Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of diffusion coefficients in live cells using fluorescence recovery after photobleaching with wide-field fluorescence microscopy

Fluorescence recovery after photobleaching (FRAP) enables characterization of quantitative dynamic properties such as diffusion coefficients of fluorescent molecules in living cells by analyzing the recovery of fluorescence intensity after photobleaching in a specific cellular compartment or area. To quantitatively determine high intracellular diffusion coefficients, a suitable optical system as well as an appropriate model for fast diffusion analysis is necessary. Here, we propose a procedure to quantify the diffusion coefficient of rapidly-diffusing fluorescent molecules that makes use of an epi-fluorescence microscope with a photobleaching laser in combination with established models for diffusion analysis. Analysis for the diffusion coefficients of tandemly oligomerized green flurescent proteins (GFPs) in living cells when changing the photobleaching times showed that photobleaching with shorter times than the diffusion speed indicated not the only way to obtain appropriate diffusion coefficients of fast-moving molecules. Our results also showed that the apparent spreading of the effective radius of the photobleached area works as a correction factor for determining appropriate diffusion coefficients of fast-moving molecules like monomeric GFPs. Our procedure provides a useful approach for quantitative measurement of diffusion coefficients in living cells. This procedure is relevant for characterizing dynamic molecular interactions, especially of fast-moving molecules, and is relevant for studies in many biological fields.
Light trapping enhancement in ordered and disordered silicon nanowire based solar cells

In this work we introduce the main principles behind efficient light trapping in silicon nanowire structures. The ultimate performance of vertical periodic crystalline silicon nanowire arrays has been determined and optimized values have been presented as a function of the nanowire length. The further improvement of the performance has been demonstrated using dual-diameter periodic silicon nanowire arrays where the already optimized nanowire structure has been used as the starting point. The improved efficiency of this densely packed structure has been compared with the reference flat films in order to evaluate theoretical improvement of the light trapping efficiency. In the last part of our work we present the efficient light trapping inside amorphous silicon nanowire based radial junction solar cells fabricated using plasma enhanced vapor-liquid-solid process.
Scalable concurrency debugging with distributed graph processing

Existing constraint-solving-based technique enables an efficient and high-coverage concurrency debugging. Yet, there remains a significant gap between the state of the art and the state of the programming practices for scaling to handle long-running execution of programs. In this paper, we revisit the scalability problem of state-of-the-art constraint-solving-based technique. Our key insight is that concurrency debugging for many real-world bugs can be turned into a graph traversal problem. We therefore present GraphDebugger, a novel debugging framework to enable the scalable concurrency analysis on program graphs via a tailored graph-parallel analysis in a distributed environment. It is verified that GraphDebugger is more capable than CLAP in reproducing the real-world bugs that involve a complex concurrency analysis. Our extensive evaluation on 7 real-world programs shows that, GraphDebugger (deployed on an 8-node EC2 like cluster) is significantly efficient to reproduce concurrency bugs within 1∼8 minutes while CLAP does so with 1∼30 hours, or even without returning solutions.
Specimen adequacy of ThinPrep sample preparations in a direct-to-vial study.

OBJECTIVE To assess specimen adequacy of the ThinPrep slide preparation method in routine use. STUDY DESIGN Two studies, a feasibility study of 299 women and a clinical study of 499 women, were conducted. A broom-type collection device was used and rinsed directly into Pre-servCyt vials. Slides were prepared with the ThinPrep 2000 device, screened and classified according to the Bethesda System. The proportion of ThinPrep slides described as "Satisfactory But Limited By: No Endocervical Component (SBLB:No ECC)" was then compared to the proportion of SBLB: No ECC slides found on conventional smears in a previously conducted clinical trial of over 7,000 patients. RESULTS For the feasibility study the proportion of ThinPrep slides described as SBLB: No ECC was 9.36% as compared to the clinical trial combined rate of 9.4% for conventional smears. For the clinical study, 4.96% of ThinPrep slides were SBLB:No ECC as compared to the 4.4% SBLB:No ECC rate for conventional smears from the same clinical trial. The proportions were statistically equivalent for both studies. CONCLUSION It is expected that the rate of representing endocervical component will be maintained when the ThinPrep preparation method is used routinely in place of the conventional cytologic smear method.
Mice lacking desmocollin 1 show epidermal fragility accompanied by barrier defects and abnormal differentiation

The desmosomal cadherin desmocollin (Dsc)1 is expressed in upper epidermis where strong adhesion is required. To investigate its role in vivo, we have genetically engineered mice with a targeted disruption in the Dsc1 gene. Soon after birth, null mice exhibit flaky skin and a striking punctate epidermal barrier defect. The epidermis is fragile, and acantholysis in the granular layer generates localized lesions, compromising skin barrier function. Neutrophils accumulate in the lesions and further degrade the tissue, causing sloughing (flaking) of lesional epidermis, but rapid wound healing prevents the formation of overt lesions. Null epidermis is hyperproliferative and overexpresses keratins 6 and 16, indicating abnormal differentiation. From 6 wk, null mice develop ulcerating lesions resembling chronic dermatitis. We speculate that ulceration occurs after acantholysis in the fragile epidermis because environmental insults are more stringent and wound healing is less rapid than in neonatal mice. This dermatitis is accompanied by localized hair loss associated with formation of utriculi and dermal cysts, denoting hair follicle degeneration. Possible resemblance of the lesions to human blistering diseases is discussed. These results show that Dsc1 is required for strong adhesion and barrier maintenance in epidermis and contributes to epidermal differentiation.
A Comparative Study of Pattern Recognition Algorithms on Sales Data

In the realm of Data Mining looking for patterns and association rules is a very critical task and has been widely studied in the past years. There exist several data mining algorithms to find Association Rules in given datasets. One of the most popular and widely used algorithm is the Apriori algorithm to find patterns and itemsets in huge datasets and getting the association rules between them. This is done to gather knowledge from otherwise unsuspecting and random data. The Fp-Growth algorithm is similarly a different algorithm which uses an extended frequent pattern prefix-tree data structure for storing critical data after compression about frequent pairs. In this paper we do a comparative analysis of the 2 most popular pattern recognition algorithms and their performance on sales data of a college canteen sales transnational database where each record consists of items purchased by customer. General Terms Pattern Recognition, Data Mining, Apriori, Fp-Growth, Frequent Itemsets, Item-pair.
Cytologic Evaluation of Low Grade Transitional Cell Carcinoma and Instrument Artifact in Bladder Washings

OBJECTIVE To identify key cytologic features for the separation of low grade transitional cell carcinomas (TCCs) from nonneoplastic lesions in bladder washings. STUDY DESIGN The cytomorphologic features of 95 bladder washing specimens showing papillary fragments, which included 50 low grade TCCs and 45 nonneoplastic lesions, were reviewed retrospectively. RESULTS Bladder washings from low grade TCCs showed papillary and irregular groups of cells with ragged borders, cytoplasmic homogeneity and subtle nuclear changes, such as increased nuclear/cytoplasmic ratio and irregular nuclear border. Bladder washings after instrumentation from nonneoplastic lesions of the bladder showed cellular specimens with cohesive, ball-shaped and papillary clusters with smooth borders lined with a denser-staining cytoplasmic collar. Reactive urothelial cells often displayed loose aggregates with irregular borders but no cytoplasmic collar. CONCLUSION In bladder washing cytology, nuclear changes and cytoplasmic homogeneity play a major role in the diagnosis of carcinoma.
Fine Needle Aspiration Cytology of Dedifferentiated Acinic Cell Carcinoma of the Parotid Gland

BACKGROUND Dedifferentiation of acinic cell carcinoma (ACC) to undifferentiated carcinoma occurs rarely and entails a poor prognosis. Most cases of dedifferentiation occur as recurrences of a previously excised ACC. More rarely the neoplasm presents with areas of well-differentiated ACC coexisting with dedifferentiated ones. CASE An 85-year-old man presented with 2 nodular areas in the right parotid area. Fine needle aspiration of both nodules was performed. In both cases cytology revealed a double epithelial component in similar proportions. The first one corresponded to cohesive groups of small to intermediate-sized, polygonal cells with round, monomorphic nuclei. They were distributed in small and larger, branching groups with acinic morphology. Intermixed with this population, irregular groups of larger, pleomorphic cells with irregular nuclei, prominent nucleoli and scarce cytoplasm were present. In addition, smears showed an abundant lymphoid background. A cytologic diagnosis of "salivary carcinoma with coexisting areas of acinic cell differentiation and high grade, undifferentiated carcinoma" was given. Histopathology revealed a well-differentiated ACC with areas of high grade undifferentiated carcinoma (dedifferentiated ACC). CONCLUSION The current case expands the cytomorphologic spectrum of ACC. Cytology may permit the preoperative recognition of dedifferentiation, allowing a more sound therapeutic approach.
Generation and characterization of mice with mesenchyme‐specific deletion of the entire ESET histone methyltransferase protein

ESET protein (also known as SETDB1) catalyzes methylation of histone H3 at lysine 9 (H3‐K9). In addition to the full‐length transcript, mouse ESET gene also gives rise to alternative spicing variants encoding truncated proteins capable of retaining interaction with other epigenetic enzymes. To completely eliminate full‐length ESET and its splicing variants, we have generated a conditional ESET allele with exon 4 flanked by two loxP sites for Cre‐mediated DNA deletion and downstream frame‐shift mutation of the entire coding region. Mating with Prx1‐Cre mice and analysis of the resultant embryos revealed that mesenchyme‐specific knockout of exon 4 completely eliminates full‐length ESET and its truncated protein products, leading to profound defects in both the flat bones and long bones, ectopic hypertrophy of growth plate chondrocytes and downregulation of Indian hedgehog protein. In addition, exon 4 deletion results in reduced thickness of articular cartilage in E17.5 embryos, whereas deletion of exons 15–16 fails to do so. These findings offer us a useful tool to further study epigenetic regulation in a truly ESET‐null background, and demonstrate that ESET plays a critical role in the control of chondrocyte hypertrophy and skeletal development.
Spontaneous Facial Mimicry is Modulated by Joint Attention and Autistic Traits

Joint attention (JA) and spontaneous facial mimicry (SFM) are fundamental processes in social interactions, and they are closely related to empathic abilities. When tested independently, both of these processes have been usually observed to be atypical in individuals with autism spectrum conditions (ASC). However, it is not known how these processes interact with each other in relation to autistic traits. This study addresses this question by testing the impact of JA on SFM of happy faces using a truly interactive paradigm. Sixty‐two neurotypical participants engaged in gaze‐based social interaction with an anthropomorphic, gaze‐contingent virtual agent. The agent either established JA by initiating eye contact or looked away, before looking at an object and expressing happiness or disgust. Eye tracking was used to make the agent's gaze behavior and facial actions contingent to the participants' gaze. SFM of happy expressions was measured by Electromyography (EMG) recording over the Zygomaticus Major muscle. Results showed that JA augments SFM in individuals with low compared with high autistic traits. These findings are in line with reports of reduced impact of JA on action imitation in individuals with ASC. Moreover, they suggest that investigating atypical interactions between empathic processes, instead of testing these processes individually, might be crucial to understanding the nature of social deficits in autism. Autism Res 2016, 9: 781–789. © 2015 The Authors Autism Research published by Wiley Periodicals, Inc. on behalf of International Society for Autism Research
Memory behavior profiler for Android applications

In recent years, the embedded devices are very popular, and the smart phone and Tablet PC are the most important consumer electronic products. When programmers design a program on PC, there are a lot of resources can be used to enhance the performance of the program. But the resources on embedded devices are limited. Thus, how to profile and optimize the programs on embedded system becomes an important design issue. In this paper, we design a profiling tool to analyze the memory behaviors of an Android application on the multi-core smartphone. The designer can improve application performance according to the profiled results. The experimental results show that the proposed tool can analyze the memory status of the profiled application.
Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits

Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges and often suffer from low statistical power due to multiple test correction. Here, we present a novel, alternative strategy for mapping epistasis: instead of directly identifying individual pairwise or higher-order interactions, we focus on mapping variants that have non-zero marginal epistatic effects — the combined pairwise interaction effects between a given variant and all other variants. By testing marginal epistatic effects, we can identify candidate variants that are involved in epistasis without the need to identify the exact partners with which the variants interact, thus potentially alleviating much of the statistical and computational burden associated with standard epistatic mapping procedures. Our method is based on a variance component model, and relies on a recently developed variance component estimation method for efficient parameter inference and p-value computation. We refer to our method as the “MArginal ePIstasis Test”, or MAPIT. With simulations, we show how MAPIT can be used to estimate and test marginal epistatic effects, produce calibrated test statistics under the null, and facilitate the detection of pairwise epistatic interactions. We further illustrate the benefits of MAPIT in a QTL mapping study by analyzing the gene expression data of over 400 individuals from the GEUVADIS consortium. Author Summary Epistasis is an important genetic component that underlies phenotypic variation and is also a key mechanism that accounts for missing heritability. Identifying epistatic interactions in genetic association studies can help us better understand the genetic architecture of complex traits and diseases. However, the ability to identify epistatic interactions in practice faces important statistical and computational challenges. Standard statistical methods scan through all-pairs (or all high-orders) of interactions, and the large number of interaction combinations results in slow computation time and low statistical power. We propose an alternative mapping strategy and a new variance component method for identifying epistasis. Our method examines one variant at a time, and estimates and tests its marginal epistatic effect — the combined pairwise interaction effects between a given variant and all other variants. By testing for marginal epistatic effects, we can identify variants that are involved in epistasis without the need of explicitly searching for interactions. Our method also relies on a recently developed variance component estimation method for efficient and robust parameter inference, and accurate p-value computation. We illustrate the benefits of our method using simulations and real data applications.
Projected Changes in Temperature Extremes in China Using PRECIS

Temperature extremes can cause disastrous impacts on ecological and social economic systems. China is very sensitive to climate change, as its warming rate exceeds that of the global mean level. This paper focused on the spatial and temporal changes of the temperature extremes characterized by the 95th percentile of maximum temperature (TX95), the 5th percentile of the minimum temperature (TN5), high-temperature days (HTD) and low-temperature days (LTD). The daily maximum and minimum temperatures generated by PRECIS under different Representative Concentration Pathways (RCPs) are used in the research. The results show that: (1) Model simulation data can reproduce the spatial distribution features of the maximum temperature (Tmax) and minimum temperature (Tmin) as well as that of the extreme temperature indices; (2) By the end of the 21st century (2070–2099), both the Tmax and Tmin are warmer than the baseline level (1961–1990) in China and the eight sub-regions. However, there are regional differences in the asymmetrical warming features, as the Tmin warms more than the Tmax in the northern part of China and the Tibetan Plateau, while the Tmax warms more than the Tmin in the southern part of China; (3) The frequency of the warm extremes would become more usual, as the HTD characterized by the present-day threshold would increase by 106%, 196% and 346%, under RCP2.6, RCP4.5 and RCP8.5, respectively, while the cold extremes characterized by the LTD would become less frequent by the end of the 21st century, decreasing by 75%, 90% and 98% under RCP2.6, RCP4.5 and RCP8.5, respectively. The southern and eastern parts of the Tibetan Plateau respond sensitively to changes in both the hot and cold extremes, suggesting its higher likelihood to suffer from climate warming; (4) The intensity of the warm (cold) extremes would increase (decrease) significantly, characterized by the changes in the TX95 (TN5) by the end of the 21st century, and the magnitude of the increase in the TN5 is larger than that of the TX95 in the national mean value. The changes in both the TX95 and TN5 are larger under the higher versus weaker emission scenario, indicating that it is essential to reduce the GHG emissions and take adaptation measures in the future.
Minocycline through attenuation of oxidative stress and inflammatory response reduces the neuropathic pain in a rat model of chronic constriction injury

Objective(s): Several lines of evidence showed that minocycline possesses antioxidant and anti-inflammatory properties. This study aimed to demonstrate the effects of minocycline in rats subjected to chronic constriction injury (CCI). Materials and Methods: In this study four groups (n = 6–8) of rats were used as follows: Sham, CCI, CCI + minocycline (MIN) 10 mg/Kg (IP) and CCI + MIN 30 mg/Kg (IP). On days 3, 7, 14, and 21 post-surgery hot-plate, acetone, and von Frey tests were carried out. Finally, Motor Nerve Conduction Velocity Evaluation (MNCV) assessment was performed and spinal cords were harvested in order to measure tissue concentrations of TNF_α, IL-1β, Glutathione peroxidase (GPx), Superoxide dismutase (SOD) and Malondialdehyde (MDA). Extent of perineural inflammation and damage around the sciatic nerve was histopathologically evaluated. Results: Our results demonstrated that CCI significantly caused hyperalgesia and allodynia twenty-one days after CCI. MIN attenuated heat hyperalgesia, cold and mechanical allodynia and MNCV in animals. MIN also decreased the levels of TNF_α and IL-1β. Antioxidative enzymes (SOD, MDA, and GPx) were restored following MIN treatment. Our findings showed that MIN decreased perineural inflammation around the sciatic nerve. According to the results, the neuropathic pain reduced in the CCI hyperalgesia model using 30 mg/kg of minocycline. Conclusion: It is suggested that antinociceptive effects of minocycline might be mediated through the inhibition of inflammatory response and attenuation of oxidative stress.
Effect of long chain branching on linear-viscoelastic melt properties of polyolefins

Abstract The aim of this review is to provide evidence that rheological testing is a potent tool for characterising polymers in the melt. An effort has been made in order to gather results in conventional and model polyolefins, and correlating them with phenomena occurring at the molecular level. We have focused our interest on long chain branching (LCB). In the case of materials containing long side-chain branches, strong effects on viscosity, elastic character and activation energy of flow are general features. Literature results mostly indicate that the effect of polydispersity on these parameters could be very similar to that expected due to the presence of LCB - notwithstanding that the effects of LCB seem to be stronger than those due to polydispersity for a given molecular weight. Different relaxation processes appear as a consequence of the presence of LCB: slower terminal relaxation behaviour than of linear counterparts, and faster additional branch relaxation at higher frequencies, clearly distinguishable from polydispersity effects. To measure the amount of LCB from limited viscoelastic data and molecular properties seems to be a suitable instrument to explain the rheological features of the different polymers, but it fails when the results are compared with measured values of LCB density in model polymers. The actual framework leads us to say that the number of branches is less important than the topology itself. Therefore, the position and architecture of the branches along the polymer main chain are the main factors that control the rheology of the material.