Miracle-dz/UniFAR-FTUs huggingface dataset:
A Large-scale Images Processing Model Based on Hadoop Platform

This paper presents a parallel processing model based on Hadoop platform for large-scale images processing, which aims to make use of the advantages of high reliability and high scalability of Hadoop distributed platform for distributed memory and distributed computing, so as to achieve the purpose of fast processing of large-scale images. The Hadoop streaming technology is used in the model. The main operations are written on shell script as the mapper of Hadoop streaming, then an assigned filelist is used as the Hadoop streaming's input. The large numbers of image files are delivered to cluster computers for concurrent image processing. The model has been implemented using virtual machines. A set of experimental results and analysis are provided.
Collagenase clostridium hystolyticum in the management of Peyronie’s disease

Peyronie’s disease (PD) is a connective tissue disorder characterized by inelastic fibrous plaques on the tunica albuginea of penis. Inelasticity induce penile deformity such as curvature, shortening, narrowing, hinging and also associated with penile pain and erectile dysfunction. The pathogenic mechanisms of the disorder are still poorly understood although physicians believed that the trauma to the tunica albuginea leads to excess inflammation in some men resulting in inflammatory mass formation in the early stage, then disruption of the normal cell architecture through deposition of collagen fibers and breaking down the elastic fibers create the “plaque”.
Laboratory Measurements of Multi-Frequency and Broadband Acoustic Scattering from Turbulent and Double-Diffusive Microstructure

Abstract : The long-term goal of the proposed research is to develop a fundamental understanding of high-frequency acoustic scattering from small-scale physical processes that occur in the ocean interior. The primary scientific objective of the proposed research is to measure, characterize, and understand the physics of high-frequency acoustic scattering from controlled, laboratory-generated microstructure, with a focus on double diffusion. The initial development of simple physics based scattering models is a secondary objective of this work.
Procurement of Bone Graft from the Iliac Crest. An Operative Approach with Decreased Morbidity*

We compared the donor site morbidity in fifty-seven consecutive patients in whom a bone graft had been procured from the iliac crest through an incision parallel to the superior cluneal nerves and perpendicular to the posterior iliac crest (the study group) with that in fifty-three consecutive patients in whom the graft had been procured through an oblique incision parallel to the posterior iliac crest (the control group). Numbness, tenderness, and pain at the donor site one and six months postoperatively were assessed by means of an interview with the patient and a review of the records. The prevalence of symptoms in the control group was greater than that in the study group. At one month, thirty-nine patients (74 per cent) in the control group had numbness, compared with twenty-five (44 per cent) in the study group (p = 0.001). At six months, thirty-one patients (58 per cent) in the control group had numbness, compared with fourteen (25 per cent) in the study group (p = 0.0002). Thirty-six patients (68 per cent) in the control group and twenty-four (42 per cent) in the study group had tenderness over the incision at one month (p = 0.005), and twenty-seven (51 per cent) and eleven (19 per cent), respectively, had tenderness at six months (p = 0.0003). Forty patients (75 per cent) in the control group and forty-six patients (81 per cent) in the study group had deep pain in the region of the iliac crest at one month, compared with thirty-two (60 per cent) and thirty-one (54 per cent), respectively, at six months. The mean analog score for pain at the donor site was 7 of 10 points in the control group and 6 points in the study group (p = 0.001) at one month and 3 and 2 points, respectively, at six months (p = 0.001).
Minimal Shape and Intensity Cost Path Segmentation

A new generic model-based segmentation algorithm is presented, which can be trained from examples akin to the active shape model (ASM) approach in order to acquire knowledge about the shape to be segmented and about the gray-level appearance of the object in the image. Whereas ASM alternates between shape and intensity information during search, the proposed approach optimizes for shape and intensity characteristics simultaneously. Local gray-level appearance information at the landmark points extracted from feature images is used to automatically detect a number of plausible candidate locations for each landmark. The shape information is described by multiple landmark-specific statistical models that capture local dependencies between adjacent landmarks on the shape. The shape and intensity models are combined in a single cost function that is optimized noniteratively using dynamic programming, without the need for initialization. The algorithm was validated for segmentation of anatomical structures in chest and hand radiographs. In each experiment, the presented method had a significant higher performance when compared to the ASM schemes. As the method is highly effective, optimally suited for pathological cases and easy to implement, it is highly useful for many medical image segmentation tasks.
Sticking your neck out and burying the hatchet: what idioms reveal about embodied simulation

Idioms are used in conventional language twice as frequently as metaphors, but most research, particularly recent work on embodiment has focused on the latter. However, idioms have the potential to significantly deepen our understanding of embodiment because their meanings cannot be derived from their component words. To determine whether sensorimotor states could activate idiomatic meaning, participants were instructed to engage in postures/actions reflecting various idioms (e.g., sticking your neck out) relative to non-idiomatic control postures/actions while reading and responding to statements designed to assess idiomatic meaning. The results showed that statements were generally more strongly endorsed after idiom embodiment than control conditions, indicating that the meaning of idiomatic expressions may not be as disconnected from perceptual and motor experiences than previously thought. These findings are discussed in terms of the mirror neuron system and the necessity of pluralistic contributions from both sensorimotor and amodal linguistic systems to fully account for the representation and processing of idioms and other figurative expressions.
Update on Expression of Plastid Genes Expression of Plastid Genes : Organelle-Specific Elaborations on a Prokaryotic Scaffold 1

Chloroplasts and their nonphotosynthetic relatives in the plastid organelle family evolved from a cyanobacterial endosymbiont (for review, see Timmis et al., 2004). The subsequent coevolution of the chloroplast and nuclear genomes produced an organelle that is eubacterial at its core but with extensive chloroplastspecific embellishments. Of the thousands of genes in the cyanobacterial ancestor, only approximately 100 are retained in chloroplast genomes. These genes fall into three categories: those encoding (1) components of the chloroplast gene expression machinery (RNA polymerase, ribosomal proteins, tRNAs, and rRNAs), (2) subunits of photosynthetic enzymes (Rubisco, PSII, the cytochrome b6 f complex, PSI, the ATP synthase, and the NADH dehydrogenase), and (3) proteins involved in other metabolic processes (e.g. ClpP, AccD, Ycf1, and Ycf2). The chloroplast proteome has a complexity of several thousand proteins and is dominated by nuclear gene products that are synthesized in the cytosol and imported into the organelle. Many of these are encoded by genes of cyanobacterial ancestry that were transferred to the nucleus and that have retained their ancestral functions. As a result, the chloroplast gene expression and photosynthesis machineries consist of proteins that are derived from two physically separate genetic systems. Detailed knowledge of chloroplast gene expression and the nucleus-encoded proteins that influence it are prerequisites for understanding nuclear-organellar cross talk and chloroplast evolution, and will aid in optimizing transgene expression in the plastid compartment. The use of genetic and biochemical approaches, together with the ability to manipulate the chloroplast genome in several species, have brought most aspects of chloroplast gene expression out of the “black box” and into the realm of concrete, mechanistic hypotheses. The intent of this contribution is to highlight new perspectives that have resulted from recent observations and instances in which current data warrant the revision of previous paradigms. For more comprehensive information, I refer the reader to recent reviews of chloroplast RNA metabolism (Stern et al., 2010), transcription (Liere and Börner, 2007; Lerbs-Mache, 2010), and translation (PeledZehavi and Danon, 2007). Mechanisms of chloroplast gene expression have been studied primarily in land plants and in the green alga Chlamydomonas reinhardtii. Here, I emphasize findings with land plants, as detailed reviews of chloroplast gene expression in Chlamydomonas have been published in a recent volume (Stern and Harris, 2009).
A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer

Metastatic spread to the liver is a frequent complication of colorectal cancer (CRC), occurring in almost half of the cases, for which personalized treatment strategies are highly desirable. To this aim, it has been proven that patient-derived mouse xenografts (PDX) of liver-metastatic CRC can be used to discover new therapeutic targets and determinants of drug resistance. To identify gene fusions in RNA-Seq data obtained from such PDX samples, we propose a novel pipeline that tackles the following issues: (i) discriminating human from murine RNA, to filter out transcripts contributed by the mouse stroma that supports the PDX; (ii) increasing sensitivity in case of suboptimal RNA-Seq coverage; (iii) prioritizing the detected chimeric transcripts by molecular features of the fusion and by functional relevance of the involved genes; (iv) providing appropriate sequence information for subsequent validation of the identified fusions. The pipeline, built on top of Chimerascan(R.Iyer, 2011) and deFuse(McPherson, 2011) aligner tools, was successfully applied to RNASeq data from 11 PDX samples. Among the 299 fusion genes identified by the aforementioned softwares, five were selected since passed all the filtering stages implemented into the proposed pipeline resulting as biologically relevant fusions. Three of them were experimentally confirmed.
Contiki Ring File System for Real-Time Applications

Wireless Sensor Nodes often need to store or cache measurement or operational data into some non-volatile memory. Many applications using low power sensor nodes are based on Contiki, which provides the COFFEE file system for data storage. As COFFEE introduces occasional long and hard to predict write delays, it can not be used in applications which have real time demands, such as sensor networks operating in industrial environments. In this paper we present an efficient implementation of a flexible Ring File System for Contiki, that can be used in real-time applications. Read and write times are predictable and adherence to Contiki's file system API allows it to be used as a drop-in replacement for COFFEE in many applications.
Modeling and performance analysis of a generalized photovoltaic array in Matlab

A generalized photovoltaic array simulation model in Matlab/Simulink environment is developed and presented in this paper. The model includes PV module and array for easy use on simulation platform. The proposed model is designed with a user-friendly icon and a dialog box like Simulink block libraries. This makes the generalized PV model easily simulated and analyzed even with a maximum power point tracker. Considering the effect of solar irradiance and temperature change, the output current and voltage of PV modules are simulated and optimized using the proposed model. The model was tested using a directly coupled dc load as well as an ac load via an inverter. The test result validates the model which can be used in related research works.
How long is too long? Effects of loop size on G-quadruplex stability

We compared here 80 different sequences containing four tracts of three guanines with loops of variable length (between 1 and 15 bases for unmodified sequences, up to 30 for fluorescently labeled oligonucleotides). All sequences were capable of forming stable quadruplexes, with Tm above physiological temperature in most cases. Unsurprisingly, the melting temperature was systematically lower in sodium than in potassium but the difference between both ionic conditions varied between 1 and >39°C (average difference: 18.3°C). Depending on the sequence context, and especially for G4 sequences involving two very short loops, the third one may be very long without compromising the stability of the quadruplex. A strong inverse correlation between total loop length and Tm was found in K+: each added base leads to a 2°C drop in Tm or ∼0.3 kcal/mol loss in ΔG°. The trend was less clear in Na+, with a longer than expected optimal loop length (up to 5 nt). This study will therefore extend the sequence repertoire of quadruplex-prone sequences, arguing for a modification of the widely used consensus (maximal loop size of 7 bases).
Telomerase antagonists GRN163 and GRN163L inhibit tumor growth and increase chemosensitivity of human hepatoma

Most cancer cells have an immortal growth capacity as a consequence of telomerase reactivation. Inhibition of this enzyme leads to increased telomere dysfunction, which limits the proliferative capacity of tumor cells; thus, telomerase inhibition represents a potentially safe and universal target for cancer treatment. We evaluated the potential of two thio‐phosphoramidate oligonucleotide inhibitors of telomerase, GRN163 and GRN163L, as drug candidates for the treatment of human hepatoma. GRN163 and GRN163L were tested in preclinical studies using systemic administration to treat flank xenografts of different human hepatoma cell lines (Hep3B and Huh7) in nude mice. The studies showed that both GRN163 and GRN163L inhibited telomerase activity and tumor cell growth in a dose‐dependent manner in vitro and in vivo. The potency and efficacy of the lipid‐conjugated antagonist, GRN163L, was superior to the nonlipidated parent compound, GRN163. Impaired tumor growth in vivo was associated with critical telomere shortening, induction of telomere dysfunction, reduced rate of cell proliferation, and increased apoptosis in the treatment groups. In vitro, GRN163L administration led to higher prevalence of chromosomal telomere‐free ends and DNA damage foci in both hepatoma cell lines. In addition, in vitro chemosensitivity assay showed that pretreatment with GRN163L increased doxorubicin sensitivity of Hep3B. In conclusion, our data support the development of GRN163L, a novel lipidated conjugate of the telomerase inhibitor GRN163, for systemic treatment of human hepatoma. In addition to limiting the proliferative capacity of hepatoma, GRN163L might also increase the sensitivity of this tumor type to conventional chemotherapy. (HEPATOLOGY 2005.)
Towards hierarchical BCIs for robotic control

There has been growing interest in brain-computer interfaces (BCIs) for controlling robotic devices and prosthetics directly using brain signals. Non-invasive BCIs, such as those based on electroencephalographic (EEG) signals, suffer from low signal-to-noise ratio, limiting the bandwidth of control. Invasive BCIs, on the other hand, allow fine-grained control but can leave users exhausted over long periods of time because of the amount of attention required for control on a moment-by-moment basis. In this paper, we address these problems using a new adaptive and hierarchical approach to brain-computer interfacing. The approach allows a user to teach the BCI system new skills on-the-fly; these learned skills are later invoked directly as high-level commands, relieving the user of tedious lower-level control. We demonstrate the approach using a hierarchical EEG-based BCI for controlling a humanoid robot. In a study involving four human subjects controlling the robot in a simulated home environment, each subject successfully used the BCI to teach the robot a new navigational task. They later were able to execute the same task by selecting the newly learned command from the BCI's adaptive menu, avoiding the need for low-level control. A comparison of the performance of the system under low-level and hierarchical control revealed that hierarchical control is both faster and more accurate. Our results suggest that hierarchical BCIs can provide a flexible and robust way of controlling complex robotic devices, satisfying the dual goals of decreasing the cognitive load on the user while maintaining the ability to adapt to the user's needs.
The sunless study: a beach randomized trial of a skin cancer prevention intervention promoting sunless tanning.

OBJECTIVE To examine the impact of a skin cancer prevention intervention that promoted sunless tanning as a substitute for sunbathing. DESIGN Randomized controlled trial. SETTING Public beaches in Massachusetts. PARTICIPANTS Women (N = 250) were recruited to participate in the study during their visit to a public beach. Intervention The intervention included motivational messages to use sunless tanning as an alternative to UV tanning, instructions for proper use of sunless tanning products, attractive images of women with sunless tans, a free trial of a sunless tanning product, skin cancer education, and UV imaging. The control participants completed surveys. MAIN OUTCOME MEASURES The primary outcome was sunbathing 2 months and 1 year after the intervention. Secondary outcomes included sunburns, sun protection use, and sunless tanning. RESULTS At 2 months, intervention participants reduced their sunbathing significantly more than did controls and reported significantly fewer sunburns and greater use of protective clothing. At 1 year, intervention participants reported significant decreases in sunbathing and increases in sunless tanning relative to control participants but no differences in the other outcomes. CONCLUSION This intervention, which promoted sunless tanning as an alternative to UV tanning, had a short-term effect on sunbathing, sunburns, and use of protective clothing and a longer-term effect on sunbathing and sunless tanning. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00403377.
Bayesian graphical models for regression on multiple data sets with different variables

Routinely collected administrative data sets, such as national registers, aim to collect information on a limited number of variables for the whole population. In contrast, survey and cohort studies contain more detailed data from a sample of the population. This paper describes Bayesian graphical models for fitting a common regression model to a combination of data sets with different sets of covariates. The methods are applied to a study of low birth weight and air pollution in England and Wales using a combination of register, survey, and small-area aggregate data. We discuss issues such as multiple imputation of confounding variables missing in one data set, survey selection bias, and appropriate propagation of information between model components. From the register data, there appears to be an association between low birth weight and environmental exposure to NO2, but after adjusting for confounding by ethnicity and maternal smoking by combining the register and survey data under our models, we find there is no significant association. However, NO2 was associated with a small but significant reduction in birth weight, modeled as a continuous variable.
Influences on Preschool Children's Physical Activity: Exploration Through Focus Groups

This study explored mothers' perceptions of influences on preschoolers' physical activity. Six semistructured focus groups with 23 mothers were conducted across a range of socioeconomic position locations. Mothers identified 4 key areas of influence: child fundamentals (eg, sex, personality), parent power (eg, rules, support), people to share with (eg, peers, adults), and places and things (eg, physical environments, toys). No substantial differences in themes were identified among socioeconomic position groups. Influences on preschoolers' physical activity are multidimensional, multifactorial, and support the use of ecological models to conceptualize and understand the influencing factors. Associations among factors influencing preschoolers' physical activity should be further investigated through quantitative research.
Foundations for structured programming with GADTs

GADTs are at the cutting edge of functional programming and becomemore widely used every day. Nevertheless, the semantic foundations underlying GADTs are not well understood. In this paper we solve this problem by showing that the standard theory of data types as carriers of initial algebras of functors can be extended from algebraic and nested data types to GADTs. We then use this observation to derivean initial algebra semantics for GADTs, thus ensuring that all of the accumulated knowledge about initial algebras can be brought to bear on them. Next, we use our initial algebra semantics for GADTs to derive expressive and principled tools --- analogous to the well-known and widely-used ones for algebraic and nested data types---for reasoning about, programming with, and improving the performance of programs involving, GADTs; we christen such a collection of tools for a GADT an initial algebra package. Along the way, we give a constructive demonstration that every GADT can be reduced to one which uses only the equality GADT and existential quantification. Although other such reductions exist in the literature, ours is entirely local, is independent of any particular syntactic presentation of GADTs, and can be implemented in the host language, rather than existing solely as a metatheoretical artifact. The main technical ideas underlying our approach are (i) to modify the notion of a higher-order functor so that GADTs can be seen as carriers of initial algebras of higher-order functors, and (ii) to use left Kan extensions to trade arbitrary GADTs for simpler-but-equivalent ones for which initial algebra semantics can bederived.
Mass properties factors in achieving stable imagery from a gimbal mounted camera

Mass properties play a role in affecting the stability of gimbaled imaging platforms. The relationship between static balance and jitter, in some measure, is previously established. The definition and role of dynamic unbalance however, is not as thoroughly understood. Leading to the discussion of dynamic unbalance, we show through the use of analytical means, the jitter resulting from static unbalance generated forces when we follow these forces through the isolation mounting, servo pointing accuracy and disturbance rejection systems using a single degree of freedom model. We then apply the qualitative results to the discussion of dynamic unbalance exploring some of the nuances of product of inertia and cross coupling response. We will offer strategies and specific methods for measuring and correcting static unbalances and the principles of reducing dynamic unbalance in gimbals in order to reduce disturbance response and ultimately improve the image resolution. Finally, we will test a method for measuring and correcting dynamic unbalance to facilitate future quantitative testing aimed toward jitter improvement.