Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel enhanced GFP‐positive congenic inbred strain establishment and application of tumor‐bearing nude mouse model

Transgenic GFP gene mice are widely used. Given the unique advantages of immunodeficient animals in the field of oncology research, we aim to establish a nude mouse inbred strain that stably expresses enhanced GFP (EGFP) for use in transplanted tumor microenvironment (TME) research. Female C57BL/6‐Tg(CAG‐EGFP) mice were backcrossed with male BALB/c nude mice for 11 generations. The genotype and phenotype of novel inbred strain Foxn1nu.B6‐Tg(CAG‐EGFP) were identified by biochemical loci detection, skin transplantation and flow cytometry. PCR and fluorescence spectrophotometry were performed to evaluate the relative expression of EGFP in different parts of the brain. Red fluorescence protein (RFP) gene was stably transfected into human glioma stem cells (GSC), SU3, which were then transplanted intracerebrally or ectopically into Foxn1nu.B6‐Tg(CAG‐EGFP) mice. Cell co–expression of EGFP and RFP in transplanted tissues was further analyzed with the Live Cell Imaging System (Cell’R, Olympus) and FISH. The inbred strain Foxn1nu.B6‐Tg(CAG‐EGFP) shows different levels of EGFP expression in brain tissue. The hematological and immune cells of the inbred strain mice were close to those of nude mice. EGFP was stably expressed in multiple sites of Foxn1nu.B6‐Tg(CAG‐EGFP) mice, including brain tissue. With the dual‐fluorescence tracing transplanted tumor model, we found that SU3 induced host cell malignant transformation in TME, and tumor/host cell fusion. In conclusion, EGFP is differentially and widely expressed in brain tissue of Foxn1nu.B6‐Tg(CAG‐EGFP), which is an ideal model for TME investigation. With Foxn1nu.B6‐Tg(CAG‐EGFP) mice, our research demonstrated that host cell malignant transformation and tumor/host cell fusion play an important role in tumor progression.
Complete Genome Sequence of a Gram-Positive Bacterium, Leifsonia sp. Strain PS1209, a Potato Endophyte

We report the complete and annotated genome sequence of a Gram-positive bacterium, Leifsonia sp. strain PS1209, a potato endophyte that was isolated from apparently healthy tubers of potato cultivar NY166. The circular genome is 4,091,164 bp long, with a GC content of 69.08%, containing 3,926 genes. ABSTRACT We report the complete and annotated genome sequence of a Gram-positive bacterium, Leifsonia sp. strain PS1209, a potato endophyte that was isolated from apparently healthy tubers of potato cultivar NY166. The circular genome is 4,091,164 bp long, with a GC content of 69.08%, containing 3,926 genes.
The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability

ABSTRACT The main transcriptional regulator of leucine biosynthesis in the yeast Saccharomyces cerevisiae is the transcription factor Leu3. It has previously been reported that Leu3 always binds to its target genes, but requires activation to induce their expression. In a recent large-scale study of high-resolution transcription factor binding site identification, we showed that Leu3 has divergent binding sites in different cultivation conditions, thereby questioning the results of earlier studies. Here, we present a follow-up study using chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate the influence of leucine supplementation on Leu3 binding activity and strength. With this new data set we are able to show that Leu3 exhibits changes in binding activity in response to changing levels of leucine availability.
Improving estimates of diving lung volume in air-breathing marine vertebrates

ABSTRACT The air volume in the respiratory system of marine tetrapods provides a store of O2 to fuel aerobic metabolism during dives; however, it can also be a liability, as the associated N2 can increase the risk of decompression sickness. In order to more fully understand the physiological limitations of different air-breathing marine vertebrates, it is therefore important to be able to accurately estimate the air volume in the respiratory system during diving. One method that has been used to do so is to calculate the air volume from glide phases – periods of movement during which no thrust is produced by the animal – which many species conduct during ascent periods, when gases are expanding owing to decreasing hydrostatic pressure. This method assumes that there is conservation of mass in the respiratory system, with volume changes only driven by pressure. In this Commentary, we use previously published data to argue that both the respiratory quotient and differences in tissue and blood gas solubility potentially alter the mass balance in the respiratory system throughout a dive. Therefore, near the end of a dive, the measured volume of gas at a given pressure may be 12–50% less than from the start of the dive; the actual difference will depend on the length of the dive, the cardiac output, the pulmonary shunt and the metabolic rate. Novel methods and improved understanding of diving physiology will be required to verify the size of the effects described here and to more accurately estimate the volume of gas inhaled at the start of a dive. Summary: Various factors affect our ability to accurately determine lung capacity during diving in air-breathing marine vertebrates; improving our estimates has implications for our understanding of the physiology and ecophysiology of these animals.
Stepped osteotomy of femoral head autograft for acetabular reconstruction in total hip arthroplasty for dysplasia of the hip: 3 to 12 years’ results

Objectives This study aims to describe a stepped osteotomy technique applied to the femoral head autograft to keep the graft volume at a sufficient level, provide primary stability, and direct cancellous-cancellous bone contact. Patients and methods In this retrospective study, 24 hips of 20 patients (5 males, 15 females; mean age 53 years; range, 43 to 68 years) with dysplasia of the hip (DDH) who underwent total hip arthroplasty with femoral head stepped osteotomy technique were evaluated between April 2003 and June 2010. Patients’ age, gender, operation side, and postoperative complications were recorded. Aseptic loosening of the acetabular cup and graft integration/resorption were evaluated radiographically. Radiological evaluations were performed according to the methods of DeLee and Charnley, and Mulroy and Harris. Functional status of the patients was determined according to the criteria of Merle d’Aubigné and Postel, and Harris hip score (HHS). Results The mean follow-up period was 5.5 years (range, 3 to 12 years). None of the patients had any complications in the early postoperative period. In all patients, the percentage of acetabular component coverage by the graft was measured as 27% (range, 19 to 38%) on average. At the last follow-up, all patients were satisfied with the result and there was no sign of clinically loosening, osteointegration was complete, and there was no radiographic evidence of graft resorption or collapse of any hip. The overall Merle d’Aubigné scores and HHSs of the patients significantly improved at the final follow-up. Conclusion This stepped osteotomy technique increases the probability of osteointegration, reduces the need for early revision, and provides reliable stability with satisfactory clinical and radiological midterm results.
Robust Control of Three Axis Gimbal System Using Finite Time Disturbance Estimation

This paper presents finite time estimation of state and disturbance for three axis gimbal system (TAGS). The system has complex coupled dynamics. Cross torques act as an additional disturbance which affects the performance. Higher order sliding mode observer (HOSMO) is proposed for estimating state and disturbance caused by cross torque together with external disturbance. The disturbance is considered as additional state and HOSMO is designed for extended state system. It is shown by simulation that a simple state feedback controller becomes robust if augmented with estimated disturbance.
Humanoid Robots and Conversational Recommender Systems: a Preliminary Study

Conversational Recommender Systems (CoRSs) implement a paradigm in which users can interact with the system to define their preferences and discover items that best fit their needs. When the CoRS is implemented as a dialog agent, user and recommender interact by exchanging text messages. However, there is little evidence on how effective the interaction is when the CoRS is implemented through a Social Humanoid Robot. In this paper, we evaluate the possibility of introducing an interface based on a Social Humanoid Robot in ConveRSE, a domain-independent framework for the development of Conversational Recommender Systems. The novel interface will be compared against the existing chatbot-based one. The objective is to discover whether the framework can adapt to the new interface without worsening user experience and accuracy. We carried out a preliminary study, which involved 20 subjects. Results proved that, even though there are differences in how users approach the system using the two interfaces, there is no significant difference in its performance.
A Simplified Model-Free Self-Evolving TS Fuzzy Controller for Nonlinear Systems with Uncertainties

This paper proposes a self-evolving Takagi-Sugeno fuzzy controller for nonlinear systems with uncertainties. The self-evolving framework is used to add and prune fuzzy rules in an online manner. Our proposed nonlinear controller is model-free and does not depend on the plant dynamics. All adjustable fuzzy parameters are tuned using a sliding surface, which is derived from the gradient descent learning method to minimize the error between the desired and the actual signals. Unlike most of the existing self-evolving controllers, where a hybrid technique is required to determine the control action, our proposed algorithm is able to construct the final control signal, which can be fed directly to control a nonlinear system. The tracking performance of our proposed controller is validated and compared with an adaptive model-based fuzzy controller in the presence of external disturbances, where better tracking results are obtained from our proposed controller.
Existence and uniqueness of solutions to uni-axial elastic-plastic wave interactions

This paper treats the propagation of stress waves through an elastic-plastic medium on the assumption of uni-axial displacement. With the further simplification to a piecewise linear stress-strain curve in terms of engineering stress and strain, wave equations are obtained for the longitudinal stress in both elastic and plastic regions, each with a distinct constant Lagrangian wave speed. The stress distribution in any region is then simply expressed in terms of two wave functions. In a general motion the medium will be divided into a sequence of alternating elastic and plastic regions separated by moving interfaces. A detailed analysis is presented for a single-interface wave interaction under general initial conditions, namely, continuous initial waves in the two directions in both elastic and plastic regions with a non-uniform yield stress in the elastic region. For different sets of initial conditions six distinct types of solution are shown to exist, and these are classified according to the direction and speed of the interface. In particular, two types involve interface speeds in excess of the elastic wave speed, not, to the authors’ knowledge, demonstrated in previous plastic wave treatments, noting the absence of possible shock formation for the present linearized stress-strain laws. Further, it is shown that stress discontinuities cannot form at the interface (or elsewhere) from initially continuous stress profiles. Associated with the different types of solution are four distinct sets of interface conditions so that there is no common form for the interaction solution. Each of the six types of solution is shown to be consistent with the elastic-plastic model only under a restricted set of initial conditions, and these sets are found to be mutually exclusive for the six types, thus deciding a unique choice for the type of single-interface solution. The six sets, however, are not inclusive of all possible initial conditions, indicating a need for multi-interface solutions in the exceptional situations. Multi-interface solutions may be possible even in the non-exceptional situations, but this possibility is felt to be unlikely. Finally, it can be noted that the analysis dealing with validity of solution is, for most cases, only local in that it applies in some small neighbourhood of the current point on the interface path, being based on expansions about this point. The results of such local analysis will therefore extend to the case of non-uniform wave speeds arising from non-linear stress-strain laws, provided that no shock is formed in the neighbourhood, but a global solution can no longer be expressed simply in terms of wave functions.
The role of CAM in high rainfall cloud forests: an in situ comparison of photosynthetic pathways in Bromeliaceae

Crassulacean acid metabolism (CAM), an advanced photosynthetic pathway conferring water conservation to plants in arid habitats, has enigmatically been reported in some species restricted to extremely wet tropical forests. Of these, epiphytic Bromeliaceae may possess absorbent foliar trichomes that hinder gas-exchange when wetted, imposing further limitations on carbon dioxide (CO 2 ) uptake. The hypothesis that the metabolic plasticity inherent to CAM confers an ecological advantage over conventional C 3 plants, when constant rainfall and mist might inhibit gas-exchange was investigated. Gas-exchange, fluorometry and organic acid and mineral nutrient contents were compared for the bromeliads Aechmea dactylina (CAM) and Werauhia capitata (C 3 ) in situ at the Cerro Jefe cloud forest, Panama (annual rainfall >4m). Daily carbon gain and photosynthetic nutrient use efficiencies were consistently higher for A. dactylina, due to a greater CO 2 uptake period, recycling of CO 2 from respiration and a dynamic response of CO 2 uptake to wetting of leaf surfaces. During the dry season CAM also had water conserving and photoprotective roles. A paucity of CAM species at Cerro Jefe suggests a recent radiation of this photosynthetic pathway into the wet cloud forest, with CAM extending diversity in form and function for epiphytes.
Effects of microbial phytase on the standardized total tract digestibility of phosphorus in soybean meal, corn, and corn co-products

25 INTRODUCTION 26 MATERIALS AND METHODS 27 RESULTS 322 vii DISCUSSION 34 LITERATURE CITED 40 CHAPTER 4: EFFECTS OF A NOVEL PHYTASE IN CORN-SOYBEAN MEAL FED TO WEANLING AND GROWING PIGS 58 ABSTRACT 58 INTRODUCTION 59 MATERIALS AND METHODS 60 RESULTS 64 DISCUSSION 67 LITERATURE CITED 70 CHAPTER 5: EFFECTS OF GRADED LEVELS OF PHYTASE ON APPARENT AND STANDARDIZED TOTAL TRACT DIGESTIBILITY OF PHOSPHORUS IN CORN AND CORN CO-PRODUCTS 89 ABSTRACT 89 INTRODUCTION 90 MATERIALS AND METHODS 91 RESULTS 94 DISCUSSION 96 LITERATURE CITED 100 CHAPTER 6: CONCLUSIONS 111
Magnetic Micromanipulation for In Vivo Measurement of Stiffness Heterogeneity and Anisotropy in the Mouse Mandibular Arch

The mechanical properties of tissues are pivotal for morphogenesis and disease progression. Recent approaches have enabled measurements of the spatial distributions of viscoelastic properties among embryonic and pathological model systems and facilitated the generation of important hypotheses such as durotaxis and tissue-scale phase transition. There likely are many unexpected aspects of embryo biomechanics we have yet to discover which will change our views of mechanisms that govern development and disease. One area in the blind spot of even the most recent approaches to measuring tissue stiffness is the potentially anisotropic nature of that parameter. Here, we report a magnetic micromanipulation device that generates a uniform magnetic field gradient within a large workspace and permits measurement of the variation of tissue stiffness along three orthogonal axes. By applying the device to the organ-stage mouse embryo, we identify spatially heterogenous and directionally anisotropic stiffness within the mandibular arch. Those properties correspond to the domain of expression and the angular distribution of fibronectin and have potential implications for mechanisms that orient collective cell movements and shape tissues during development. Assessment of anisotropic properties extends the repertoire of current methods and will enable the generation and testing of hypotheses.
Stub Loaded Dual-Mode Dipole Antenna for Wide Bandwidth in a Compact Size

In this paper, a compact and broadband dual-mode dipole antenna is proposed. Mode compression is utilized to achieve broad bandwidth in a compact-sized antenna. Third-order mode of the dipole antenna is compressed in the vicinity of the fundamental mode. This is done by loading stubs to the dipole arms. The loading point and the stub size play a crucial role to achieve broad bandwidth. The proposed antenna was fabricated. Antenna measurements were also carried out to validate the simulation results. Good compliance is observed in the simulated and measured results.
Using Human-Imprinted Chicks to Evaluate the Importance of Forbs to Sage-Grouse

Abstract Although several studies have indicated the importance of forbs in brood habitats, no studies have quantified direct effects of the amount of forb cover on sage-grouse (Centrocercus urophasianus) chicks. In 2002 and 2003, we conducted field experiments in Middle Park and Moffat County, Colorado, USA, respectively. Our objective was to quantify effects of 3 levels of forb cover in brood habitat on mass gain and feather growth of human-imprinted sage-grouse chicks. The results indicate that increasing forb cover in brood areas with <20% forb cover may lead to increased chick survival and grouse productivity.
Effects of Variable Life History and Insect Herbivores on Reproduction in Solidago macrophylla (Asteraceae) on an Elevational Gradient

Abstract This study documents variation in the number of florets per flower head and the number of flower heads per flowering shoot for individuals of Solidago macrophylla, a perennial composite, on an elevational gradient in the White Mountains of New Hampshire, and asks if variation in floret distribution vs. plant insect attack predicts variation in reproductive success. Fifteen populations were censused over 2–3 yr to document the number of florets per head, the number of heads per shoot, aphid infestation and seedling emergence per flowering shoot. Additionally, levels of seed predation by tephritid flies were measured during the final year. Flowering shoots in populations at higher elevations produced significantly more florets per head and fewer flowering heads than flowering shoots in populations at lower elevations. Overall, populations at lower elevations produced more florets than populations at higher elevations. However, this difference in reproductive potential did not result in differential reproduction in either 1993 or 1994. Populations at higher elevations had fewer plants with aphids than populations at lower elevations. In 1993 neither aphid infestation levels nor floral life history traits predicted the mean number of emerging seedlings per shoot in the greenhouse. In 1994 the percent of flowering shoots per population with aphids was a significant negative predictor of the mean number of emerging seedlings per shoot in the greenhouse, whereas the number of seed predators per head per shoot was a significant positive predictor of the number of emerging seedlings. Floral life history traits did not predict reproduction in 1994. Finally, patterns of seedling emergence over the environmental gradient resulted in a greater opportunity for selection in lower vs. higher elevation populations.
An Arctic-Alpine Lichen New to England

Note, Collema nigrescens rarely has isidia, but when present they are globular or slightly flattened, and are most prevalent on diseased or damaged parts, The thallus is thicker than in Csubnigrescens3 ((60) 90 = 150Athick when moist as against 60 IOOJU in the latter), and more densely pustulate and ridged; the apothecia are numerous, and the spores 50 90 (112) x 3 4,5^ as against (34) 40 75 x 6-5 (7)p in C, subnigrascens,
Recruitment and Dominance of Quercus rubra and Quercus alba in a previous Oak-Chestnut Forest from the 1980s to 2008

Abstract This study documents 25 y of change in the abundance of Quercus rubra (northern red oak) and Quercus alba (white oak), in a previous chestnut (Castanea castanea)-oak forest in the Southern Appalachians of the eastern U.S.A. Spatially explicit data from 1983–1984 and 2007–2008 of individually mapped trees on two plots in southwestern Virginia were used to examine how the basal area and density of all tree species changed, with specific attention to recruitment, growth, and mortality patterns of Q. rubra and Q. alba. Since the 1980s there has been an increase in the number of shade tolerant trees, primarily Acer pensylvanicum (striped maple), and a decrease in the number of shade intolerant and intermediate shade tolerant trees, including both Q. rubra and Q. alba. We found a negative correlation between A. pensylvanicum abundance and Quercus seedling abundance and a positive correlation between light availability and Quercus seedling abundance. Both Q. rubra and Q. alba have experienced self-thinning, and the previous oak-chestnut forest will likely become increasingly dominated by maples and other shade tolerant species.
Satellite and Ground Based Rainfall Measurement Relationship in Kurdistan Region, Iraq

Remote sensing [RS] of hydrologic processes is becoming increasingly popular tool for frequent, consistent, reliable and cost-effective hydrologic data collection and monitoring. Remote Sensing and space borne measurement systems are in use to observe, detect, and monitor hydrologic parameters such as precipitation, evapotranspiration, soil moisture, and vegetation, etc. However, the satellite-based measurements are prone to errors due to a number of factors related to the atmosphere, environment, sensor sensitivity, and the instrument itself. Remote Sensing data need proper analysis, calibration, and validation before its implementation to real life problems. Amongst other hydrologic measurements, rainfall is also measured by satellites. The Tropical Rainfall Measuring Mission [TRMM] was one of the main satellites deployed for precipitation measurements. Like other Remote Sensing measurements, rainfall measurements are also affected by a variety of factors, which necessitate verifying its validity with some reference measurements. In this study, the TRMM measurements are compared with the ground-based measurements, for six gauging stations in Iraqi Kurdistan Region for years between 2000 and 2016, by using various methods. These include arithmetic differences, Pearson's correlation coefficient R, relative bias and root mean square error [RMSE]. It is found that a strong to medium correlation exist between the point measurements and the corresponding satellite pixel measurements.
Red–blue plots for detecting clusters in count data

A new index and four new graphical displays, termed "red-blue" plots, are presented to study and measure clustering in spatially referenced count data. The index can detect clusters in the form of patches, comprising several nearby large counts, and in the form of gays, comprising several nearly small counts. The new methods quantify the degree to which the count for each sample unit contributes towards the overall degree of clustering, either as part of a patch or as a gap; provide tests of nonrandomness to detect clustering; and facilitate a comprehensive definition of the size and dimension of a cluster. The methods are illustrated using aphid field data.