Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Superoxide-producing NAD(P)H Oxidase in Kidney*

During phagocytosis, gp91 phox , the catalytic subunit of the phagocyte NADPH oxidase, becomes activated to produce superoxide, a precursor of microbicidal oxidants. Currently increasing evidence suggests that nonphagocytic cells contain similar superoxide-producing oxidases, which are proposed to play crucial roles in various events such as cell proliferation and oxygen sensing for erythropoiesis. Here we describe the cloning of human cDNA that encodes a novel NAD(P)H oxidase, designated NOX4. The NOX4 protein of 578 amino acids exhibits 39% identity to gp91 phox with special conservation in membrane-spanning regions and binding sites for heme, FAD, and NAD(P)H, indicative of its function as a superoxide-producing NAD(P)H oxidase. The membrane fraction of kidney-derived human embryonic kidney (HEK) 293 cells, expressing NOX4, exhibits NADH- and NADPH-dependent superoxide-producing activities, both of which are inhibited by diphenylene iodonium, an agent known to block oxygen sensing, and decreased in cells expressing antisense NOX4 mRNA. The human NOX4 gene, comprising 18 exons, is located on chromosome 11q14.2-q21, and its expression is almost exclusively restricted to adult and fetal kidneys. In human renal cortex, high amounts of the NOX4 protein are present in distal tubular cells, which reside near erythropoietin-producing cells. In addition, overexpression of NOX4 in cultured cells leads to increased superoxide production and decreased rate of growth. The present findings thus suggest that the novel NAD(P)H oxidase NOX4 may serve as an oxygen sensor and/or a regulator of cell growth in kidney.
The genetic rescue of two bottlenecked South Island robin populations using translocations of inbred donors

Populations forced through bottlenecks typically lose genetic variation and exhibit inbreeding depression. ‘Genetic rescue’ techniques that introduce individuals from outbred populations can be highly effective in reversing the deleterious effects of inbreeding, but have limited application for the majority of endangered species, which survive only in a few bottlenecked populations. We tested the effectiveness of using highly inbred populations as donors to rescue two isolated and bottlenecked populations of the South Island robin (Petroica australis). Reciprocal translocations significantly increased heterozygosity and allelic diversity. Increased genetic diversity was accompanied by increased juvenile survival and recruitment, sperm quality, and immunocompetence of hybrid individuals (crosses between the two populations) compared with inbred control individuals (crosses within each population). Our results confirm that the implementation of ‘genetic rescue’ using bottlenecked populations as donors provides a way of preserving endangered species and restoring their viability when outbred donor populations no longer exist.
Fibrolamellar hepatocellular carcinoma in ascitic fluid: A case report with cytohistological correlation

The fibrolamellar variant of hepatocellular carcinoma (FL‐HCC) is distinguished from other hepatocellular carcinoma's (HCC) by its unique clinical and pathological features. Cytological features of this tumor on fine needle aspiration have been described earlier. We report a rare case of a 17‐year‐old African American male with metastatic FL‐HCC, diagnosed by body fluid cytology. The patient presented with ascites and computed tomography (CT) scan revealed multiple omental masses and liver lesions. The fluid sample was obtained along with the omental biopsy and was found positive for metastatic fibrolamellar hepatocellular carcinoma. The fluid cytology showed atypical polygonal cells with enlarged nuclei, prominent nucleoli, and abundant granular cytoplasm. Cytomorphologic features of FL‐HCC presenting in body fluids have been rarely described before. This case enriches the cytopathology literature by providing awareness of this tumor presenting as metastasis in body fluids, especially in young individuals with liver lesions. Presence of a concurrent biopsy specimen provided cytohistological correlation, as it remains the gold standard for the accuracy and reliability of cytological diagnoses. Diagn. Cytopathol. 2016;44:757–760. © 2016 Wiley Periodicals, Inc.
Causal discovery of linear acyclic models with arbitrary distributions

An important task in data analysis is the discovery of causal relationships between observed variables. For continuous-valued data, linear acyclic causal models are commonly used to model the data-generating process, and the inference of such models is a well-studied problem. However, existing methods have significant limitations. Methods based on conditional independencies (Spirtes et al. 1993; Pearl 2000) cannot distinguish between independence-equivalent models, whereas approaches purely based on Independent Component Analysis (Shimizu et al. 2006) are inapplicable to data which is partially Gaussian. In this paper, we generalize and combine the two approaches, to yield a method able to learn the model structure in many cases for which the previous methods provide answers that are either incorrect or are not as informative as possible. We give exact graphical conditions for when two distinct models represent the same family of distributions, and empirically demonstrate the power of our method through thorough simulations.
Semantic-Based Privacy Protection of Electronic Health Records for Collaborative Research

Combined health information and web-based technologies can be used to support healthcare and research activities associated with electronic health records (EHRs). EHRs used for research purposes demand privacy, confidentiality and all information governance concerns are addressed. However, existing solutions are unable to meet the evolving research needs especially when supporting data access and linkage across organization boundaries. In this work, we show how semantic methods can aid in the specification and enforcement of policies for privacy protection. This is illustrated through a case study associated with the Australasian Diabetes Data Network (ADDN), the national paediatric type-1 diabetes data registry and the Australian Urban Research Infrastructure Network (AURIN) platform that supports Australia-wide access to urban and built environment data sets. Specifically we show that through extending the eXtensible Access Control Markup Language (XACML) with semantic capabilities, we are able to support fine-grained privacy-preserving policies leveraging semantic reasoning that is not directly available in XACML or other existing security policy specification languages.
Design of a crawler with bounded bandwidth

This paper presents an algorithm to bound the bandwidth of a Web crawler. The crawler collects statistics on the transfer rate of each server to predict the expected bandwidth use for future downloads. The prediction allows us to activate the optimal number of fetcher threads in order to exploit the assigned bandwidth. The experimental results show the effectiveness of the proposed technique.
Effect of phenol extraction of group A streptococcus on titer and specificity of fluorescent M-typing antisera.

Vaccines were prepared from three M-serotypes of group A Streptococcus both by conventional heating procedures and by extraction with phenol. The antisera elicited by these vaccines were conjugated with fluorescein and examined by immunofluorescence for titer and specificity. The sera elicited by phenol-extracted cells showed no cross-reactivity in the case of two strains and reduced crossreactivity with the third. In all cases, phenol-extracted vaccines elicited higher titers than did heat-killed cells. It is suggested that this procedure for vaccine production may facilitate immunofluorescent screening for M-serotypes.
Analyst-Ready Large Scale Real Time Information Retrieval Tool for E-Governance

With the proliferation of the Internet and rapid development of information and communication infrastructure, E-governance has become a viable option for effective deployment of government services and programs. Areas of E-governance such as Homeland security and disaster relief have to deal with vast amounts of dynamic heterogeneous data. Providing rapid real-time search capabilities for such databases/sources is a challenge. Intelligent Foraging, Gathering, and Matching (I-FGM) is an established framework developed to assist analysts to find information quickly and effectively by incrementally collecting, processing and matching information nuggets. This framework has previously been used to develop a distributed, free text information retrieval application. In this chapter, we provide a comprehensive solution for the E-GOV analyst by extending the I-FGM framework to image collections and creating a “live” version of I-FGM deployable for real-world use. We present a Content Based Image
Partially adaptive arrays application for MU-MIMO mode in a MmWave small cells

In this paper we provide detailed system level performance analysis of MU-MIMO mode in the millimeter wave (mmWave) small cells (Wi-Fi hotspots) environment. Traditional way of MIMO implementation assumes a single RF chain per antenna element, with all spatial processing done in the baseband. To overcome high pathloss in the mmWave bands, the large-aperture, very high gain arrays with a large number of elements (several hundreds) are required. Therefore we introduce partially adaptive arrays with reduced number of degrees of freedom which are implemented based on the modular antenna arrays (MAA) architecture. The scalable practical design of MAA allows creation of large-aperture, high-power antenna arrays with reduced number of RF chains at cost of decreasing the adaptability. Employing recently proposed quasi-deterministic (Q-D) model for millimeter-wave channels, it was shown that partially adaptive MAA have very small degradation in comparison with ideal fully adaptive array (FAA) in a realistic scenarios. It was shown that application of MU-MIMO mode in a mmWave small cells allows achieving up to 15-30 Gbps total throughput per cell in a multipath environment (university campus scenario) with practical antenna array design.
Detection of hypercholesterolemia using hyperspectral imaging of human skin

Hypercholesterolemia is characterized by high blood levels of cholesterol and is associated with increased risk of atherosclerosis and cardiovascular disease. Xanthelasma is a subcutaneous lesion appearing in the skin around the eyes. Xanthelasma is related to hypercholesterolemia. Identifying micro-xanthelasma can thereforeprovide a mean for early detection of hypercholesterolemia and prevent onset and progress of disease. The goal of this study was to investigate spectral and spatial characteristics of hypercholesterolemia in facial skin. Optical techniques like hyperspectral imaging (HSI) might be a suitable tool for such characterization as it simultaneously provides high resolution spatial and spectral information. In this study a 3D Monte Carlo model of lipid inclusions in human skin was developed to create hyperspectral images in the spectral range 400-1090 nm. Four lesions with diameters 0.12–1.0 mm were simulated for three different skin types. The simulations were analyzed using three algorithms: the Tissue Indices (TI), the two layer Diffusion Approximation (DA), and the Minimum Noise Fraction transform (MNF). The simulated lesions were detected by all methods, but the best performance was obtained by the MNF algorithm. The results were verified using data from 11 volunteers with known cholesterol levels. The face of the volunteers was imaged by a LCTF system (400- 720 nm), and the images were analyzed using the previously mentioned algorithms. The identified features were then compared to the known cholesterol levels of the subjects. Significant correlation was obtained for the MNF algorithm only. This study demonstrates that HSI can be a promising, rapid modality for detection of hypercholesterolemia.
Spectral Properties of Unitary Cayley Graphs of Finite Commutative Rings

Let $R$ be a finite commutative ring. The unitary Cayley graph of $R$, denoted $G_R$, is the graph with vertex set $R$ and edge set $\left\{\{a,b\}:a,b\in R, a-b\in R^\times\right\}$, where $R^\times$ is the set of units of $R$. An $r$-regular graph is Ramanujan if the absolute value of every eigenvalue of it other than $\pm r$ is at most $2\sqrt{r-1}$. In this paper we give a necessary and sufficient condition for $G_R$ to be Ramanujan, and a necessary and sufficient condition for the complement of $G_R$ to be Ramanujan. We also determine the energy of the line graph of $G_R$, and compute the spectral moments of $G_R$ and its line graph.
Mechanical and abrasive wear behavior of glass and basalt fabric-reinforced epoxy composites

Multipass two-body abrasive wear behavior of basalt and glass fabric-reinforced epoxy composites have been carried out by using a pin-on-disc machine. Basalt and glass fabric-reinforced epoxy composites have been fabricated by hand layup technique. The mechanical properties of basalt and glass fabric reinforced epoxy composites were evaluated. Abrasive wear performance was evaluated at ambient temperature using 400 grade Silicon Carbide paper as a counter face. The elemental compositions of fabricated composites were quantitatively analyzed by using energy dispersive X-ray spectroscopy. The abrading wear mechanisms have also been studied by worn surface analysis using scanning electron microscopy. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Unsupervised Analysis of Structured Human Artifacts

Unsupervised Analysis of Structured Human Artifacts by Taylor Berg-Kirkpatrick Doctor of Philosophy in Computer Science University of California, Berkeley Professor Dan Klein, Chair The presence of hidden structure in human data—including natural language but also sources like music, historical documents, and other complex artifacts—makes this data extremely difficult to analyze. In this thesis, we develop unsupervised methods that can better cope with hidden structure across several domains of human data. We accomplish this by incorporating rich domain knowledge using two complementary approaches: (1) we develop detailed generative models that more faithfully describe how data originated and (2) we develop structured priors that create useful inductive bias. First, we find that a variety of transcription tasks—for example, both historical document transcription and polyphonic music transcription—can be viewed as linguistic decipherment problems. By building a detailed generative model of the relationship between the input (e.g. an image of a historical document) and its transcription (the text the document contains), we are able to learn these models in a completely unsupervised fashion—without ever seeing an example of an input annotated with its transcription—effectively deciphering the hidden correspondence. The resulting systems have turned out not only to work well for both tasks—achieving state-of-the-art-results—but to outperform their supervised counterparts. Next, for a range of linguistic analysis tasks—for example, both word alignment and grammar induction—we find that structured priors based on linguistically-motivated features can improve upon state-of-the-art generative models. Further, by coupling model parameters in a phylogeny-structured prior across multiple languages, we develop an approach to multilingual grammar induction that substantially outperforms independent learning.
On Boosting Sparse Parities

While boosting has been extensively studied, considerablyless attention has been devoted to the task of designing good weaklearning algorithms. In this paper we consider the problem of designing weak learners thatare especially adept to the boosting procedure and specifically the AdaBoost algorithm. First we describe conditions desirable for a weak learning algorithm. We then propose using sparse parity functions as weak learners, which have many of our desired properties, as weak learners in boosting. Our experimental tests show the proposed weak learners tobe competitive with the most widely used ones: decisionstumps and pruned decision trees.
Basic studies on sonoporation with size- and position-controlled microbubbles adjacent to cells

We have been studying a sonoporation technique that uses one-shot exposure of short-pulsed ultrasound to cells with attached microbubbles. Here, we introduce a new observation system developed for elucidation of sonoporation mechanisms. An inverted-type microscope was equipped with optical tweezers that enable position control of a microbubble. A Laguerre-Gaussian (LG) beam, a Gaussian beam with a dark spot at the center, was used to trap a microbubble with a refractive index lower than that of the surrounding water. The LG beam was produced using a phase-only spatial light modulator and 1,065-nm laser light. Results of basic experiments showed that the tweezers can trap bubbles of 1-30 μm in diameter suspended in water, and the minimum optical power for trapping bubbles of 5 μm in diameter was around 10 mW. Sonoporation experiments were carried out using size- and position-controlled bubbles placed on cell membranes or placed at separated positions from cells, and the results indicated the importance of the newly developed system for elucidation of sonoporation mechanisms.
Multiple‐image radiography for human soft tissue

Conventional radiography only provides a measure of the X‐ray attenuation caused by an object; thus, it is insensitive to other inherent informative effects, such as refraction. Furthermore, conventional radiographs are degraded by X‐ray scatter that can obscure important details of the object being imaged. The novel X‐ray technology diffraction‐enhanced imaging (DEI) has recently allowed the visualization of nearly scatter‐free images displaying both attenuation and refraction properties. A new method termed multiple‐image radiography (MIR) is a significant improvement over DEI, corrects errors in DEI, is more robust to noise and produces an additional image that is entirely new to medical imaging. This new image, which portrays ultra‐small‐angle X‐ray scattering (USAXS) conveys the presence of microstructure in the object, thus differentiating homogeneous tissues from tissues that are irregular on a scale of micrometres. The aim of this study was to examine the use of MIR for evaluation of soft tissue, and in particular to conduct a preliminary investigation of the USAXS image, which has not previously been used in tissue imaging.
Registration completeness in the Norwegian Arthroplasty Register

Introduction A high degree of registration completeness is necessary in order to obtain unbiased and accurate register-based study results. We investigated the completeness of registration in the national Norwegian Arthroplasty Register (NAR). Material and methods Registration completeness for the years 1999–2002 was calculated as a percentage, with the number of joint replacements reported to the NAR as numerator and those reported to the Norwegian Patient Register (NPR) as denominator. While the NAR received information directly from the orthopedic surgeons on a voluntary basis, the NPR, which is mandatory, received information from the electronic administrative patient records of the hospitals. Results Registration completeness in the NAR was 97% (97% for primary operations; 101% for revisions). Completeness was 98% (97%; 106%) for hip replacements, and for knee replacements it was 99% (99%; 97%). Hip and knee replacements represented 95% of all operations. However, completeness was poorer for less common joint replacements and poorest for ankle implants (82%; 40%) and wrist implants (52%; 14%). In the NAR, completeness of registration of revisions involving only removal of one or more prosthetic parts was lower than for exchange revisions for all types of joint replacement. For hip implants, 76% of the removal revisions (80% of Girdlestone procedures) were reported, and for knee implants the figure was 62%. According to NPR statistics, removal procedures accounted for 9% of all revisions of hip and knee replacements. Interpretation In the NAR, registration completeness of hip and knee replacements was high both for primary operations and exchange revisions. For some of the less common joint replacements, completeness was low and may—if not improved—compromise prosthesis survival studies. The lower registration completeness of removal revisions also needs to be improved. ▪
Enhanced Gastrointestinal Motility with Orally Active Ghrelin Receptor Agonists

The orexigenic peptide ghrelin has been shown to have prokinetic activity in the gastrointestinal (GI) system of several species, including humans. In this series of experiments, we have evaluated the prokinetic activity of novel, small-molecule ghrelin receptor (GhrR) agonists after parenteral and peroral dosing in mice and rats. Gastric emptying, small intestinal transport, and fecal output were determined after intraperitoneal and intracerebroventricular dosing of GhrR agonists, using ghrelin as a positive control. These same parameters were evaluated after oral gavage dosing of the synthetic agonists. Regardless of dose route, GhrR agonist treatment increased gastric emptying, small intestinal transit, and fecal output. However, fecal output was only increased by GhrR agonist treatment if mice were able to feed during the stimulatory period. Thus, GhrR agonists can stimulate upper GI motility, and the orexigenic action of the compounds can indirectly contribute to prokinetic activity along the entire GI tract. The orexigenic and prokinetic effects of either ghrelin or small-molecule GhrR agonists were selective for the GhrR because they were absent when evaluated in GhrR knockout mice. We next evaluated the efficacy of the synthetic GhrR agonists dosed in a model of opiate-induced bowel dysfunction induced by a single injection of morphine. Oral dosing of a GhrR agonist normalized GI motility in opiate-induced dysmotility. These data demonstrate the potential utility of GhrR agonists for treating gastrointestinal hypomotility disorders.
Design and characterisation of low-cost thick-film piezoresistive force sensors for the 100 mN to 100 N range

Two simple low-cost thick-film force sensor designs are optimised, characterised and tested in this work, combining calculations of sensor element and joint stresses, joint strength characterisation and measurement of complete sensors. All sensors are based on standard hybrid substrates. Our results show that a single sensor geometry cannot cover such a wide range of forces in an optimal way. For small forces (100 mN to ca. 2 N), simple cantilever force sensors are an excellent solution, achieving reasonable precision with a very simple design and compatibility with an SMD (surface mount device) assembly process with solder or conductive glue. Characterisation of solder joint strength shows that such joints can reliably withstand the bending moments resulting form the loading of the cantilever sensor up to ca. 2 N. Above this force, both solder joint and cantilever strength become critical in the cantilever design. Therefore, a 3-point or 4-point bending beam geometry must be selected, thereby extending the force range to ca. 100 N.