Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying cellular dynamics in mice using a novel fluorescent division reporter system

The dynamics of cell populations are frequently studied in vivo using pulse-chase DNA labeling techniques. When combined with mathematical models, the kinetic of label uptake and loss within a population of interest then allows one to estimate rates of cell production and turnover through death or onward differentiation. Here we explore an alternative method of quantifying cellular dynamics, using a cell fate-mapping mouse model in which dividing cells can be induced to constitutively express a fluorescent protein, using a Ki67 reporter construct. We use a pulse-chase approach with this reporter mouse system to measure the lifespans and division rates of naive CD4 and CD8 T cells using a variety of modeling approaches, and show that they are all consistent with estimates derived from other published methods. However we propose that to obtain unbiased parameter estimates and full measures of their uncertainty one should simultaneously model the timecourses of the frequencies of labeled cells within both the population of interest and its precursor. We conclude that Ki67 reporter mice provide a promising system for modeling cellular dynamics.
Omega-3 fatty acids upregulate Nrf2 expression and attenuate apoptosis, inflammation, and fibrosis in a rat model of cyclosporine-induced nephropathy

Background: Cyclosporine A (CsA)-induced kidney injury is characterized by renal impairment with inflammatory cell infiltrations, apoptosis, fibrosis, and hypoxic injury. It is not clear whether omega-3 fatty acids (O-3 FAs), which have anti-inflammatory and antioxidant roles, affect nuclear factor erythroid 2-related factor 2 (Nrf2) expression. The aim of this study was to investigate whether O-3 FAs affect Nrf2 expression and exert anti-inflammatory, anti-apoptotic, and anti-fibrotic effects in CsA-induced nephropathy. Methods: Male Sprague-Dawley rats were divided into control, CsA-treated, and CsA-treated with O-3 FA groups. Nrf2 expression was measured by Western blots and immunohistochemical staining. Results: Kidney function was impaired in the CsA-treated rats compared to the controls. Caspase-3 and caspase-7 were activated in the CsA-treated group, and the Bax/Bcl2 ratio was higher. O-3 FAs attenuated these apoptosis-related changes. ED-1 and inhibition of kappa B (IĸB) protein expression were significantly upregulated in the CsA-treated group. Compared to the control group, O-3 FA supplementation attenuated the increased expression of ED-1 and IĸB related to inflammation. Smad2/3, Smad4, and transforming growth factor-β 1 were activated in the CsA group, and O-3 FA treatment prevented these changes related to renal fibrosis. The expression of Nrf2 was reduced in CsA-treated rats, but Nrf-2 was increased by O-3 FA treatment. Conclusions: We suggest that Nrf2 is a potential mediator induced by O-3 FA supplementation and that it attenuates pro-inflammatory pathways, fibrotic processes, and apoptosis. Further studies are needed to elucidate the crosstalk between Nrf2 expression and signals related to O-3 FA treatment.
PAX7 and MyoD Proteins Expression in Response to Eccentric and Concentric Resistance Exercise in Active Young Men

Objective: Satellite cells play an important role in muscle regeneration, which this process can be affected by different genes including PAX7 and MyoD. Exercise training known as an important strategy for mediating the satellite cell’s function. Therefore, the main purpose of the present study is to investigate the changes in PAX7 and MyoD protein expression in response to eccentric and concentric resistance exercise in healthy young men. Materials and Methods: In this semi-experimental and cross-sectional study, 10 healthy men (age range 18-30 years old) participated. They were randomly divided into two equal groups (n=5) to perform one of two high-intensity eccentric or concentric knee extensions muscle contraction protocols. The contractions included a maximum of 12 sets of 10 repetitions, with a 30 second rest time interval between sets. PAX7 and MyoD protein expression was assessed using Immunohistochemistry analysis from the Vastus Lateralis muscle needle biopsy samples that have been taken 24 hours before and 3 to 4 hours after the end of the exercise protocol. Results: We observed that the PAX7 protein expression level increased significantly after eccentric (47.75%) and concentric (39.21%) (P=0.01) intervention. While, the MyoD protein expression level reduced (38.14%) significantly following acute eccentric resistance exercise (P=0.01). Conclusion: It seems that eccentric or concentric muscular contraction modulates the expression of PAX7 and MyoD protein expression in the skeletal muscle, with further effects observed in eccentric resistance exercise.
Design Techniques for Minimizing Manufacturing Variations in Surface Micromachined Accelerometers

In an effort to improve performance and reduce die area and cost, we have developed an open-loop surface-micromachined accelerometer, the ADXL76. The deposition and etching processes which define the dimensions of the sensing structure can have a wide variation in their characteristics, which can lead to large variations in output sensitivity. This paper describes techniques which were used to design an accelerometer structure that is significantly less sensitive to these dimensional variations. Symmetry was used throughout the structure. In addition to the global four-fold symmetry of the overall structure, local symmetry in the series capacitor unit cells and tether environments was used. This included adding extra etch uniformity structures which make the etch environment around the tethers equivalent to the etch environment around capacitor gaps. The use of these etch uniformity structures increased the correlation between the tether width and the capacitor gap by almost a factor of 4. In addition, the sensors nominal geometry was optimized to minimize the variation of the output sensitivity due to etch and warpage variations. Using these techniques, the ADXL76 accelerometer demonstrated a factor of 2 reduction in the standard deviation of pre-trim sensitivity as compared to an equivalent design that did not use these techniques. This improved sensitivity distribution allows for a smaller trim range, which results in the use of less die area and a faster trim. In addition, the improved correlation between the as-fabricated tether width and capacitor gap allows for more accurate trimming. Thus the overall post-trim sensitivity distribution is much improved as compared to previous closed-loop accelerometer designs.
A High-Certainty Visual Servo Control Method for a Space Manipulator with Flexible Joints

This paper introduces a novel high-certainty visual servo algorithm for a space manipulator with flexible joints, which consists of a kinematic motion planner and a Lyapunov dynamics model reference adaptive controller. To enhance kinematic certainty, a three-stage motion planner is proposed in Cartesian space to control the intermediate states and minimize the relative position error between the manipulator and the target. Moreover, a planner in joint space based on the fast gradient descent algorithm is proposed to optimize the joint’s deviation from the centrality. To improve dynamic certainty, an adaptive control algorithm based on Lyapunov stability analysis is used to enhance the system’s anti-disturbance capability. As to the basic PBVS (position-based visual servo methods) algorithm, the proposed method aims to increase the certainty of the intermediate states to avoid collision. A physical experiment is designed to validate the effectiveness of the algorithm. The experiment shows that the visual servo motion state in Cartesian space is basically consistent with the planned three-stage motion state, the average joint deviation index from the centrality is less than 40%, and the motion trajectory consistency exceeds 90% under different inertial load disturbances. Overall, this method reduces the risk of collision by enhancing the certainty of the basic PBVS algorithm.
Photoemission from Silicon Photodiodes and Induced Changes in the Detection Efficiency in the Far Ultraviolet

Photoemission from semiconductor photodiodes exists as a spurious effect in the detection of radiation in the far ultraviolet. The magnitude of this photoemission effect in silicon transfer standards has been measured and found to be significant in the spectral region from 5 nm to 165 nm. The efficiency of these photodiodes in the more conventional semiconducting mode was altered by this photoemission as much as 14% under some conditions of operation. Application configurations which virtually eliminate the influences of photoemission have been identified and should be employed. The possibility of using these photodiodes in a photoemissive mode (as solar-blind detectors) was found to be limited by the temporal instability and spatial uniformity of the devices tested.
Numerical diffusion in stratified lake models

Three-dimensional numerical models that solve the shallow water equations on a coarse fixed-grid, are limited in their ability to predict internal wave evolution, by the cumulative effects of numerical diffusion. Numerical diffusion of the metalimnion alters the internal response of the basin, and precludes simulations on seasonal to annual time scales. The discrete solution of the equations of motion leads to unintentional smoothing of advected gradients, which irreversibly increases the thickness of the metalimnion. The hydrostatic approximation exacerbates numerical diffusion by steepening internal basin-scale waves due to nonlinear effects until limited by numerical diffusion and dissipation. This steepening enhances horizontal gradients at the wave front which increases numerical diffusion locally, leaving a diffused metalimnion in the wake of the wave front. A method for correcting the numerical diffusion of mass based on conservation of background potential energy is proposed.
Development and Implementation of Efficient Noise Suppression Methods for Emission Computed Tomography

In PET and SPECT imaging, iterative reconstruction is now widely used due to its capability of incorporating into the reconstruction process a physics model and Bayesian statistics involved in photon detection. Iterative reconstruction methods rely on regularization terms to suppress image noise and render radiotracer distribution with good image quality. The choice of regularization method substantially affects the appearances of reconstructed images, and is thus a critical aspect of the reconstruction process. Major contributions of this work include implementation and evaluation of various new regularization methods. Previously, our group developed a preconditioned alternating projection algorithm (PAPA) to optimize the emission computed tomography (ECT) objective function with the non-differentiable total variation (TV) regularizer. The algorithm was modified to optimize the proposed reconstruction objective functions. First, two novel TV-based regularizers—high-order total variation (HOTV) and infimal convolution total variation (ICTV)—were proposed as alternative choices to the customary TV regularizer in SPECT reconstruction, to reduce “staircase” artifacts produced by TV. We have evaluated both proposed reconstruction methods (HOTV-PAPA and ICTV-PAPA), and compared them with the TV regularized reconstruction (TV-PAPA) and the clinical standard, Gaussian post-filtered, expectation-maximization reconstruction method (GPF-EM) using both Monte Carlo-simulated data and anonymized clinical data. Model-observer studies using Monte Carlo-simulated data indicate that ICTV-PAPA is able to reconstruct images with similar or better lesion detectability, compared with clinical standard GPF-EM methods, but at lower detected count levels. This implies that switching from GPF-EM to ICTV-PAPA can reduce patient dose while maintaining image quality for diagnostic use. Second, the 1 norm of discrete cosine transform (DCT)-induced framelet regularization was studied. We decomposed the image into high and low spatial-frequency components, and then preferentially penalized the high spatial-frequency components. The DCT-induced framelet transform of the natural radiotracer distribution image is sparse. By using this property, we were able to effectively suppress image noise without overly compromising spatial resolution or image contrast. Finally, the fractional norm of the first-order spatial gradient was introduced as a regularizer. We implemented 2/3 and 1/2 norms to suppress image spatial variability. Due to the strong penalty of small differences between neighboring pixels, fractional-norm regularizers suffer from similar cartoon-like artifacts as with the TV regularizer. However, when penalty weights are properly selected, fractional-norm regularizers outperform TV in terms of noise suppression and contrast recovery. Development and Implementation of Efficient Noise Suppression Methods for Emission Computed Tomography By Jiahan Zhang B.S., Nankai University, 2011
Conoidin A, a Covalent Inhibitor of Peroxiredoxin 2, Reduces Growth of Glioblastoma Cells by Triggering ROS Production

Compounds that cause oxidative stress have recently gained considerable interest as potential anticancer treatment modalities. Nevertheless, their efficiency may be diminished by the antioxidant systems often upregulated in cancer cells. Peroxiredoxins (PRDXs) are antioxidant enzymes that scavenge peroxides and contribute to redox homeostasis. They play a role in carcinogenesis and are upregulated in several cancer types. Here, we assessed the expression pattern of PRDX1 and PRDX2 in glioblastoma (GBM) and examined the efficacy of their inhibitors in GBM cell lines and patient-derived GBM cells. Both PRDX1 and PRDX2 were upregulated in GBM compared to non-tumor brain tissues and their considerable amounts were observed in GBM cells. Adenanthin, a compound inhibiting PRDX1 activity, slightly decreased GBM cell viability, while conoidin A (CONA), a covalent PRDX2 inhibitor, displayed high toxicity in GBM cells. CONA elevated the intracellular reactive oxygen species (ROS) level. Pre-treatment with an ROS scavenger protected cells from CONA-induced death, indicating that ROS accumulation plays a crucial role in this phenomenon. Menadione or celecoxib, both of which are ROS-inducing agents, potentiated the anticancer activity of CONA. Collectively, our results unveil PRDX1 and PRDX2 as potential targets for GBM therapy, and substantiate the further exploration of their inhibitors.
Temporal constraints on (non-)epistemic readings: Further evidence from Korean

This paper investigates how modal readings are affected by temporal interpretation in natural language sentences, by taking a close look at the Korean swu - construction which can receive multiple modal readings. Previous work on the swu -construction has attributed its modal readings to syntactic structures (e.g. Ha 2007; Chung 2007; Kim 2010) or lexical ambiguity (e.g. Mun 2016; Lee 2017). I discuss empirical and theoretical problems with these approaches, and provide a non-ambiguity analysis, following Kratzer’s (1981; 1991) view that distinct modal readings are contextually determined. I argue that the modal readings are determined by modal-temporal interactions at the semantics-pragmatics interface. Utilizing Condoravdi's (2002) notions of Temporal Perspective (TP) and Temporal Orientation (TO), I provide a novel empirical finding that the non-epistemic readings are available only with future TOs while the epistemic modal reading is not temporally constrained in the swu - construction. I develop a compositional analysis of the temporal interpretation, and account for the (un)availability of (non-)epistemic readings in terms of the temporal constraints on the modal bases, along the same line as Condoravdi (2002) and Rullmann & Matthewson (2018). The analysis proposed in this paper is shown to be empirically and theoretically superior to the previous analyses of the swu - construction, and provides further crosslinguistic support for the theory of modal-temporal interactions proposed by Rullmann & Matthewson (2018).
Pan Arab Journal of Rhinology Pan Arab Journal of Rhinology

Objective: Allergic fungal rhinosinusitis is a fungal infection of paranasal sinuses that often associated with bone destruction with extension outside the sinonasal framework. The objective of this report is to further define these findings as they relate to this disease. Study design: This is a prospective non-randomized case series study. One hundred twenty-three patients with allergic fungal rhinosinusitis were enrolled in this study. Radiological evaluation for every patient was done in the form of computed tomography and\or magnetic resonance image in order to define bone erosion and sinus expansion associated with this type of rhinosinusitis. Results: One hundred and twenty-three cases of proven allergic fungal sinusitis were evaluated. The mean age of the study group was 35.4 and the SD 13.1. The age range was 13 to 61 years. Males comprised 68.3 % of the patients and females 31.7 %. Among 123 enrolled patients, 57.9% of study group showed affection with 54.3% had bone erosion, 21.4% had expansion and 24.3% had both erosion and expansion lesion, 80% of them showed the lesion unilaterally versus 20% had bilateral affection. Conclusion: Bone invasion is a characteristic feature of allergic fungal sinusitis. Orbital and skull base invasion in these cases is not an uncommon finding. Bone invasion should be addressed during evaluation of every case of allergic fungal sinusitis. According to the results of this study, orbital invasion mostly occurs through the medial wall, followed by the roof of the orbit, and lastly through the floor.
Retransmission Reduction using Checkpoint based Sub-Path Routing for Wireless IoT

Wireless IoT has been one of the major breakthroughs of the current decade. It has improved the quality of life and has also aided in several improvements in domains like healthcare. Effective routing and energy conservation has been the major challenges in creating and maintaining a successful IoT network. This work presents a checkpoint based routing model, CSPR, to improve the transmission efficiency by reducing retransmission. This work selects checkpoints in the network prior to transmission. The checkpoints are used to build the final path. This process ensures that the routes created are dynamic and reactive, leading to improved security and increased path reliability. Comparison with existing routing model shows improved network lifetime and reduced selection overhead levels, exhibiting the high efficiency of CSPR.
Perfectly Secure Asynchronous Agreement on a Core Set in Constant Expected Time

A major challenge of any asynchronous MPC protocol is the need to reach agreement on the set of private inputs to be used as input for the MPC functionality. Ben-Or, Canetti and Goldreich [STOC 93] call this problem Agreement on a Core Set (ACS) and solve it by running n parallel instances of asynchronous binary Byzantine agreements. To the best of our knowledge, all results in the perfect and statistical security setting used this same paradigm for solving ACS. This leads to a fundamental barrier of expected Ω (log n ) rounds for any asynchronous MPC protocol (even for constant depth circuits). We provide a new solution for Agreement on a Core Set that runs in expected O (1) rounds, is perfectly secure, and resilient to t < n 4 corrup-tions. Our solution is based on a new notion of Asynchronously Validated Asynchronous Byzantine Agreement (AVABA) and new information theoretic analogs to techniques used in the authenticated model. We show a similar result with statistical security for t < n 3 .
Utilization of Chicken Meat in terms of Physical and Chemical Contamination

Chicken meat products in the presentation process need to pay attention to quality and safety. The nutritional content of broiler chicken meat is quite high when it is stored for more than 2 days it will be easily damaged. This study aims to determine the utilization of ginger by curing method on broiler chicken meat. The research treatments were as follows: T0: Control chicken meat, T1: Chicken meat with the addition of 1% ginger powder, T2: Chicken meat with the addition of 2% ginger powder, T3: Chicken meat with the addition of 3% ginger powder. The scores given are: (1) do not like; (2) rather like; (3) likes; and (4) really like it. Assessment based on a score of 1 - 4 was given by the panelists on the questionnaire that had been provided. The panelists who were asked to carry out the organoleptic assessment were panelists with slightly trained criteria of 8 people. Before carrying out the organoleptic assessment, the panelists were introduced to the material (sample) to be tested by practicing organoleptic testing. The results showed that the T3 treatment was the best treatment in the sensory tests conducted. Based on sensory data regarding the use of chicken meat that is free from physical and chemical contamination, it can be concluded that the quality of chicken meat can be improved in several ways, one of which is by adding ginger so that sensory quality increases. Ginger is proven to be able to reduce the fishy smell of chicken meat and its bioactive components can prevent physical and chemical damage to chicken meat.
AneurysmsHistology in Elastase-Induced, Saccular A Proposed Ordinal Scale for Grading

BACKGROUND AND PURPOSE: The elastase-induced aneurysm model in rabbits, though widely applied, still offers no quantitative or qualitative metric for histologic outcome. This study is aimed at producing such a scale to evaluate outcome and facilitate meaningful, preclinical comparison among devices proposed for aneurysm treatment. MATERIAL AND METHOD: Elastase-induced aneurysms were created and embolized in 30 rabbits. Aneurysms were harvested between 2 and 24 weeks. Specimens were embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The scale comprised 3 subcategories: extent and degree of recanalization/coil compaction; neck healing, based on thickness and type of tissue across the neck; and dome healing. Neck healing was assessed by both gross and microscopic inspections. Compaction was assessed by using both the angiographic and histologic images. Dome healing was assessed by using the microscopic images only. Data were analyzed with either analysis of variance for the quantitative data or Kruskal-Wallis tests when analyzing the nonparametric data. RESULTS: We noted a significant main effect for healing over time ( P (cid:1) . 0016). Post hoc tests showed that, at 2 weeks, the mean score was 1.4 (cid:2) 0.8, as compared with a mean score of 7.2 (cid:2) 1.6 for the 24-week time point ( P (cid:1) . 05). Further, significant differences in healing between narrow-necked (6.0 (cid:2) 1.3) and wide-necked aneurysms (3.5 (cid:2) 1.1) were seen at 4 weeks ( P (cid:1) . 0433). The dynamic range of the scale also appears to be appropriate, because there was adequate range at the upper portion of the scale to reflect improved healing that might be achieved with future devices. CONCLUSIONS: This scale is a potentially relevant outcome measurement tool for elastase-induced aneurysms after endovascular therapy. Future studies are still required to confirm its practical relevance.