Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiated human airway organoids to assess infectivity of emerging influenza virus

Significance Influenza virus infection represents a major threat to public health worldwide. There is no biologically relevant, reproducible, and readily available in vitro model for predicting the infectivity of influenza viruses in humans. Based on the long-term expanding 3D human airway organoids, we developed proximal differentiation and further established a 2D monolayer culture of airway organoids. The resultant 3D and 2D proximal differentiated airway organoids can morphologically and functionally simulate human airway epithelium and as a proof of concept can discriminate human-infective influenza viruses from poorly human-infective viruses. Thus, the proximal differentiated airway organoids can be utilized to predict the infectivity of influenza viruses and, more broadly, provide a universal platform for studying the biology and pathology of the human airway. Novel reassortant avian influenza H7N9 virus and pandemic 2009 H1N1 (H1N1pdm) virus cause human infections, while avian H7N2 and swine H1N1 virus mainly infect birds and pigs, respectively. There is no robust in vitro model for assessing the infectivity of emerging viruses in humans. Based on a recently established method, we generated long-term expanding 3D human airway organoids which accommodate four types of airway epithelial cells: ciliated, goblet, club, and basal cells. We report differentiation conditions which increase ciliated cell numbers to a nearly physiological level with synchronously beating cilia readily discernible in every organoid. In addition, the differentiation conditions induce elevated levels of serine proteases, which are essential for productive infection of human influenza viruses and low-pathogenic avian influenza viruses. We also established improved 2D monolayer culture conditions for the differentiated airway organoids. To demonstrate the ability of differentiated airway organoids to identify human-infective virus, 3D and 2D differentiated airway organoids are applied to evaluate two pairs of viruses with known distinct infectivity in humans, H7N9/Ah versus H7N2 and H1N1pdm versus an H1N1 strain isolated from swine (H1N1sw). The human-infective H7N9/Ah virus replicated more robustly than the poorly human-infective H7N2 virus; the highly human-infective H1N1pdm virus replicated to a higher titer than the counterpart H1N1sw. Collectively, we developed differentiated human airway organoids which can morphologically and functionally simulate human airway epithelium. These differentiated airway organoids can be applied for rapid assessment of the infectivity of emerging respiratory viruses to human.
Evidence for Three-Toed Sloth (Bradypus variegatus) Predation by Spectacled Owl (Pulsatrix perspicillata)

Abstract We detected the nighttime death of a radio-collared three-toed sloth (Bradypus variegatus) with an automated radio telemetry system in a Panamanian moist forest. Forensic evidence collected at the fresh carcass, including five pairs of zygodactyl puncture wounds, and the consumption of only soft tissue, suggests that the predator was a large owl, probably Pulsatrix perspicillata. Telemetry data, feces in the sloths' rectum, and old sloth feces at the base of the tree near the carcass suggest that the sloth was descending to the ground to defecate when it was killed. If correct, this is the first record of P. perspicillata killing such a large prey, highlighting the importance of crypsis, and not self-defense, as sloths' anti-predator strategy. This event also suggests there are high risks for sloths climbing to the ground to defecate, a puzzling behavior with no clear evolutionary advantage discovered yet.
The use of velocity-based training in strength and power training-A systematic review

Background: The intensity or load of a strength training exercise is commonly considered to be the most important factor contributing to muscular strength and power. Traditionally in strength training, intensity is defined as the percentage of the maximum weight that can be lifted once i.e. 1 repetition maximum. For power development exercises, the velocity can be used to measure the intensity. A linear position transducer is able to measure kinetic and kinematic variables. Velocity-based training refers to the usage of a linear position transducer to track movement velocity of an exercise and thus, using velocity, rather than load, as a measurement of intensity. Purpose: The purpose of this systematic review was to provide an analysis of the existing velocity-based training research utilizing a linear position transducer. The study also aimed to investigate the validity and reliability of different commercial linear position transducers for kinetic and kinematic measurements. Method: A systematic review was conducted from 19 studies on velocity-based training that met the selection criteria and underwent a quality assessment. Results: It was possible to predict the 1 repetition maximum using velocity and the minimal velocity threshold was stable across different relative intensities. Performing squats at either maximal velocity, or stopping at a velocity loss of <40% could significantly improve 1 repetition maximum, increase mean velocity during a set of squats as well as vertical jump performance. Two linear position transducer were found to have excellent validity and reliability for both kinetic and kinematic measurements. Conclusion: Velocity-based training was beneficial for enhancing neuromuscular adaptions and could be used to predict the 1 repetition maximum. When using of a linear position transducer for power development, it is suggested that it is valid and reliable for both kinetic and kinematic measurements.
Synthesis, characterization and applications of maghemite beads functionalized with rabbit antibodies

Magnetic nanoparticles (NPs) have attracted great attention owing to their applications in the biomedical field. In the present work, maghemite (γFe2O3) NPs of 6.5 nm were prepared using a sonochemical method and used to prepare magnetic beads through silanization with 3-aminopropyltrimethoxysilane (APTS). Subsequently, amino groups in the resulting APTS-γFe2O3 beads were converted to carboxylic acid (CARB-γFe2O3) through the succinic anhydride reaction, as confirmed by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy and dynamic light scattering (DLS) measurements. The size of these beads was measured as 12 nm and their hydrodynamic diameter as 490 nm, using TEM analysis and DLS, respectively. The CARB-γFe2O3 beads were further functionalized by immobilizing rabbit antibodies on their surfaces; the immobilization was confirmed by flow cytometry and ionic strength. The samples were further characterized by Mössbauer spectroscopy and DC magnetization measurements. Studies on magnetic relaxivities showed that magnetic beads present great potential for application in MR imaging.
Modular pathway engineering of key carbon‐precursor supply‐pathways for improved N‐acetylneuraminic acid production in Bacillus subtilis

N‐acetylneuraminic acid (NeuAc) is widely used as a nutraceutical for facilitating infant brain development, maintaining brain health, and enhancing immunity. Currently, NeuAc is mainly produced by extraction from egg yolk and milk, or via chemical synthesis. However, its low concentration in natural resources and its non‐ecofriendly chemical synthesis result in insufficient NeuAc production and environmental pollution, respectively. In this study, improved NeuAc production was attained via modular pathway engineering of the supply pathways of two key precursors—N‐acetylglucosamine (GlcNAc) and phosphoenolpyruvate (PEP)—and by balancing NeuAc biosynthesis and cell growth in engineered Bacillus subtilis. Specifically, we used a previously constructed GlcNAc‐producing B. subtilis as the initial host for NeuAc biosynthesis. First, we constructed a de novo NeuAc biosynthetic pathway utilizing glucose by coexpressing glucosamine‐6‐phosphate acetyl‐transferase (GNA1), N‐acetylglucosamine 2‐epimerase (AGE), and N‐acetylneuraminic acid synthase (NeuB), resulting in 0.33 g/l NeuAc production. Next, to balance the supply of the two key precursors for NeuAc biosynthesis, modular pathway engineering was performed. The optimal strategy for balancing the GlcNAc module and PEP supply module involved the use of an engineered, unique glucose and malate coutilization pathway in B. subtilis, supplied with both glucose (for the GlcNAc moiety) and malate (for the PEP moiety) at high strength. This led to 1.65 g/L NeuAc production, representing a 5.0‐fold improvement over the existing methods. Furthermore, to enhance the NeuAc yield on cell, glucose and malate coutilization pathways were engineered to balance NeuAc biosynthesis and cell growth via the blocking of glycolysis, the introduction of the Entner–Doudoroff pathway, and the overexpression of the malic enzyme YtsJ. NeuAc titer reached 2.18 g/L, with 0.38 g/g dry cell weight NeuAc yield on cell, which represented a 1.32‐fold and 2.64‐fold improvement over the existing methods, respectively. The strategy of modular pathway engineering of key carbon precursor supply pathways via engineering of the unique glucose‐malate coutilization pathway in B. subtilis should be generically applicable for engineering of B. subtilis for the production of other important biomolecules. Our study also provides a good starting point for further metabolic engineering to achieve industrial production of NeuAc by a Generally Regarded As Safe bacterial strain.
Interrepetition Rest Set Lacks the V-Shape Systolic Pressure Response Advantage during Resistance Exercise

Resistance exercise may lead to an aneurysm due to dangerous levels of systemic hypertension. Thus, a minimized pressure response during exercise may guarantee safer training. For that, we analyzed an interrepetition rest design (IRD) hypothesizing that it would produce a lower systolic blood pressure (SBP) response in comparison with a continuous design (CD). Additionally, we studied the effect of accumulated repetitions on the increasing SBP rate during the first continuous set. Fifteen healthy participants (age: 24 ± 2 years; SBP: 113 ± 8 mmHg) performed leg presses, with 40 repetitions and 720 s of total rest, structured in an IRD of individual repetitions (resting time: 18.5 s), and in a CD of five sets of eight repetitions (resting time: 180 s). Analyses reported an increase (p = 0.013) in the mean peaks of SBP in the IRD (162 ± 21 mmHg), versus the CD (148 ± 19 mmHg), while both augmented versus baselines (p < 0.001). Additionally, the linear model estimated a progressive increase of SBP of around 7 mmHg per repetition. Summarily, the IRD produced a higher mean of the SBP peaks during the 40 repetitions due to lacking the v-shape advantage in comparison with the CD.
Treatment Success of Hip and Core or Knee Strengthening for Patellofemoral Pain: Development of Clinical Prediction Rules.

CONTEXT Patellofemoral pain (PFP) is a common injury that interferes with quality of life and physical activity. Clinical subgroups of patients may exist, one of which is caused by proximal muscle dysfunction. OBJECTIVES To develop clinical prediction rules that predict a positive outcome after either a hip and core- or knee-focused strengthening program for individuals with PFP. DESIGN Secondary analysis of data from a randomized control trial. SETTING Four university laboratories. PATIENTS OR OTHER PARTICIPANTS A total of 199 participants with PFP. INTERVENTION(S) Participants were randomly allocated to either a hip and core-focused (n = 111) or knee-focused (n = 88) rehabilitation group for a 6-week program. MAIN OUTCOME MEASURE(S) Demographics, self-reported knee pain (visual analog scale) and function (Anterior Knee Pain Scale), hip strength, abdominal muscle endurance, and hip range of motion were evaluated at baseline. Treatment success was defined as a decrease in visual analog scale score by ≥2 cm or an increase in the Anterior Knee Pain Scale score by ≥8 points or both. Bivariate relationships between the outcome (treatment success) and the predictor variables were explored, followed by a forward stepwise logistic regression to predict a successful outcome. RESULTS Patients with more pain, better function, greater lateral core endurance, and less anterior core endurance were more likely to have a successful outcome after hip and core strengthening (88% sensitivity and 54% specificity). Patients with lower weight, weaker hip internal rotation, stronger hip extension, and greater trunk-extension endurance were more likely to have success after knee strengthening (82% sensitivity and 58% specificity). CONCLUSION The patients with PFP who have more baseline pain and yet maintain a high level of function may experience additional benefit from hip and core strengthening. The clinical prediction rules from this study remain in the developmental phase and should be applied with caution until externally validated.
Flagellum couples cell shape to motility in Trypanosoma brucei

Significance Trypanosoma brucei is a highly invasive pathogen capable of penetrating deeply into host tissues. To understand how flagellar motility facilitates cell penetration, we used cryo-electron tomography (cryo-ET) to visualize two genetically anucleate mutants with different flagellar motility behaviors. We found that the T. brucei cell body is highly deformable as defined by changes in cytoskeletal twist and spacing, in response to flagellar beating and environmental conditions. Based on the cryo-ET models, we proposed a mechanism of how flagellum motility is coupled to cell shape changes, which may facilitate penetration through size-limiting barriers. In the unicellular parasite Trypanosoma brucei, the causative agent of human African sleeping sickness, complex swimming behavior is driven by a flagellum laterally attached to the long and slender cell body. Using microfluidic assays, we demonstrated that T. brucei can penetrate through an orifice smaller than its maximum diameter. Efficient motility and penetration depend on active flagellar beating. To understand how active beating of the flagellum affects the cell body, we genetically engineered T. brucei to produce anucleate cytoplasts (zoids and minis) with different flagellar attachment configurations and different swimming behaviors. We used cryo-electron tomography (cryo-ET) to visualize zoids and minis vitrified in different motility states. We showed that flagellar wave patterns reflective of their motility states are coupled to cytoskeleton deformation. Based on these observations, we propose a mechanism for how flagellum beating can deform the cell body via a flexible connection between the flagellar axoneme and the cell body. This mechanism may be critical for T. brucei to disseminate in its host through size-limiting barriers.
The Role of Mean Absolute Deviation Function in Obtaining Smooth Estimation for Distribution and Density Functions: Beta Regression Approach

Smooth Estimation of probability density and distribution functions from its sample is an attractive and an important problem that has applications in several fields such as, business, medicine, and environment. This article introduces a simple approach but novel for estimating both functions in one process to have smooth curves for both via left mean absolute deviation (MAD) function and beta regression approach. Our approach explores estimation of both functions by smoothing the first derivative of left MAD function to obtain the final optimal smooth estimates. The derivation for these final smooth estimates under conditions of nondecreasing distribution function and nonnegative density function are performed by applying beta regression of a polynomial degree on the first derivative of left MAD function where the degree of polynomial is chosen among the models that have less mean absolute residuals under the constraint of nonnegativity for the first derivative of regression vector of expected values. A general class of normal, logistic and Gumbel distributions is derived as proposed smooth estimators for the distribution and density functions using logit, probit and cloglog links, respectively. This approach is applied to simulated data from unimodal, bimodal, tri-modal and skew distributions and an application to real data set is given.
Probability of beef tenderness in confined cows - a meta-analytic approach

This study aimed to assess the probability of meat tenderness in confined cows. For this purpose, CAPES and SciELO platforms were searched for papers under this subject published in Brazil between 2000 and 2015. A total of 43 articles were found, of which eleven were used. Those selected approached the finishing of confined cows and specified animal genetic group, breed, and age at experiment start. Moreover, all these studies evaluated sensory and organoleptic characteristics of meat, following the same method. Each variable was analyzed by logistic regression, using the LOGISTIC procedure of SAS. The factors were evaluated by odds ratio (OR), in which changes in the probability of meat tenderness were estimated by means of an add-on function in regression variable units. Animal age at the beginning of termination, percentages of zebuine blood and heterozygosity, and marbling score are factors that affect (p < 0.30) the chance of beef tenderness. The probabilities of obtaining a tender meat increase when age at termination beginning and zebuine genotype participation are reduced, as well as when heterozygosity (via crosses) and meat marbling score increases.
Structural Changes in the E. coli Ribosome During Assembly and Cellular Stress

ii Acknowledgments. iii List of Tables . ix List of Figures . x CHAPTER 1: Introduction . 1 1.1 The ribosome . 1 1.2 In vitro ribosome assembly . 2 1.3 In vivo ribosome assembly in eubacteria . 4 1.4 In vivo RNA probing using hydroxyl radical and DMS probing . 8 1.5 Regulation of ribosome assembly and rRNA synthesis . 11 1.6 Ribosomal response to bacterial starvation. 12 1.7 Specific aims . 13 CHAPTER 2: Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting . 22 2.
BIFFOA: A Novel Binary Improved Fruit Fly Algorithm for Feature Selection

Feature selection is an important method to reduce the number of attributes of high-dimensional data and an essential preprocess work in classification. It eliminates irrelevant, redundant, and noisy features improves the performance of the model and reduces the computational burden. Fruit fly optimization algorithm is a new algorithm proposed in recent years, which imitates the foraging behavior of fruit fly. To the best of our knowledge, it has not been systematically applied to feature selection. This paper uses the fruit fly optimization algorithm as a search strategy and designs a wrapper-based feature selection method, named binary improved fruit fly optimization algorithm (BIFFOA). Besides, four different strategies based on evolutionary population dynamics (EPD) and new mutation operators are employed to enhance the BIFFOA. The extensive experiments on 25 datasets (see Table 1) show that the performance of the BIFFOA is better than several state-of-the-art algorithms.
Role of the South Pacific Convergence Zone in West Antarctic Decadal Climate Variability

Regional atmospheric circulation along coastal West Antarctica associated with the Amundsen Sea Low (ASL) mediates ice shelf melt that governs Antarctica's contribution to global sea level rise. In this study, the South Pacific Convergence Zone (SPCZ) is identified as a significant driver of ASL variability on decadal time scales. Using the Community Earth System Model, we impose a positive sea surface temperature anomaly in the SPCZ that reproduces an increase in convective rainfall in the southwest SPCZ that has been observed in recent decades, consistent with the negative phase of the Interdecadal Pacific Oscillation (IPO). Many of the major climate shifts across West Antarctica during the 2000‐2014 period when the IPO was negative can be explained via a teleconnection over the ASL emanating from the SPCZ. Knowledge of these relationships significantly enhances our understanding and interpretation of past and future West Antarctic climate variability.
Geospatial delineation and mapping of groundwater potential in Embu County, Kenya

Integration of Remote Sensing (RS) and the Geographical Information System (GIS) approaches in the field of groundwater resources management is a breakthrough. The RS and GIS geospatial approaches can enhance the assessment, monitoring, and conservation of groundwater resources. In this study, RS and GIS geospatial techniques were applied with the aim of identifying groundwater potential zones in Embu County, Kenya, based on selected multi influencing factors. Lineament layer was obtained by processing Landsat 8 ETM+ image using Principal Component Analysis in ENVI®4.7 and automatic extraction from Principal Component Image using the LINE module in Geomatica software. The resultant groundwater potential map showed that approximately 78% of the total area ranged from ‘high’ to ‘very high’ zones indicating that almost half of the study area has good groundwater potential. About 20% showed moderate potential while only 2% fell under the low potential zone. The proposed study approach can be used as a new way of modeling geospatial data for identification and mapping of groundwater potential zones. The study findings are useful to first-hand information planners and local authorities for assessment, planning, management and administration of groundwater resources in Embu County.
Cookin’: Interactive Cooking Assistant

This report focuses on an interactive system that helps people during cooking by guiding them through the steps of a recipe which is obtained with the Spoonacular API. This involves both text and speech instructions that the system gives to the user, while the user can interact with it by using their voice and poses. In literature, these systems have been explored before, but only certain parts were implemented or it only gave limited feedback during cooking. This system guides a user completely through the process by reading out the equipment, ingredients and steps. Each multimedia component, speech and visuals, will be explored separately and then each component will be connected to the actual system by a user interface. This results in a system that works with textual input at the start, and voice commands and poses during the process where machine learning is used for the recognition of poses and the speech is made more efficient by using more words to recognize commands. Speech recognition is done with the Google Speech Recognition API and Kinect is used for the detection of the joint coordinates of poses. Training is done on a dataset which contains the arm coordinates and that can be extended. For classifying, the k-nearest neighbor algorithm was used since it gives the highest accuracy (99.76%) and is also relatively fast. The value for k is chosen to be 8, based on the amount of poses and a noise class. In the future, other multimedia components can be added to the infrastructure, since it is easily adjustable.