ranged from . 34 to . 73 and . 33 to . 51, respectively.
Association between body mass index and sperm quality and sperm DNA integrity. A large population study

This study aimed to analyse whether the functional quality of spermatozoa is associated with body mass index (BMI). Semen samples were obtained from 1824 men undergoing fertility evaluation/treatment. Semen analysis was performed using World Health Organization (WHO) criteria, and morphology was evaluated with the motile sperm organelle morphology examination (MSOME). The percentages of sperm DNA fragmentation (using TdT (terminal deoxynucleotidyl transferase)‐mediated dUTP nick‐end labelling (TUNEL) assays), sperm chromatin packaging/underprotamination (using chromomycin A3/CMA3), mitochondrial damage (using MitoTracker Green) and apoptosis (using annexin V) were also assessed. At least 200 spermatozoa were examined in each evaluation. The following BMI values were used as cut‐off points: ≤24.9 kg/m2, 25–29.9 kg/m2 (overweight) and ≥30 kg/m2 (obese). High BMI negatively affects sperm concentration, vitality, motility and morphology (p < .05). Conversely, high BMI does not seem to be associated with impaired sperm DNA integrity, as assessed by DNA fragmentation, sperm protamination and sperm apoptosis (p > .05). However, increased BMI is associated with increased mitochondrial damage in spermatozoa (p < .05). In conclusion, given the adverse consequences of obesity and the possible effect of male BMI on assisted reproduction technology (ART) outcomes, the benefits of weight reduction should be discussed when counselling couples interested in fertility treatment.
Correlates of intensity-specific physical activity in children aged 9–11 years: a multilevel analysis of UK data from the International Study of Childhood Obesity, Lifestyle and the Environment

Objectives Physical activity (PA) can provide numerous physical and psychological health gains, yet a low proportion of children in England are sufficiently active to accrue benefit. Analysing the correlates of PA from a socioecological perspective may help to identify factors that promote versus discourage PA. The purpose of the present study was to: (1) assess the relationships between a wide range of potential correlates and intensity-specific PA and (2) explore which correlates are associated with meeting government PA guidelines. Design, setting and participants Cross-sectional study on children aged 9–11 years from the South West of England (n=425; 183 males). Outcome measures A mixture of self-reported and objective measures (eg, body mass index (BMI), accelerometer-derived PA, self-reported sport participation, etc) were collected from child participants, parents and school teachers. After adjusting for covariates (ie, age, sex and accelerometer wear time), multilevel modelling techniques were employed to examine the relationships between potential correlates and light-intensity, moderate-intensity and vigorous-intensity PA, as measured with an ActiGraph GT3X+ accelerometer. Generalised linear mixed modelling was used to analyse the correlates associated with government-recommended levels of PA. Results Computer use shared a negative association whereas parent support for PA showed a positive relationship with light-intensity PA. In terms of moderate-intensity PA, computer use and BMI z-score shared a negative association whereas positive relationships were found for sport participation, active transport and for outdoor time after school. Children at schools with 25%–49% of pupils attending school sport/PA clubs did more moderate-intensity PA than those attending schools with lower participation rates. For vigorous-intensity PA, a negative relationship was observed for BMI z-score, and positive associations for self-efficacy, active transport, parent support and the presence of crossing guards on routes to school. Correlates associated with meeting the PA guidelines were BMI z-score (negative), sport participation, active transport and outdoor time after school (all positive). Conclusion Results demonstrate that factors pertaining to the individual, home and school environment may play an important role in understanding the correlates of differing PA intensities in children. Trial registration number NCT01722500.